Drexel CoAS E-Learning Transcripts

Open Notebook Science in 15 minutes

2008-11-26T16:22:00.000-05:00

Open Notebook Science in 15 minutes

Jean-Claude Bradley: All right. So, I will try to explain to you these two concepts of the synthesis of anti-malarial compounds and Open Notebook Science in the next 15 minutes. Well, this is actually a pretty good time to give this talk. This week we actually got our Wikipedia entry for Open Notebook Science. And it turns out that it required a lot of peoples coordinate efforts. And it required a body of work before we were able to do this. But, if you go on Wikipedia, you can learn a lot more that I don't have time to explain today.

The idea of Open Notebook Science is basically to report the work that you do in the laboratory in real time or as close as you can to real time, so that the entire world knows as much as you do about your research. Like I said, there are a number of references here that you can take a look at the background of this. But, the motivation is that - well, it should be self evident that it's a way to do faster science compared to either not disclosing some things or significantly delaying them.

And I think, it's also a way of doing better science, which is not immediately obvious, but hopefully I will show you some examples of how that can be.

OK, now to the synthesis part. So, we are a synthetic organic chemistry group and our target is malaria, specifically Falcipain-2. Malaria, as you should know, is a disease that is spread by mosquitoes. And here's actually the malarial parasite inside of the red blood cell. And it uses the enzyme Falcipain-2 to metabolize hemoglobin. So, if we can inhibit that enzyme, it could be a way to basically stop the process of it replicating.

And so, what we have done is we have collaborated with a group at the Indiana University, Rajarshi Guha. And he does the docking, which basically means that he takes the Falcipain-2 in the computer and tries to dock molecules and see if they fit or not. If they fit, there's a chance that it might inhibit it. And so, he tells us which compound to make. And then we make them and we ship them off to UCSF where Phil Rosenthal does the testing.

So, this is a collaboration done completely openly, and people can join in or they can follow what we are doing well before the publications come out. So, I am not going to talk too much about the nuts and bolts of it, but, suffice to say that we use blogs, wikis and all these different social networking sites to try to make this system fully hosted and fully replicatable by anyone else in the world who might want to do a similar thing. And that's happened. And I can surely talk to you if you are interested in seeing the different groups that have done that.

I was telling you about it's a way of doing better science and really comes down to where's the beef when you talk about your experiments. So, this is a blog post here, where we are talking about doing different things. And it says "See experiment 150 for more information." So, this is Ugi reaction that I will be mentioning over and over in this talk.

And if you click on that link, it takes you to the lab notebook page experiment 150. And this actually looks very similar to what it would look like in a paper notebook. And that's on purpose. We wanted to make things easy as possible for people to get involved with Open Notebook Science.

So, you have an objective, and you have all these different hyperlinks. So, one of the things that you can link to - and then this is a pretty long page, I am just going to skip through it giving you examples. You can hit that Ugi edit link and it takes you to an entry in ChemSpider. ChemSpider is a free database. It has over 21 million compounds. You can do such sorts of searching. You can do all kinds of things for free. And I don't have to worry about that on my server.

So, that's what we are trying to achieve here. We are trying to get high quality information processing without having to become computer scientists to do it. And it's becoming really possible to do.

We also link to the docking procedure that our collaborator Rajarshi uses. Again, here the idea is that this is replicatable. Someone who has done docking before should be able to get enough information from this page to generate the same compounds in the same order; all right? So, these are called SMILES codes and they are convenient ways of representing molecular structures, and you can just dump them in spreadsheets. So, it's a pretty convenient way.

Again, this is all made explicit, so you don't have to ask the researcher for permission. You can just go and look at the results.

Another very helpful thing is our spectra. If you know anything about organic chemistry you know that the basis of it is spectra, especially NMR spectra. And there's actually a very neat way - if you have your NMR spectrum in a JCAMP format, you can run JSPEC view so that someone who does not know anything about the Java or anything, just hits this link and this spectrum pops up, and it's actually interactive.

So, you can use your mouse and drag across any peak and it will expand. Again, here - this is what I am talking about doing better science, you know. May be, you didn't expand that peak in your paper. May be you didn't talk about it. But, if I am trying to replicate this where I am trying to extend your research, maybe I am interested in that peak. Maybe I want to measure it. And so there are just more details.

So, by the time we end up with the final conclusions and it's says "This Ugi product was within 59% yield." You don't have to take our word for it. It's all backed up - either well or poorly - but it's all backed up, exactly what's supporting our statement.

If you are not familiar with the wiki, the reason that we use it for a live notebook is that every time there's a change made, it tells you who made the change and exactly when. And we have a third party time stamp for it. So, we can claim that we knew what we knew exactly when. And we are not running the time stamp. It's run on a third party that's well respected. So, that could be interesting down the road to settle claims.

We can compare any two versions, and using wiki spaces it lets you - basically shows you the stuff in green is the stuff that was added, and the stuff in red was deleted. So, it's a really nice way to understand what people are good at, right? Because this is a collaboration, many people in the lab working together, certain people are good at some thing and other people are good at other things. And this is a really good way to keep a track of all that.

Now, to find information, that's actually a big issue. Obliviously, if we just left it in the wiki like that - I mean we have tags. We have ways for searching for the information. But, you don't want to have to do that if you are interested in seeing the collection of experiments that we have run.

So, we've run this Ugi reaction several times and we have modified the conditions. So, we have used different staring materials, different solvent amounts, and different concentrations. And we have sometimes gotten a nice precipitate that was pure product and sometimes we don't. So, we are trying to understand that. And we are using these Google docs as a way of sharing that information in a very convenient way.

So, this is a spreadsheet. It works very similar to Excel but it's free and it's hosted. So, I will show you an example of an opportunity we had recently to use a robot from Mettler-Toledo. And we are able to actually automate this optimization of this reaction. This was done in collaboration with Dr. Owens. He did some statistical analysis, which I want have time to get into. But, the idea here is that we wanted to find the highest yields - the condition for the highest yields.

So, we modify concentration, we modify the solvent, and we modify the excess of some of the reagents. So, we actually did these reactions in little tubes that had a filter at the tip. So, the robot added the four different components. And then it precipitated or it didn't. And if did. We just washed it and then weighed the results. And of course took an NMR to make sure that we actually got the compound.

So, this is a picture of the robot. And it's basically just a syringe that goes and takes the liquid out and puts them. An interesting thing about using a robot is that you get automatically the log of what the robot did. And it pays attention all the time. So, it will record what it is it think it did. That's a double edged sword. It gives you a lot of information. If you want to debug things, yeah, you absolutely have some good data to look at.

But, it also means because you are able to do so many more experiments, you have to be even more vigilant about systematic errors. And we've had that problem. And so, you end up doing a thousand experiments before you find the problem, all right.

But, once you get it working, actually, this can be extremely useful. So, just to go to the final results here. So, we did these experiments and we had enough material to publish a paper. So, here's another use of the wiki where we actually wrote the paper in the wiki. So, every single draft was saved. And we can go back and see exactly how the paper was written.

And the really nice thing about having a notebook to point to is... See, I can have reference nine to 11 be the melting point of the compound, and I can specify the batch that it was taken from - from experiment 99, whereas the proton NMR was taken from experiment 203, sample A 11. So, that information is typically not part of a typical publication. You assume that the guy knows what he is doing and that he actually characterizes his compounds properly. While that is not always the case as we find out painfully. So here we can actually go and see if there is a problem with the specific batch if we are not getting the same information.

Now, where we actually submitted this paper is kind of interesting. It's called the Journal of Visualized Experiments, JoVE. So, there is a written part to this that I just showed you; that is what we wrote on the wiki. And they actually sent some camera people to record our experiments. And so, this is now under peer review. And we should hear back shortly about this. And I don't see any problems and I don't expect any problems.

So, this will be a nice way to communicate with video as well. So, there are so many tools now that make communicating your science faster without losing anything. Another thing that the physicists have been using for a while is pre-print servers. So, chemistry really didn't have a good pre-print server - well, they did, but that's a whole other story; it's no longer working. So, Nature actually recently came up with this Nature Precedings, which is a pre-print server and it's backed with the editorial filter of the Nature Publishing Group. If you are not familiar with Nature, it's one of the most well-respected publishers out there.

So, if they basically say that this has good scientific quality, it's probably true. And so, we can before publication in JoVE or any peer review journal that we choose to publish in, we can actually link to this document. People can comment on this document. They can vote on it. They can give us feedback. You can have versioning on here. All kinds of things you can do.

Normally, we have a paper out, you just tell people "Well, it's going to come out next week," and when it does "Here's the link." Well here, now, you can actually give the link and you can have [inaudible 10:39].

So, the bottom line here is we did find a maximum yield - 66%. We went in with a yield of about 49 to 50% - we got some increase. But, the major result of this was really to prove that we could optimize the reactions in robotics.

Now, so far as the malaria project, that's actually important because that's how we make our compounds with Ugi reaction. Recently, we've actually gotten some results about this. We have four compounds that actually are active in inhibiting the enzymes, and they are also effective in inhibiting the infection of plasmodium falciparum. And these are in the micromolar range. So, it's not bad. I mean, it's definitely publishable stuff.

And there are different stories here. We used one receptor area on the enzyme here. We used another receptor here. I don't have time to get into it, but it's kind of interesting the results that are coming out of this. And again, this is out into the open. And we never know who is going to stop by and collaborate.

A last little story. I recently did a little trip in the UK. And my friend here Cameron Neylon who also does open notebook science - although, he uses a different system than I do, we had the chance to spend a day in the lab to do experiments. And one of the things that evolved from my trip is a very simple project using open notebooks. And we spent the day measuring solubilities. So, we took a bunch of compounds and we took a bunch of organic solvents, and measured the solubilities. And then, we reported these solubilities in a Google doc.

Now, this is actually very interesting. So, for Boc-glycine and methanol, we are measuring 4.4 molar. And you notice that that's in green. And down here, for D-glucose and methanol, we do get a number, right, and it's 0.05. But, I put it in red and I don't actually include that number in my final results, because I am not satisfied that I am going to stand behind these. I don't think that 1.8 milligrams in the way that we were measuring it is good enough to report this.

But, what if you want a ballpark estimate? You can still access my number and you have all the details of the context in which it was taken. So, again, that's better science, I think. And what we are trying to do with this project - it's actually related to the malarial project in the sense that we can measure solubilities, report them publicly, and then build models; and Rajarshi Guha is going to help us build models of solubility - we should be able to predict the yields of these Ugi reactions in different solvents.

So, the idea is, for this Ugi product, you should do it in 51% methanol, 4% ethanol and the rest is acetonitrile. So, that will be a very powerful thing that can be used not just for our project, but really anyone could. And sort of to get this ball rolling, I set up this Open Notebook Science Challenge. And what it is, it is essentially we are asking people from around the world to contribute their measurements so long as they link them to a well maintained notebook. And if they do that then we can use these results, and we can publish with them, and we can do everything that we do as scientists.

And we have a sponsor. Aldrich's is actually volunteered to ship compounds anywhere in the world to encourage people to do this. So, I am very excited about this. It's a new initiative. And I think it has a good chance of working.

And there are so many people to thank here. Khalid is my grad student. Kevin Owens you just heard from. Tim Bohinsksy is an undergrad who just started to working in my lab, his term measuring solubilities. James is also an undergrad. Tom Osborne is the Mettler-Toledo rep who was very patient and took a lot of time to bring us the robot for us to get these results.

Antony Williams is the guy who runs the ChemSpider, the database that I showed you for molecules. Andrew Lang actually put our results into Second Life. Because of the briefness of this talk, I wasn't able to get into that. But, you can visualize the optimization of the reaction using 3D plastic. You can rotate it in Second Life. So, Andy did that. And of course, Cameron from Southampton.

So, that's it. Any questions?

iSchool Open Notebook Science talk

2008-11-24T13:24:00.002-05:00

iSchool Open Notebook Science Talk

Jean-Claude Bradley: I would like to tell you today about Open Notebook Science. My talk is based on the work we did in chemistry in terms of making anti-malarial compounds and measuring solubilities. But, I have actually put this talk together in a way to sort of minimize the chemistry and focus more on the IT aspects of it. Hopefully, by the end of it, you will understand pretty well what it is we are doing.
This really comes as, there are several themes that have been emerging the past few years in science and in teaching and one of them is actually openness. There are a few people here who are doing more open teaching in terms of recording their lectures and making them open on iTunes. All of these things are progressing.
The same thing is happening in research. We are going from a world where we have a traditional lab notebook, which is unpublished and will never see the light of day unless somebody writes a paper about it and going to more and more open forums. Traditional journal articles are more open, but people have to pay for it, and so it's limited to only certain a sub-set of people.
Recently, people are talking about open access journal articles. Again, that's more open, because the articles are free to access; however, generally the authors have to pay for the cost, so it's not generally a totally free deal.
At the end of the spectrum, we have Open Notebook Science. The idea of that is total transparency in the research process. We want to make available the actual lab notebooks of the students in real time or as close to real time as possible for the world to see so that's what I'll be talking to you about.
Now, my job is a little bit easier as of the past couple of weeks because we now have our Open Notebook Science entry in Wikipedia. If you're more interested in looking at some references, we've got some things coming out in Cell, CD News and Nature. So, with this kind of accumulating scholarship, it actually is starting to really take shape. I'll tell you about some of the people, besides myself, who are involved in this.
Again, I am going to start from the IT perspective instead of the chemistry. The way that I always like to talk about this, which of this happens to be usually my last line for the chemists, is we're moving from a world where we have human-to-human communication. That's what science has really been from the very beginning, one scientist telling another scientist what they did or trying to avoid what the other scientist did.
Right now, I think we are in a very interesting phase where we are starting to have humans communicating with machines and back and forth in terms of scientific information. Eventually, I think that the whole scientific process will get done by machines talking to machines, but I think in order to get to that point we have to go through this period where we have to somehow find a compromise so that both humans and machines can access the same information and talk to each other.
That comes down to what is the information that chemists actually manipulate. There's this concept of what's a fact. What's true? What's false? If we find a number, how sure can we be that it is close to the true value? We have to remember and students often forget this, that there really are no facts they're just measurements embedded within assumptions. The problem with the way that chemistry, especially, is being currently communicated even in traditional journals is that those assumptions are not made explicit. It is very difficult to tell exactly what was done or what the author actually did or didn't do.
Open Notebook Science maintains the integrity of the data providence from the lab notebook all the way to whatever documents happen to come out of that. So, if somebody wants to question a number, they can just click through and have access to the original lab notebook page.
Here, we are moving from a concept of trust and there is actually a lot of trust today in science. If someone that you know writes a paper, you are more likely to think that it's correct or more likely to be more valued than if someone else writes it, or if an article comes out in a certain journal you may give it more credibility than in another.
We have that in all the three fields. Chemistry has its own journals where if there's a yield that shows up, you know that you can't trust it because it's a certain journal, which I won't say which it is, but as chemists, we all know those. That's really based on trust. I think that if we start to move away from trust and move to just simply providing proof, if you provide sufficient proof you don't need trust anymore because the machine or the person has to back up everything that they're claiming.
Let me give you a very specific example. Here, we are looking at the solubility of 4-chlorobenzolvide. Solubility is just how much of a compound goes into solution, very, very simple chemical concept. It should be something fairly easy to answer. You should just basically look it up in literature. It turns out that a lot of these measurements have not been done surprisingly. Very, very simple things but you can't access them.
It should be a very simple thing. Give a couple of under grads some compounds and a scale and just let them go. Well, it's not that simple. If you look at the values that our students have been obtaining, you'll see here a high number five to one to 3, and then there's a number here 0.07. That number was collected along with all the other numbers since we're just reporting results.
As a chemist I looked at that and it didn't make any sense at all because these compounds are actually pretty similar chemically. It would be extremely surprising for them to have very different properties. Either, we discovered an extremely interesting phenomenon or, as is more likely the case, there is a problem with the way the measurement was done.
That particular measurement, by looking at the lab notebook, I'm going to actually look at the specific experiment for a bunch of slides and show you that we were able to uncover the fact that this compound was operating in the speed back, the machine that basically lets us find out how much is dissolved.
We redid the experiment and now we get a value of 3.6 moles. That number makes more sense so that number is validated according to what I think based on what I saw of the experiment where the first number is rejected. In the literature, you will not get to dig down into the original proof for this.
Let's take a look at what is actually in the lab notebook page. We're missing a little bit of the screen here. Up here, it says log, so this is the log section of the lab notebook. It basically has just a sequence of what the students did and what they observed. That's how you are supposed to keep a lab notebook in organic chemistry.
I have highlighted a couple of things here. Unfortunately, there's a section missing and the section that is missing actually said did not measure the amount of time vortexed. The lab notebook just doesn't tell me the stuff that the students did. It tells me what they didn't do whereas if I were using a trust-based system I would assume: oh, this person probably measured the time they did this. They probably measured the pressure, but unless you actually check, you actually can't know that.
Down here is the same thing. There are actually times here that are missing from the screen. I can actually see how long they put it in and what they did or didn't measure.
The other thing that we can actually drill down to is the rationale of the findings. We can make those explicit. This is actually a discussion and conclusion section off that same page, and it basically talks about the data. It talks about the raw data. Some of this, I wrote. My student wrote another part. Someone else might have come in and actually added to it. It explains the rationale of why we think that 0.07 number is incorrect.
You can look at the raw data, but you can also look at the rationale of the scientist. Again, this is not typically provided in a paper because this is actually just developing. You can also look at the actual documents that are offered up as proof.
Here, we actually have pictures. You can see here that there are some interesting things. These are after evaporation so we would expect to have all dry solids here, but you can see that the one on the left actually still has a bit of liquid left in it. Is that a problem? In this particular case, it turns out it's not a huge problem, but you're made richer by knowing that there was a potential issue here.
You'll notice also that number 46 is all covered in white, and it looks different from the other ones. I would look at that number a little bit more cautiously because it looks like it actually burst and started to bubble over while it was evaporating. Those are the things, again, that are not provided in a typical research article in chemistry.
Down here this is actually on Flickr. Everything that we're using is as open as possible. This is the nice thing, that you can get random people coming in and making their own contribution or using the data in a way that you wouldn't expect. This guy thought that it was a good looking picture. It had nothing to do with chemistry, but that doesn't matter. This is the Web 2.0 type of information sharing.
We also make use of YouTube. That actually is a very efficient way to record experiments because, again, instead of asking the student to write every detail of what they did you could just do a quick video, and I can actually ask myself questions: did we hook this up correctly? Where is the thermometer? All kinds of things that are gone if they don't record it.
Here, we are actually using very short clips. We're not talking about recording the entire experiment over hours. We are talking about a 30-second clip. Show me your setup and then they don't have to write it up. This is a way of learning....

Audience Member: It seems like 20th century technology where you have to make animate recordings that are translated into digital as opposed to, maybe, in the future having smarter machines that automatically record what you're doing.

Jean-Claude: Yes.

Audience Member: ...a chance to measure temperature and stuff like that.

Jean-Claude: That's where we're headed. In fact, I'll show you a robot that we've used exactly in that way. The thing is, you know, we don't have robots for everything, and we don't have all the stuff accessible. We have to do what we can with what we have. But I agree, if all this could be automated, it would certainly be a lot easier.
The other things that we show are the calculations. This is a really simple measure. You are basically just seeing how much material dissolves in a certain amount of liquid, and you're just measuring it. It turns out there are a lot of calculations in that. You have to weigh the empty vial. You have to weigh it with the liquid. You have to weigh it after it evaporates.
It's clear that there are a lot of places where you can make mistakes. If you see a number that looks strange, I would come here first to actually take a look at the calculation. Maybe, the student made a mistake. If they did make a calculation mistake, then, at least, I know that and I can deal with it. I can drill down to see exactly where the problem might be.
Here, we're making pretty extensive use of Google's spreadsheets. It's a really great way to share any kind of calculated information like this, and you can do all kinds of calculations. It's totally free and hosted.
The other nice thing about the Google spreadsheets is it's not that dangerous to make them open for editing because you can see the history. If someone comes in and just completely deletes all of your values, it's a little bit annoying. It hasn't happened yet, but it's not a big deal. You can just basically go back to a previous version, and it will restore it.
This is nice because we can now make these spreadsheets editable to anybody, so someone can come in here and actually mark something up and write a comment. You can color code something. It becomes so much more flexible than having to give people permission to come in and modify a certain spreadsheet.
Now, if you've gathered we use a Wiki actually for the lab notebook itself, There's a couple of reasons for that. The main one is that the Wiki gives you a page history. I can see every single version since the beginning of that experiment. I can see who made the contribution. By comparing two versions, I can see what each person added at each point.
We're using Wiki spaces, and Wiki spaces show the changes in green by the stuff that's added. It shows the stuff in red by stuff that's deleted. Often times, I will write a comment and ask a student a question, and then they will address the question and remove my comment. That's exactly what happened here. The red stuff was my original question.
This is actually also a great tool for interacting with students, especially graduate students where that's what they are supposed to learn how to basically report on science and how to make conclusions from their data set.
It doesn't end with just pictures. There are all kinds of different data formats. In chemistry, we are very big on spectra. That's how we prove that we made certain things. That's how we prove purity of things, and NMR is by far the most useful of those special techniques.
Here, we're making use of JSPEC view and the JCAMP-DX format. Are any of you familiar with that, JCAMP? It's a very handy format. It's open. It supports any XY data, and you can convert a lot of the proprietary software or, say, file systems into different instruments into a JCAMP format.
Once you have it as a JCAMP format, you can put it up on the web in a way that a browser can interact with the data. You don't need for the person to download software to view it. It runs in Java. Basically, they click on a link. It pops up the spectrum. If you drag your mouse across, you can actually expand any peak that you want. Unfortunately here, because we're missing half a screen, you can't see that, but there's actually a very detailed peak. You cannot see the details in the original spectrum.
This is a big deal because in a traditional publication you do supply supplementary materials, but it's generally in the format of a PDF. You cannot zoom into a PDF peak, and there's a lot of information there in terms of purities, in terms of all kinds of things that you would like to get at to figure out what happens.
Getting into indexing, again unfortunately, we are missing part of the screen here. I'll try to describe it as best I can. Over here, there is a list of compound names. So, we're looking at a list of solvents, like toluene, ethanol and vanillin that I'll be talking about. We can represent these different molecules using different things, like INChIs and InChlKeys and SMILES code. Anybody here work with those? OK, one person.
Basically, these are the contemporary way of representing molecules using linear text. If you want to represent toluene, you could type toluene, but there are many names for it. Methylbenzene is another name. How can you represent that in a way that a machine, for example, could read it unambiguously?
So, there are SMILES, InChls and InChlKeys. I would certainly be happy to talk to anybody about the details of those, but the InChlKey is always the same length no matter how big the molecule is. That's nice for indexing in Google.
For example, if we click on this link which is vanillin, you can see that it pops up my lab's work, and it also pops up some paper where that particular compound shows up. These are starting to be used more and more. They have huge advantages in terms of compressing information and making it sure that it's absolutely corresponding to the molecule you want.

Audience Member: What are the InChls?

Jean-Claude: The InChl, you actually can't figure them out. You'd have to look them up, but there are web services so you can use Self. You can use different kinds of web services.

Audience Member: Self is not representative of the structures.

Audience Member: But, InChl is represented of its structure and its connectivity is represented here.

Jean-Claude: The InChl, actually, the big reason why the InChl started to be used - just for small molecules the InChl are fine, but when you have molecules that are medium sized they are so big that Google can't index them anymore and that's a problem.

Audience Member: Now, we're taking [muffled voice].

Jean-Claude: These things are fairly recent. InChl is pretty recent. It's only in the past couple of years. InChlKeys is, maybe, one year.

Audience Member: [muffled voice]

Jean-Claude: The problem with the cast is the copyright. That's the big problem.

Audience Member: What about abstracts?

Jean-Claude: Chemical abstracts? People do use them, but if you're talking to people that are interested in indexing a lot of stuff without having to worry about the legal aspects, they tend to stay away from the cast number. That doesn't mean you'll find them on Wikipedia. You'll find them in a bunch of places, but, yeah, you will definitely find them. But, the whole copyright issue is actually a big problem with that.

Audience Member: Since you're interrupting, let me say that as a reader I would much rather have trust than proof, that is, who do I trust? I'd like to trust, read like a proof. But, to have every reader have to go back and verify things from the beginning, it seems to be a very great burden.

Jean-Claude: The point is you only do it when you have to. The reason that I looked at that number is because it didn't make sense in the context of the other numbers. I didn't drill down to every other number.
Right now, you cannot do that from publication. The peer review process does not cover that at all. So, that is the problem right now. My only option in a paper is that I have to email the author and hope that they respond by sending me the information that I want and that just doesn't happen very seamlessly.

Audience Member: Proof is needed by the reviewers, and that is proven by me in advance.

Jean-Claude: Yeah. So, basically, use trust for as long as you can get away with it, but when you are trying to repeat an experiment and you can't, you're kind of stuck with the whole trust issue.
I don't know if it's a post-doc who wrote that up. I don't know if it's a new student. Why not just give me the proof? I mean, it's really not that big of a deal. They already have all this information. It is just a question of making it open and having people access it.

Audience Member: Recent publications are devoted to doing this sort of thing, producing validated data over, let's say, a sequence of temperature, pressure, and this sort of thing. Is it that there are so many chemical compounds out there and so many different variables that even the publications that are devoted to that would work beyond this in the old days, I think. [crosstalk] just can't do it all.

Jean- Claude: I mean, there is so much to do that people haven't done them. Quite frankly people and companies probably have done these measurements and have no benefit in sharing them. So, there is a lot of that kind of thing as well.
But the level of detail that I am talking about, even if you look at it in this database, I don't think that you can access... Let's say that you challenged a number in this data base. They're not going to send you the lab notebook pages where they got that information from. And that is what we are talking about. We are talking about transparency at the level of no insider information from the research group to the rest of the world.
So, there may be stuff that was added in the past hour, that is incorrect, by my students. And that's OK. We accept that as part of the process of working in the open. That is no different that any other place where we work in the open.
OK. So, one of the main databases that we do use is ChemSpider. In fact, the CEO is coming tomorrow, Tony Williams - two o'clock, Disquay 109. It is a great opportunity. He will be talking about all this and he will be doing a demo if you want to interact with him. But, this is really a fantastic resource for manipulating organic chemicals.
What we do for the lab notebook... I don't want to be running software on my servers that will actually do substructure searching, that will be doing any kind of analysis like that. With ChemSpider I can actually farm that out. And this is free and hosted for you, for anyone to do.
You basically just link from the molecule to this and then it gives you all this information. It gives you the smiles, the InChl, the InChlKey.

Audience Member: And the empirical formula, is what it gives.

Jean-Claude: OK. Empirical formula, yes. What we normally call it. But, that doesn't have enough information to...

Audience Member: [muffled voice]

Jean-Claude: Yes. Certainly that would be what we file under that.

Audience Member: Where is ChemSpider pulling this in from?

Jean-Claude: ChemSpider is pulling it all over the place. They have links to the vendors. Down here you see experimental properties, melting point, and boiling point. They are actually links from ChemSpider to where they got them from. It could me an MSDS sheet. It could be any number of things.

Audience Member: Does this generate on the fly? Do they go out and get this stuff when you ask for it or has it harvested a lot?

Jean-Claude: ChemSpider has already harvested, like, over 21 million compounds.

Audience Member: So, you would call this a search engine for the invisible web, the chemical properties, which works like Google.

Jean-Claude: Yeah, that's a good way to look at it; a search engine for the chemical invisible web.

Audience Member: How does this compare to the Walstein that was acquired from Crossfire?

Jean-Claude: Well, it's free first of all.

Audience Member: What's that?

Jean-Claude: And it's free.

Audience Member: And it's not in German!

Audience Member: How complete is it?

Jean-Claude: Yeah, Walstein is certainly superior in terms of reactions, but this has actually started to compete with... If you're looking for properties like a boiling point, things like that, it is actually getting pretty comparable, I think, we used in the past year. This is all new stuff here. Going in the next five years, this is going to change. It is going to be totally unrecognizable. Right now, as of today, this is the state of the art.

Audience Member: [muffled voice]

Jean-Claude: We still pay for it. Drexel still has Walstein, SciFinder, and all those pay services, and they're still useful. As long as they still provide information that these sites don't we're still going to keep using them and teaching them.

Audience Member: So, you're not against this empirical overview of the literature associated with ChemSpider and Walstein?

Jean-Claude: Each database has its own things they provide. ChemSpider, for our purposes, is extremely useful because it has these key things. Like if we want to generate the InChlKey, for example, this is by far the easiest way to do so. Go on ChemSpider, put your compound in, and then you have the InChlKey, you can copy and paste.
So, there is a whole bunch of things. You've got synonyms...

Audience Member: Is there sufficient meta data for a program, not a person, to go and find information, that it will point to some arbitrary substance and then take it and use it somewhere else?

Jean-Claude: Yeah, there are web services that you can hook up. Now, you can't get all the information because of licensing issues. Like some of these properties you can get them on one page, but you can't download 10,000 of them. So, there are those kinds of limitations. But, ChemSpider tries to be very good about providing everything they can in the form of a web service. So, that makes it very useful.

Audience Member: OK.

Jean-Claude: The other nice thing about ChemSpider is we can also upload the raw data, like the raw spectra, and they're also in JCamp format. JSpecview looks at it. And as of, actually, yesterday we can deposit our solubility properties. So, Tony actually made a special parameter for us to put our solubility properties.
That is going to be very interesting as people... If you want to find the solubility in methanol you are going to be able to, over time.
OK. Let's see how much time I have here. This is until 1:30, right?

Audience Member: That's right.

Jean-Claude: OK.
So, this is something that I am very exited about, that also happened quite recently in the past few weeks. I told you about Open Notebook Science and I set up an Open Notebook Science Challenge, which is for people from around the world to actually do solubility measurements of certain kinds of organic compounds and report them to the central place. So, we actually have 127 measurements now. There are just a variety of solvents. There's different people that did similar techniques, but not exactly the same techniques.
We just recently got funding from Submeida for these Open Notebook Science Awards. And Drexel students are eligible for them. Actually, any student at a university in the States or in the UK is eligible for them. They are $500 a piece and there's ten of them over the next ten months.
This is kind of neat because we have judges that are chemists, that are either in academia or high up in industry, who will actually give feedback to students on their lab notebook. So, the student might put a report and a judge might come in and say, "You didn't provide enough information." or "This is wrong." or "Look at this." So, what we are trying to do is have a peer reviewed Open Notebook. That is something that hasn't been done and I think this is going to be very exciting.
It requires something of a challenge to get everyone motivated to actually do it. So, these are not big awards, but they're interesting enough that we have five students now contributing to this. It will be very interesting to see, in the next ten months, how this is going to play out.
This is what we have so far. Each one of these experiments can have 20 to 40 solubility measurements. That is not a big number, but, like I said, they cover about 127. And these all link to the lab notebooks.
You will see on the top here there is a summary data. So, again, we don't expect people to click through every experiment to find what they're looking for. There should be easy ways of accessing that information. And again, Google Doc is a really good way to do that.
Here, I have validated solubilities. What does that mean? It means that I have decided that I don't see anything wrong with these data points at this time. Now that could change tomorrow, but I feel comfortable enough to put them up on here. And they link back - you see these links, experiment 208, 205 - these link back to the actual notebook pages. So, if you want to see how these numbers are generated you can.
Here, it just shows up as a nice look-up. You can see the solubility, and it's got the smiles there which is another way, it's like an InChl - the solvent and the solute. And so this is a very large spreadsheet. And Google Docs can't handle very large volumes, but this will probably work for at least the first thousand entries that we have. That's roughly what we're looking at in the next few months.
Now, this is where it got really exciting in the past week, is that - I don't know if you guys have heard of Google Visualization API - anybody try to use that here? This is very cool stuff. So, Google Docs, again, it's free, it's hosted; and they actually have an API where you can query it and you can return results. So, if I search for Vanoline, it gives me all the measurements of Vanoline to date in all the different solvents.
Unfortunately, we're missing the key part here, which is the names of the solvent because the screen isn't big enough! But, it turns out that some of these are actually farther away then we might expect. On the right, you can see one of those examples. So, for methanol, we get values ranging from 2.8 to 4.2. So, this is the same experiment, run by different people, and we're getting values that are pretty far apart.
It actually tells us we have a mean of 3.2, and we have a standard deviation of 1.4. So, how do you interpret that? Well, if I were to only give you the mean and the standard deviation, you could probably use that for some purposes. But, maybe you want to see what that one looks like it's very big - which is actually one that I personally did. It looks like it's out of the rest of the group.
You might want to look at what's different about that experiment from the other ones. From the live notebooks I'm starting to think that it has to do with how long they were vortexed - how long they were actually mixed. Because it may take actually a longer time than you think to reach a saturated solution. But, then again, we can only ask that question because we have access to the raw data.

Audience Member: ... sciences, in the field of chemistry, a kind of passive knowledge of what actually happens at the lab bench. I am thinking about medical experiments [inaudible] biology - DNA extraction, these sorts of things. There is something that you couldn't learn even from the best value. You can get the rest of people's take to the shelf over the sink - you can share that.
But still, the only way to learn how to do these things or to do them correctly was to go to somebody in the lab and actually physically do the experiment. This is something that is still kind of missing, it seems to me, and could be even exacerbated in this reliance on 'he's done it' and you get a lot to think of that.

Jean-Claude: Well, this is stuff you have to record anyway. We're just making it public.

Audience Member: Right.

Jean-Claude: We're not really changing the workflow.

Audience Member: Right. But, there is a question of truth, and replicability. At some point, you also have the human.

Jean-Claude: No. That's the whole point. If you have a lab notebook and links to all the raw data, you don't need the human.

Audience Member: So, you know exactly what the pH of the water coming out of that faucet is?

Jean-Claude: If we measured it. Then again, there are some chemists who are better than others, and that's the point of this too is to show ways of recording science that's better. And if they didn't record it, you'd want to know that they didn't record it.

Audience Member: At what point are the things not rationally recordable. I'll give you an example from clinic indexing. A kind of customer, a former colleague of mine, Paddy Goodman; well, someone wanted a photograph of the squish ivy on the mantelpiece in the Oval Office. Now, photographs of the wall, these are indexed. What do you record in an image that is retrieval-worthy for some purpose? What do you record in a laboratory experiment that somebody is going to be concerned about down the road? Because you cannot.
I would argue, 'record everything.' So what is being recordable and what you wish - 'Damn, I wish I'd recorded that!' - later on.

Jean-Claude: And that's happened; and that's the conclusion of some experiments. 'We should have recorded this and guess what, next time we do.'

Audience Member: So, how does that information gets shared out so the people know this?

Jean-Claude: That's what this is for.

Audience Member: Thanks. So, this is how you do it?

Jean-Claude: There is no other mechanism that exists right now to enable that sharing except if you happen to work closely with someone. Yeah, this is really the point of Open Notebook Science.

Audience Member: But isn't your point here, that assuming all four of those measures in your notebook, then yours would surely spend more of the time on mixing, and that would be different.
Or, yours would show you measured the mixing time, and theirs would show they didn't.

Jean-Claude: That's in fact the case, yeah. With some of those they did not measure the mixing time. So, now that brings the question...

Audience Member: But, at least it's a clue...

Jean-Claude: It's a clue.

Audience Member: ...and, of course, it maybe a red herring because that may not be what affected it.

Jean-Claude: Exactly, but at least we could design that experiment. Yes. Yeah, there is not one way to do this measurement; you can evaporate, you can also use UV; there's a bunch of different tools you can use. And that's the whole point of this is you don't want people to have to go through each thing; you don't want to have to Google stuff to find it. You want to have this interface. Or you can access this now, and you can add your own intelligence to this. You don't need to know the chemistry to use this. But, you may find an anomaly to give to the chemist, and then the chemist can look in to what's causing this anomaly.
But, yeah, all these numbers should be very close to each other and they're not, so there is something... Somebody is not doing it right.
So, down here, you see there is a link. This number - that first one - it's experiment 207, sample number three. You click on that it takes you to the lab notebook, and you will see that in fact, that is my experiment. That I did with my collaborator from Southampton.

Audience Member: I think you would have done...

Jean-Claude: That's the point. That everything - yeah. That you maintain the chain of where the data came from at all points in time.

Audience Member: It is a broad...

Jean-Claude: Yes.

Audience Member: ... what we did then, holding them.

Jean-Claude: I mean, it's very surprising in chemistry that the whole concept of providence is really not widespread. You can open up a book of melting points, and it doesn't usually tell you where they got those numbers from; but it's from a trusted source. I don't know if that meets...

Audience Member: ...physics and references in the last part of the...

Jean-Claude: Well, they may reference the actual papers but I can tell you when you read those papers that there's often not a lot of information. But, at least here, you can see how much information was recorded.

Audience Member: Lot of detail with it.

Jean-Claude: Well, in fact, patents is probably the reason that chemists are so hyper about keeping a lot of notebooks. Because those are the legal documents that you use in a court case when you want to prove that you were first. And now, we're trying to do the same thing - in using them openly in real-time for another purpose is not legal. Things are actually very hard to fake when you have to provide all the raw data. Things are easy to fake if all you have to do is put a number in a table. Oh, that was my yield!
It's very difficult to fake all the raw spectra, to fake all the weights, to fake all that stuff would be so difficult that you would get caught.

Audience Member: [muffled voice]

Jean-Claude: It's actually easier to just be truthful than to try to figure it out!

Audience Member: This is an excellent tool for researchers in, say, academia. Is there any thoughts about how this might integrate into the workflow of say, a pharmaceutical company or an optical...

Jean-Claude: Well, this is certainly available to the pharmaceutical companies. If they wanted to find out what solvent to do a reaction, they could certainly find that information on our site. So, going forward we're going to have more and more values, and that's something that I hope will be copied as well, but, yeah absolutely. And there's not any intellectual property issues, everyone comes on board collaborating, making things open, so that simplifies things a lot.

Audience Member: It means that the private companies will know this is a resource, but probably they are not going to participate.

Jean-Claude: That's what they're doing now..

Audience Member: It's different now. They might do a version of this internally for their own research, and would that become a standard tool that they can use live?

Jean-Claude: I mean, that's actually what they're doing with ChemSpider, because they don't want people to see what they're searching - they can get a copy of ChemSpider for a fee.
So, there are basically different business models emerging from this. I'm coming at it from the standpoint of we want good data, we want to report good data, and we want to publish the stuff. That's what we're doing, but, absolutely, it can get pretty tricky.
Anybody here working on RDF? Maybe we should talk later because I want to make sure that I do cover this thing with the robots. I have very little time.
We were talking about workflows before even if we didn't use that term: protocols, workflows. We have actually been converting what we wrote to be human readable into a very standard format that machines can read.
Basically, it says here common name methanol InChlKey. It gives you the InChlKey, and then it gives you the volume in milliliters. This can be scraped pretty easily and can be put into a database, for example. Is anybody working with people at MyExperiment? They're basically very heavy in the bioinformatics area.
What they call an experiment really means taking information, submitting it to BLAST search or something like that, and then getting information back. Some of these can actually be pretty tricky with lots of web services being called, so there's a place in my experiment where you can upload those.
In the past two weeks, they've actually opened up what they take as a workflow to include what I have on the right there, which are physical transformations or physical workflows, not just converting information. So, this is potentially very exciting. MyExperiment people are very heavily invested in this, so I think that there's definitely a future.

Audience Member: Is there actually a workflow notation they do on the...?

Jean-Claude: There is a specific notation for their bioinformatics queries, but right now, I think they just decided, "Look, just open it up for people with physical processes." I guess, they're going to look later at standardizing those. No, right now ,it's just a page.
Chemical Markup Language: anybody here involved a little bit? That's something else we haven't discussed.
There are always these different ways of making things machine-readable. I would like to talk a little bit about the use for it. The reason I got involved in solubilities is that we were trying to make compounds as anti-malarial agents. If we can predict the solubilities, we can actually figure out how to get good yields off of our target compounds. It just hadn't been done, so that's why we're doing it.
In parallel with recording the values, we are working with Rajarshi Guha at Indiana University who's actually doing modeling to predict the solubilities. So, in the coming months that would be very interesting to see what the predictions are verses what we've observed. Let me skip through here.
Rajarshi is doing docking. Is anybody doing docking? You basically have an enzyme and a small molecule, and you try to dock into it to try to inhibit it. Here we're also using Google Docs to report on the results of those docking runs, and again we're using Google Docs to do that as a very simple way of sharing information.
Just to tell you about the robots a little bit, this is the Ugi reaction that we're actually doing to make these anti-malarial compounds. We wanted to see if we could optimize this by using robots. So, Rajarshi lent us their mini mapper system, which is basically just the syringe on an arm. It can go and pick up some liquid and deliver it at different positions.
We were able to do 48 reactions in parallel. These are little filter tubes about this big. The idea is that you have the robot add the four solutions, changing the parameter slightly, and then it precipitates. We filter and weigh it, and the weight is the yield of the reaction. The nice thing as was mentioned earlier about a robot is the robot actually spits out its own log of what it did.
That can be very useful from the standpoint of figuring out what it thinks it did, which is not necessarily what it did. This actually can be more problematic than having a human do it because you're doing a lot of reactions in parallel. If you have a systematic error, you sometimes don't know why you're having a problem. We had that problem.
The machine wasn't programmed carefully, and what happened was we didn't realize it wasn't changing the solvents completely. We were getting numbers definitely, but as a chemist I was looking at the numbers and saying, "Something is wrong." It took awhile actually. We did probably over 1000 experiments before we knew what the problem was.
Eventually, we did do it. We recorded, so this is the calculation part of that. We wrote this up on a Wiki. Now, we're talking about a document that its intended audience, or its intended vehicle, is actually a standard journal. We wanted to write this to see, first of all, if a publisher would take it. Will he take a paper that was written in the open? The answer was yes. The publishers will definitely do it.
We submitted this, and the nice thing about this is that we can actually link to individual lab notebook pages from the journal article. Down here, it says the melting point was taken from experiment 99, for the proton the NMR was taken from experiment 203. Right now, there's not a mechanism in chemistry that will actually do that because the lab notebooks are not made public or even available.
But here, because we do have those documents available, we can point to them. That means that basically that was a different batch than that one, and in a traditional article you don't make that distinction. You trust people that all of their stuff is the same quality.
If you're interested in automatic markup of documents, tomorrow Tony Williams will be talking about this in the ChemSpider talk. This is basically software that goes through a document and it figures out the chemical, and then you can see that it actually knows how to draw it. This kind of markup is actually very, very interesting going forward.
This paper, which is still under peer review, should appear in the Journal of Visualized Experiments where they actually send a team of people to do a camera recording of our experiments as well. So, there's the written, there's the video, and this will be the first example for us of having a peer-reviewed article linking back to the lab notebooks.
Another handy thing you can use these days is Nature Precedings. If you're familiar with Archive that handles a lot of the physics preprints. Nature Precedings will handle more broadly. It's nice because it does have the editorial approval of Nature, a nice DOI, and a nice author list that you can use.
While my article is pending under peer-review at JoVE, I can actually put it up on Precedings. I can talk about it, I can give people a link, and they can download it. This is actually a very handy tool and very complementary to the peer-review process.

Audience Member: Publishers don't care....

Jean-Claude: No, many publishers don't care. What they don't want you to do is to take the final document with all of the editing that they did on a PDF copy and make that available. That's more the issue. They really don't have a problem with text. That's not the case for ACS, but it is the case for many others.
Some people are asking about Second Life. We don't have enough time, but we can do a lot of the same things looking at spectral and molecules. We have an eCrystals repository where people can submit the 3D structures of their molecules. That's another way we can make things open. We can report on the activities of the various compounds.
I find outcomes in terms of the malaria project is we actually have nine compounds, which show activity against the enzyme, and we have four that show activity against infection of the malaria parasite into the red blood cells. This is neat because this has not been written up yet, but the information is available to anyone who actually wants to use it.
There are other people who are doing Open Notebook Science. Gus Rosania up in Michigan also works on drug transport, and all of his students are using the same Wiki approach. Cameron Neylon from the University of Southampton is also doing the Open Book Science, but he's not using the Wiki. He's using a modified blog engine to do much of the same thing as we are.
I'd just like to thank my students. I think, I've run out of time, right?

ITConversations Jean-Claude Bradley Interview

2008-07-09T15:15:00.003-04:00

ITConversations Jean-Claude Bradley Interview

Announcer: Jean Claude Bradley, an associate professor of chemistry at Drexel University, is a pioneering practitioner of open notebook science. On this edition of Interviews with Innovators, Bradley explains to host Jon Udell that he believes scientific research happens better and faster when the entire process is transparently narrated online. From IT Conversations.

[music]
Phil: Hi, and welcome to IT Conversations. I'm Phil Windley, the executive producer. Today, I'm happy to bring you another program from Jon Udell's Interviews with Innovators. This program is made possible by Microsoft's Channel nine and Channel 10.
Announcer: By joining as a paid member, you'll not only help keep the Conversations Network on the air, you'll also have access to our Premium Edition programs without promotional messages. Just click on the "Join Now" button on our website to learn more. Our audio files are delivered by Limelight Networks, the high performance content delivery network for digital media.
Phil Windley: And now, here's Jon Udell.
Professor Jean Claude Bradley: So, I started to do open notebook science in the summer of 2005. I've been a professor at Drexel since '96, and I've worked in several labs, doing gene therapy work, making DNA chip type of chemistry, and my background is a synthetic organic chemistry PhD.

So, I have experience in different labs. And one of the things that you notice if you work in a lab is that most of the stuff that you do never gets seen by anybody. As a chemist, you do an experiment, and you have a lab notebook, which is generally paper. I understand the industry, they're moving more towards the electronic notebook systems. But, there, also, the control is pretty tight. So, effectively, it's pretty similar to the kind of exposure that you'd have with paper.

At least, within your own company, you could share things. But, in terms of other people that you don't know benefiting from what you've done, I always wondered if there would be a way to do that.

And it really took until about 2005, when social software technologies were really very, very easy to use. And there are plenty of examples of people using blogs and wikis and these kinds of things, and you could get free, fully hosted services that would be inconceivable just a few years earlier. Because that's the other thing that was really important to me. I want to spend my time being a chemist. I don't want to spend my time managing a server.
Jon Udell: Yeah.
Professor Bradley: In chemistry, if you want to do a lot of the high end technical stuff, with respect to computers, you try to find a student that is comfortable, or even interested in, programming work as well as chemistry. And that's actually not that easy to find.
Jon: Yeah. That's always a bottleneck. So, I just want to ask. You mentioned that an idea here was for you to be able to share your work with other people so that they could benefit from it. But, I assume that there is an inverse thing happening here, too, which is that perhaps other people can help you with your work when they see what you're doing or what you're trying to do.
Professor Bradley: Yes. I mean, originally, I don't know what my expectations were in terms of what would happen. Theoretically, people could come in and start to comment on our experiments. And we have had that. We did get a few comments from people that just came out of the blue. But, mainly, people are not that willing to go out and do that. The main benefit that I've seen, from our end, is really to be able to find new collaborators that we would have otherwise not found.
Jon: Yes.
Professor Bradley: So, it's data finding data.
Jon: Yeah, exactly. So, explain how that actually happens for you, what the process looks like.
Professor Bradley: OK. So, the notebook that we're using, the actual lab notebook where each page is an experiment, that's on a wiki. I use Wikispaces. It's free. It has a Creative Commons by attribution license by default if you have the free account. And their service has been great. They have great functionality. No limitations on the free account. The pages look pretty similar to what they would in a book, except that we can do more stuff, like we can link to the raw data, actually.

So, if someone wants to dig to a particular spectrum, or they want to zoom in to something, or they want to verify a statement that the student or the PI made, they can do that. So, that's a requirement, that our lab notebook on Wikispaces is our official lab notebook. Students are free, certainly, to use paper for any purpose they wish, but the official lab notebook has to be on the wiki.
Jon: And who has been discovering and exploring these notebook pages and the data behind them?
Professor Bradley: Well, we get about 150 to 200 hits a day. And its people that vary from the educational side of this, which we haven't really talked about, to people looking for the NMR of like this morning, something was looking for the NMR of crotonic acid. If your listeners don't know what that is, it's basically just information about a compound. You wouldn't think to use Google as your first resource for that, but honestly people are using Google. I find myself using it ahead of using anything else, just because it's so quick.

And the fact that people are actually getting the information that they're looking for. I mean, we have taken the NMR of crotonic acid, and people can actually look at that and dig into any part of the spectrum that they want to.

So, I see a lot of that kind of stuff happening, where people are looking for very specific information. They might be looking for a boiling point of a solvent or something like that. And I know from their hits that, most of the time, I think, they're actually finding what they're looking for.
Jon: OK.
Professor Bradley: But, people are not very willing to contact you about that. So, I know what they were looking for. I know that they found it. But, I don't know if they went on and actually did an experiment from that, because that's something that I can't control. I can't actually contact the people because all I know is their location.
Jon: Yeah. But, you did mention that, through this process of exposing your work on the blog, you've come into contact with people who have become collaborators.
Professor Bradley: Yes. So, I didn't say "never." I just said most of the time; people don't end up contacting you. But, once in a while, you do, in fact, intersect with someone who is interested in open collaboration, and they're willing to participate. They have the skills to actually do something.

For example, we're making anti malarial compounds. So, one of our collaborators is Rajarshi Guha, from Indiana University, and he does docking calculations. So, he basically uses just a computer to tell us which compounds we should make. And then, since we're the synthetic organic group, we can actually go out and make those compounds, and the have them tested somewhere else. For example, Phil Rosenthal's group at UCSF has tested our compounds for anti malarial activity.

So, those are the kinds of collaborators that I'm very excited to be able to interact with, because they're doing exactly the part of the process where we're not the expert.
Jon: Yeah. So, in the normal course of events say, 15 years ago you would have run into people like this at conferences, or you would have read papers that they had written. In other words, it's not that there was no way for people to discover collaborators and to get together. Is it just a question of, it's one of those differences in degree becoming a difference in kind, kind of a thing?
Professor Bradley: Well, it has to do with speed, essentially...
Jon: Yeah.
Professor Bradley: Because it's very true. I mean, I can write a paper, and someone can find that paper. But, in order to actually get to the point of having a paper, you already have had to do a lot of work that actually works into a nice, little story. And a lab notebook isn't like that. A lab notebook is basically just stuff that you tried, and you try to get to a conclusion as quickly as you can, with sometimes limited information. And so that's a totally different kind of interface.

But, I should say. You were asking about the whole system. The lab notebook is definitely an integral part of the system. But, there's also a blog. There's also use of other social software, like FriendFeed and all these different, additional ways to connect up with the information.

But, regardless of how I talk about it, I'm always able to put a link. So, if I make a comment on my blog that's higher level, I don't want to repeat all the experimental details. I can just shoot a link over.
Jon: Yeah.
Professor Bradley: If someone has an issue, they can look at that. And I think, that's more where the utility is, if anyone wants to dig into any statement, they can. It doesn't mean that everybody's going to do that. It's only going to be the people who have a vested interest in a particular reaction, for example, that might bother.
Jon: Yeah. But, it's there if they choose to follow it.

So, there are, well, a variety of reasons why this isn't the dominant way things are done yet. And I guess we don't know if it will become the dominant ways things are done. But, talk about some of the push back, the reasons why, for publishing and tenure issues or for competitive issues, people would tend to not want to go this route. And how do you have that conversation with people?
Professor Bradley: Well, yeah, you're absolutely right. I mean, there are a lot of issues to consider, and they get brought up often at conferences. I really like to see the people's opinions on that. Although, at these conferences, to be fair, it's a self selected group, so a lot of the people there will be open already to openness.

But, you're absolutely right. In terms of doing traditional research, depending on the field but in organic chemistry, it's generally fairly secretive people do talk about their early results at conferences sometimes. But, this whole openness like you has, like with the genome or some specific datasets like that, and is not part of the culture in chemistry.

You also have the issue of intellectual property. So, obviously, if I'm doing my work in real time, I'm showing everything that's going on. I don't have time to protect it.
Jon: Right.
Professor Bradley: Now, in the US, you could still get away with that, but it's just easier to just not deal with the intellectual property. There are plenty of areas in science where intellectual property doesn't even come up, like cosmology, and there are still people interested in doing that.

So, I think, for chemistry, what kind of shocks people sometimes is that they sort of assume that everything they're doing can be turned into a profitable patent. But, the reality is that, most of the time, that's not true, and it's also a lot of hassle to actually go through, and it's very expensive for the institution.

So, it's really not that different than sending a paper out. As soon as that paper goes out, and if you haven't submitted at least a preliminary patent, you're not going to be protected. So, that's an issue that you have to wrestle with.

It's not something that I'm trying to convince people to convert to. I'm just basically saying I have a hypothesis that making your research fully transparent and as close to real time as possible is going to actually produce a qualitatively different kind of science progress. And that's going to require the cooperation of some people, but not necessarily the majority of scientists.
Jon: That's a good point. That's a good point. So, this network effect could be very powerful, but involve relatively few notes, in fact.
Professor Bradley: That would be fine.
Jon: Yeah.
Professor Bradley: Yeah. For me, I also want to move towards more automation, where machines are actually designing experiments, executing them and analyzing them, and then sharing their results. And in order to get to that kind of a system, for me it's obvious that everything has to be open, because, if not, the barrier that you have to go over to pay for services and try to get special permission to access people's data, it's just so large that it's just not going to happen very soon.

But, if all this information is open, anyone in the world who wants to, for example, look for correlations in our data, they can write a script, they can read it, and they can say, "Well, look, why don't you try this experiment?"

And ultimately, we'd like that entire process to be fully automated. So, one of the things that we're actually looking at this week, we have Mettler Toledo, they're doing a trial with us. They brought in one of their automatic reactors. They were going to see if they can get people to suggest experiments for us to do during this trial of a few weeks.

So, ultimately, I have a destination beyond the human to human collaboration. My view on it is skewed with respect to that. And you don't need to get the majority of people contributing to have that effect.
Jon: You said, in passing, something kind of provocative: that the machine would be designing the experiments. What did you mean by that?
Professor Bradley: So, we're mixing these compounds together, and we actually don't know right now what the governing factors are on getting pure products as precipitates.
Jon: So, it's kind of a large possibility space. And if you could automate the sort of march through that space, then you'd like to do that.
Professor Bradley: Yeah. And that's not going to be us doing that. That's going to be people from the artificial intelligence community, or from the bioinformatics community, who may take an interest. And I can't predict that. All I can do is I can make it available, and I can make it as convenient as possible for people to get the information.

And so, I'm using things like Google Docs, Google Spreadsheets, as ways of quickly sharing information, the summaries of the lab notebook, and getting people to put reactions that they want to do in another Google spreadsheet. So, now there's the opportunity to make the Google spreadsheet completely public. I don't know if you're aware of that.

And so, that's actually pretty cool. So, that means that people don't have to register and log in and do all kinds of things.
Jon: Yeah.
Professor Bradley: They can just find it, dump their information. And ultimately, I'm in control. But, if I see that we have the ability to run an extra few reactions, why not? And that would be something that the whole world would benefit from.
Jon: [laughs] That's a really interesting take on this that I hadn't heard before.

So, you've talked a little bit about this kind of machine to machine possibility. In the human domain, I guess there's still an awful lot of what I tend to call tacit knowledge involved in understanding how you actually get a result from an experiment, which involves a lot of variables that you may not even perfectly understand yourself. And so I know that you've been very active in the use of screencasting as a way of kind of capturing... Well, you should talk about, actually, how you see that sort of show and tell piece of it fitting into the picture.
Professor Bradley: Yeah. In terms of screencasting well, following your lead, of course I think, it's a fantastic technology. And I've used it pretty extensively for teaching. All of my classes in organic chemistry are recorded, and students can access them from anywhere. And it really does replace, in the sense of a classroom kind of interaction or I should say a lecture style interaction with students, it really does replace it.

If you have a really good screencast, good audio, everything that you do on the screen is recorded, students can get exactly the same kind of information that they can in a live classroom. That's actually allowed me to stop doing lectures, and assigning the screencasts in the same way that I would assign a book chapter.
Jon: Ahead of class?
Professor Bradley: Yeah. I mean, there is no lecture anymore in my course. It's all workshops.
Jon: Yeah.
Professor Bradley: So, the students watch the screencast, do the problems, and then they come to the workshops and I can help them one on one.
Jon: Mm hmm. Mm hmm.
Professor Bradley: So, it's a fantastic technology, very simple. It reminds me very much of the social software, because of how simple it is and the leverage that it has.
Jon: So, in this case, you said that having seen the screencast, which replaced the lecture; they then can come and receive really kind of individualized instruction. Is that actually happening kind of one on one? And if so, what's the continuing role for getting the class together as a group, physically?
Professor Bradley: I don't see a purpose of getting the entire class as a group together.
Jon: Really?
Professor Bradley: My objective is the students learn the skills that I outlined in my syllabus.
Jon: huh.
Professor Bradley: I test them on that, and if they understand the material, they will do better on the test. So, my role as a teacher is I'm looking at the student learning. That's what I'm focused on. And if that requires me to spend three and a half hours with a group of a couple of students because that's how they learn best, that's fine. If other students can just go out I get a lot of pre med, and they're very busy. If they can do very well, and if they can understand the material from the screencast and from reading the book, that's great, too.
Jon: Yeah.
Professor Bradley: I know that some teachers do take it personally, this whole attendance thing. But, to me, leverage the technology. Keep remembering what it is that you're trying to do as a teacher, and if you can do it as effectively with technology, you don't necessarily have to be face to face.
Jon: So, I assume this is at least somewhat controversial. [laughs] You're in a business which, for a thousand and more years, has been kind of predicated on the lecture format to a group of people assembled in one place.
Professor Bradley: Yeah. Yeah. And they are still getting that, in the sense of the screencasts are simply recordings of those lectures. It's just that they can pause it. They can fast forward through it. It is still the lecture format.
Jon: They don't have to take notes. Yeah. Yeah. Oh yeah.
Professor Bradley: They are still used to someone's going to write something on the board and somebody's going to explain something, so I think, it's not that difficult for them to migrate from that.

And the big controversies about doing podcasting classes: will students still come in? It depends what the intention of the professor is. If you actually do take it personally that your students are not going to show up, and you do things like leave out certain things from the podcasts or you only give audio if you leave things out on purpose, then of course they're not going to do as well if they don't come in.

But, I'm not approaching it like that. I'm just approaching it: can I replace the lecture interface? And I do think that we can do that. It works pretty well, actually.
Jon: And then, so talk a little bit more about this other aspect, the sort of face to face, personalized instruction. How is that evolving? Because there's time constraints on that. So, how do you manage your time?
Professor Bradley: It depends on how many students come. Like they just had a test yesterday, so there was a pretty heavy review session today. If a few students have a similar problem, I might just go to them, have them work together. If there's only one student that has that particular problem, I have no difficulty with just working with them one on one.
Jon: Right.
Professor Bradley: I typically will not give them the answer. So, they'll show me what they're doing, I'll give them a hint, and then I'll move on to the next student or next group of students. And I'll rotate like that. And I think, that works pretty well. Sometimes it's a little bit strained, like the last 15 minutes of the last workshop for the final exam. Yeah, it's going to get a little not everybody's going to get their questions answered, necessarily. But, all the other workshops, really, there is plenty of time to do that and does it well.
Jon: There are all sorts of things that you can imagine once you eliminate that particular constraint of "we're all in the classroom together at the same time." And one of those is that, well, your class is one of a number of classes that are going on in various parts of the country, various parts of the world.

So, at the same time, there actually are other people who are teaching and other people who are learning the same subject. And then, if you relax the same time constraint, while there's the class that did this the year before and the year before that, and also in these other locations. Do you know what I mean?
Professor Bradley: Yeah.
Jon: There's this notion that there's a kind of a wide area kind of collaboration that we can at least imagine would reshape the process of education in pretty interesting ways. Have you had a sense of how that could develop?
Professor Bradley: Yeah. I think, one of the best ways of doing that is through Second Life.
Jon: Really?
Professor Bradley: Because my students have extra credit assignments where they need to represent like a reaction that they learned in class onto Second Life. And we now have tools that allow us to build molecules pretty easily like full 3D molecules that are realistic looking using some tools that Andy Lang has actually developed with me. And so I've had my students do that. And they also can take quizzes in Second Life.
Jon: So, you're saying the molecular modeling is being done in Second Life, or it's being done in some tool which then imports the thing into Second Life?
Professor Bradley: Yeah. I mean, technically, it's done. What we need to figure out is the SMILES, or the InChI code, for your molecule.
Jon: The which code?
Professor Bradley: It's called SMILES.
Jon: OK.
Professor Bradley: It's a way of representing a molecule with a string of text.
Jon: Yeah, OK.
Professor Bradley: And that you can get from a number of places. We typically use like ChemSpider, or ChemSketch.
Jon: OK.
Professor Bradley: They're both free. And you can just draw the molecule and just export the SMILES. And then you basically go in Second Life. I give them this little machine. It's called a rezzer.
Jon: Yeah.
Professor Bradley: And they simply talk to it. They just dump the SMILES there, and the molecule, it actually hits a couple of servers to minimize the molecule to make it look realistic. And it uses that information to build it right in front of you. It's pretty neat, I have to admit. The first time the students actually see the molecule being built in 3D in front of them, it's great.

And the nice thing with these new tools is I don't have to spend any time whatsoever talking about scripting or anything like that. It's very, very simple.
Jon: What's the Second Life connection here? In other words, you could refer a student to a web page that would launch something that would build the molecule and enable them to view it in a 3D fashion. But, there's more to this, I assume, right? There's this notion that, well, there's kind of a shared space that they're virtually present in. And so, what's the significance of that in this context?
Professor Bradley: Yeah. The power of Second Life, a lot of people don't realize. It's not so much the 3D world; it is the network. And so, what you do is these molecules are basically presentations. They just happen to be in 3D instead of in a poster format.

Although they do have to write a little something about what the molecule is, and if they're doing a reaction, they explain what it is, and other people can come and visit it. So, that's one place where there could be an interaction with other organic chemistry students from around the world, or with even teachers who teach chemistry.
Jon: So, this is actually occurring? And if so, can you kind of characterize what that interaction is like? Are people kind of standing around watching a molecule being built in Second Life and having a conversation about chemistry? I mean, is that what's actually happening?
Professor Bradley: Well, the building of the molecule may or may not happen in front of other people. It depends on who happens to be there.
Jon: OK.
Professor Bradley: But, these presentations are left there.
Jon: So, people can walk up to them after the fact and...
Professor Bradley: Yeah. On various islands. Like we have Drexel Island. We have Nature Island, called Second Nature. There's American Chemical Society Island, where I've participated in some of the construction there. So, there are these even chemistry specific resources, where you're pretty likely to find chemists there, especially on a place like American Chemical Society Island. So, definitely there's networking possibilities.
Jon: So, in that case, then, it's a question of, on the one hand, you have synchronous communication, like, "Is the person here now? Can I talk to them?" But, more broadly, there's asynchronous communication, which wouldn't really require Second Life at all. It could just happen on the web, right? So it may be, actually, a broader opportunity.
Professor Bradley: Yeah. I mean, if you think about Second Life as primarily a tool for connecting people together, there are a lot of asynchronous interactions. For example, there's a chemist who, nearby to my lab area on ACS Island, built a peptide. And she was looking at it and wondering if the chirality was right on the different atoms. I wasn't there when she had that issue. But, she IM'ed me. And what happens in Second Life is, if you're not there, it goes to your email.
Jon: Right.
Professor Bradley: So, I get this email. She has a question. So, I log in a couple of hours later. She's not there. But, I go to her peptide, which is in 3D, and I look at it, and I confirm that, yeah, in fact this is the wrong chirality for this amino acid. And so I leave her a message.
Jon: Yeah.
Professor Bradley: And then, maybe next time, we're both there at the same time and we can talk about it synchronously. But, you can absolutely interact with people asynchronously as well.
Jon: Yeah. Although, I guess what I'm getting at here is the fact that this is occurring in Second Life is kind of tangential, in a way, right? Like it all could happen in other ways on the web.
Professor Bradley: The thing is that Second Life is very sticky, so you are more likely to find people doing stuff. Whereas, if you just went to a chat room, for example, I don't think that would work very well in chemistry, because it's difficult to show what's going on. There's not a sense of identity. The avatar effect is actually very powerful, in terms of people identifying with their avatar. And most students, after a couple of times in, want to know how to change their avatar to look like something else.
Jon: Mm hmm.
Professor Bradley: And that's the kind of involvement that you will not find in a lot of these other social software kind of interactions. So, yeah, it is actually different in that sense, I have to admit.
Jon: This is a little bit of a tangent, this whole thing, but since you brought it up. I mean, my sense right now is that, as a mainstream kind of phenomenon, Second Life is gated by the pretty intense amount of UI machinery and sort of conventions that need to be mastered in order to just navigate and be in the space in an effective way. Do you know what I mean? It's like there's a fair amount of overhead there for people to get over.

And I think, we're like a generation or two away from this being a naturalistic enough kind of an interface, that people will spend way less time figuring out how to drive their avatars around and can focus more on what's actually happening in the environment. Do you think that's a reasonable observation?
Professor Bradley: Yeah. That is a very important factor if you consider using Second Life. And that's where the workshops are extremely handy; because the students bring their laptops, and it takes like five to 10 minutes to get a student, totally naive to being able to do everything they need to do walk around, fly around, click on a quiz, build a molecule. And that happens very easily if we're in the same place at the same time.

But yes, if I just tell you, "Go onto Second Life," most people will get pretty frustrated because you end up on these orientation islands, where the purpose is more general. They're trying to show you how to do all kinds of different things. But, I don't need my students to learn all kinds of different things. I just need them to fly, walk, teleport, maybe talk, chat with who they want, and add a friend.
Jon: Yeah.
Professor Bradley: Then, if they want to change their appearance, for example, that's great. But, you shouldn't make that a necessary thing in order to participate in the process.

And again, I can't overemphasize how important it is. That face to face time with the student's laptop can make that process almost painless.
Jon: Or, I guess, actually capturing in a screencast some of the instruction that you do in that face to face environment. So, that also could be...
Professor Bradley: Yeah, absolutely. I haven't done that. I've thought of doing that. I mean, students also have issues with their computer. I can tell if their video card isn't good enough to run Second Life...
Jon: Yeah. Yeah.
Professor Bradley: Yes, the screencast would help a little bit, but it's really nice to have that face to face.

So, yeah. I mean, it's just a factor. And once you take that into account, then it becomes pretty usable. Now, I don't make Second Life mandatory in my class. That's a whole different question.
Jon: Right. Right.
Professor Bradley: If I have 200 students, it's not feasible for me to do that.
Jon: Right. Right. Right.
Professor Bradley: Yeah.
Jon: So, [laughs] I didn't realize you were so deeply into that. That's interesting to hear.

I'm a little bit skeptical about it, just because I'm trying to focus, in my own work and in my own stuff, on things that are, I would say, more accessible to everybody, and where the barriers to entry are lower.

So, here's the thing. Even when you strip away all of the technological barriers so, if everybody had the right gear and the right amount of bandwidth and things like that there's still sort of like conceptual hurdles that people have to get over, right? I mean, you crossed a huge conceptual hurdle when you got into open notebook sites, right? There's no high tech really going on there.

I mean, yeah, you mentioned that while it helps to have these services kind of floating on the net that we can just use for this purpose. But, it's more sort of getting the idea, right? That intuition that you have, that by operating in this transparent way, the science will progress faster and better than it otherwise could, right?
Professor Bradley: That's the hypothesis, yeah.
Jon: Yeah. And that's just a question of getting the idea in your head and then having a sense of how to use some pretty basic, very readily available technologies. So, blogs and wikis had been around for quite some time before this idea started to take hold. You know what I mean? In other words, I'm trying to say it's more of a conceptual breakthrough that isn't really gated to any particular technology at all.
Professor Bradley: Right. And that comes up when we talk about other sciences that may not have the traditional paper notebook. I don't know. I mean, I'm just saying, if you focus on making your science as transparent as possible I like to say, try to have no insider information. In other words, someone observing what you're doing would be able to come to the same conclusions as your internal group.

So, if that gets done with a wiki, that's fine. Everybody's using a slightly different system. And that's what's very interesting to see, that we're learning about not only their science, but also about how they think about science, as they construct their notebook.
Jon: So, tell me this, then, since we would all agree there is an appropriate role for competition and there are also, obviously, lots of ways where cooperation is appropriate, we are always kind of struggling to find that balance. It is not an 'either or' kind of thing. We need to have the right ingredients in the right proportions.

And so, from that perspective how do you see weaving in the appropriate aspects of the competitive nature of science into this environment where, in fact, there is also this transparent work happening? How do you reconcile those things?
Professor Bradley: Well, you are making a supposition that competition is necessary for science to progress, and I don't think that is correct.
Jon: OK. Well, good.
Professor Bradley: Because I think, competition if you have a company and you have a business moral that is based upon intellectual property, then absolutely. Then, you have to build the way that you work in such a way that you are going to be able to protect these compounds and then solve them or whatever you want to do.

In terms of actually getting science done, in the sense that today we are able to do something that we weren't able to do yesterday because we understood something new. Maybe, we didn't understand anything. Maybe, it's purely empirical. Like we just know how to make these compounds precipitate. It will take a year to figure out why exactly, but if we are able to control reality in some new way, then I think, that can be done without competition.
Jon: Setting aside the intellectual property aspect of it, there is just the notion that while being the first one to discover something is really different from being someone who comes along afterward or even someone who made the discovery just slightly after the first person did.

There is a kind of I guess you could call it a game behavior which is, I think, kind of fundamental to human nature. Where I was sort of going with this though is that one of the, I think, still unfulfilled uses of technology in particular the stuff that looks like or can be made to look like games is that there are ways to leverage that sort of game behavior and that competitive instinct which can be useful.

For example, a lot of social software is a way for people who are active and who make contributions to take credit for the contributions that they've made, and there can be positive aspects to the kind of competition that is engendered by that architecture.
Professor Bradley: Yeah, I think, in that sense competition can be useful. Like recently I submitted a proposal to the Gates Foundation. Part of the idea is to give prizes to the first people who predict that a compound would be active and make the compound and then test the compound and it turns out to have a minimal activity. Giving out a prize for the first three people who actually do that, I think, there is an element of competition there, but it is not where people are going to work secretly.
Jon: Exactly. This is really just a kind of this line of thinking here. A while ago I interviewed a guy, Ned Gulley, who works at MatWorks, and he designed a contest for Matlab programmers which have turned into a really interesting thing because it is a contest, but it is also a contest that also happens in framework where ultimately all of the code that you write is transparent.

If you are working toward a solution, you can clone other people's codes. You can tweak it. You can completely change it, and so there is this fascinating kind of interplay between. You know, there are incentives for sharing, and there are also incentives for not sharing. And people are kind of walking the line between those two sets of incentives as they play this game.

It is just a real interesting kind of social experiment in terms of how we leverage the competitive instinct in ways that can be most useful and productive in an environment where ultimately it is all transparent.
Professor Bradley: Yeah, that is a great example. It is very analogous, absolutely. You know, in terms of just talking about the simplicity of the software...
Jon: Yeah.
Professor Bradley: One of my biggest surprises when I was doing this initially, naively I thought that you just use a blog to record the experiments.
Jon: Yeah.
Professor Bradley: It seemed to me to makes sense because you have one post. You can describe one experiment, and then have people comment on it. And then, create a new experiment. That actually didn't work very well, and the reason is there is so much editing that goes on in terms of recording the science. And the wiki is because you are able to access any individual version. You are able to see when conclusions were made, when errors were found and corrected. You are able to see who did each particular contribution.

So, in terms of the software, people do want attribution and using something like a wiki breaks down each person's contribution to such a fine level that, I think, it makes sense for people to participate because you will get credit for exactly what you did. And that is a very special kind of technology that allows you to actually do that. If we did not have wikis I don't think that we would still be doing it at this point.
Jon: Or more broadly, version control.
Professor Bradley: Right, easy version control.
Jon: Yeah. No, I think, that's right, actually. This is an area where relatively few people have yet to experience that effect. Programmers take it for granted. Programmers have been working in source control systems for many years and have at this point an intuitive sense of what it's like to be in an environment where, like you said, each contribution is individually tracked and can be rolled back and so on. Those people who have gotten deeply involved in working in the wiki environment also have developed a sense of that.

But, I think, that is still probably a new experience to most people, the fact that things can work this way that these things can be tracked in this granular way?
Professor Bradley: Yeah, and not everyone is necessarily comfortable working with the wiki right away.
Jon: Right.
Professor Bradley: It is a minor issue that can be addressed, but that's part of the reason that we use multiple technologies. We also use a mailing list, for example. It sounds very 'old school,' but it turns out that it has a very good role to play for certain kinds of interactions, especially debugging stuff. It has to work pretty well.

You know, it's not like one of the technologies took over. It is all these pieces that actually fit very nicely together. They are all free, and anyone who wants to replicate any part of the system can do so overnight, basically.

That's another reason why I worked with the specific tools that I did because it is always frustrating if you see something that you like that you want to do, and oh, you have to buy software. That's a big limitation for people getting involved.

That's another very special thing that has happened in the past years that wasn't there several years ago.
Jon: I think, I read that you are also sort of the e learning coordinator for Drexel at large. Is that true?
Professor Bradley: For the College of Arts and Sciences at Drexel, I am the e learning coordinator.
Jon: Maybe, to kind of close out, you can say a little about how because we have talked a lot about science and chemistry in particular, but what your view is of how these things are playing out in other disciplines at the school.
Professor Bradley: Well, one of the projects that I was involved with pretty heavily is setting up Drexel Island on Second Life. We have about 30 groups on there. And that's been an interesting process, to see what people find to be helpful, what kind of use they make of the technology. A lot of it is basically just advertising their department or class, whatever. And everybody has a different take on it.

And I think, that's been my main focus, in addition to helping people with screencasting. But, in the past year, that's probably been the most intense thing.

You've mentioned that you have some reservations about it, and I absolutely understand that. I was actually not that caught on it for a long time, because it felt like it was using technology just for its own sake. But, I had a friend, Beth Ritter Guth, who was teaching English, and she invited me to her class in Second Life. And once I saw how the avatars interacted together and how it was really different than anything else, I got interested.
Jon: How would you characterize what you saw happening there?
Professor Bradley: It's very personal. In other words, you turn and you can see an avatar. And you have to remember, when you're looking at an avatar, especially for someone who's been around there for a while, that's them. That's who they want to be. Because you can be whatever you want to be. So, you're actually looking at them, in a sense, even more deeply than you would in person, because you can't change everything about yourself in person.

So, there's that very personal connection that you absolutely do not get from a chat room. Because we're still using chat. Or you can use voice. In fact, voice has been a recent addition. And it's kind of interesting: we still don't tend to use it, even though sometimes three or four people are gathered and everybody has voice. You can tell because there's a little white dot that shows up on the avatar's head. But, people still like to use chat.

So, there is something interesting about that, in terms of this kind of barrier. I think, it has to do with some kind of privacy. People still feel a little bit more private when they're using chat.
Jon: We still need to kind of get at why it is that... So, earlier, you said, well, there really isn't an important reason anymore for people to gather together in the physical space of the classroom. At the same time, we're saying, well, there may be a reason why it's interesting and important for people to gather in these virtual spaces. So, why?
Professor Bradley: Well, to meet people. I mean, I think, from my perspective, I introduce my students to organic chemistry. And that has to do with content. It has to do with principles. But, it also has to do with getting involved in the world of chemistry in general.
Jon: OK.
Professor Bradley: And right now, that's the big opportunity with Second Life, is that doing very minimal things, I can bring a couple of students in who may even be tech averse. And then I can see, once they realize that they can meet new people that become interesting. They can meet their classmates, of course, who they might not have seen because they were taking everything online.
Jon: [laughs] You have to admit, there's a certain kind of circularity to this, right? Its like, [laughs] "We could have just gone to the physical place and met. But, we're not doing that, so now we have to go to this virtual place to meet. But, if we're all students at the same university on the same campus, we actually could have met in the same physical place."
Professor Bradley: I think, it has to do with the term "have to." This is just an additional channel that they can use. So, it's not something that they must do. If I hold a class and I have an attendance policy, I'm saying, "You guys must come here." OK?
Jon: Right.
Professor Bradley: And that locks me up from doing other things.
Jon: Yeah. Yeah. Really, what we're trying to get to and you started to go there with this example from the English class. What she was saying, what this teacher was saying is that there are aspects to the quality of interaction that can occur in that environment which are qualitatively different and, in some ways, for some purposes, better. Right?
Professor Bradley: Yes. It all has to do with this long tail, I guess. Most students don't participate in it, and that's absolutely fine. And it benefits a certain sub population of the class; just as having a certain kind of workshop with students benefits them in a way that it doesn't benefit other students.

Using the screencasting, that buys me time. And that's the important part of the screencasting. So, by doing that, I'm able to do the Second Life. I'm able to use molecule models, for example, physical molecular models that I can pull out, and we can look at things that are difficult to see on paper.
Jon: So, in terms of, when you said "long tail, " it sounds like what you really were getting at there was that in a class full of kids, as we know, there are going to be a few who are outgoing and social and will perform well and communicate effectively and actually end up taking up a lot of the airtime in that setting. And this is, again, generally true for many modes of electronic communication, not just Second Life.

But, in these other modes, it becomes possible for people who have sort of different comfort levels, different amounts of extroversion versus introversion, and different styles of communication, to flourish where they might not have flourished so well in the face to face environment.
Professor Bradley: Yeah, exactly. And again, the student is in control of this. I think that they're getting their best value with the model that offers different possibilities.

They take a test after a couple weeks, all right? Now, if they get a poor result on that test, at that point we need to figure out, "What is it that you need to be doing? Maybe you thought you could do this class completely online, but it turns out that, no, you've got to come in for one workshop a week." And I can simply advise them of that. From my experience, I know that's exactly what they need. And all I can do is basically just tell them, "These are the options you have in my class. And if I think that you can benefit from Second Life, I'll help you with doing that."
Jon: That's a good way to put it. Yeah.
Professor Bradley: Yeah. And that's all it is, really.

If you were asking me, "What was the benefit of Second Life?" I was sort of looking at the most beneficial thing that could possibly happen is that they would meet someone that, later on, they would end up doing a co op at a company because they met somebody from there, or they would do a PhD somewhere. And those are the kinds of connections that are kind of difficult to make for students who are undergrads, like sophomores. And I think that that can have a tremendous benefit.

But no, I couldn't expect 200 students to go through that process. I mean, most of the students are busy enough just worrying about getting the basic material down.
Jon: Yeah. Yeah.
Professor Bradley: But, it's an interesting possibility and something that I had not really contemplated before I got involved with it, as to why it is a powerful tool. For me, it comes down to the networking, either in teaching or research.
Jon: Well, we're not going to solve it on this call, but it is still to be explained what's the sort of qualitative difference between this style of interpersonal communication and social networking that happens, or can happen, in Second Life, versus the style that is happening in a variety of other environments online, right?
Professor Bradley: Well, a really good example is a chat room. I'm sure you have a lot of experience with going to a chat room. There's 10 people already having conversations and you don't really know what's going on, and you're trying to figure it out. Well, in Second Life, because everyone has an avatar, you can approach a group of people, and you see who's talking to each other.

You can face a certain person, or you can even IM one of the people from the group. It sounds strange, but there's a huge effect. It really feels like you're actually there. To the left of you are Juan, and to the right of you is Mary. And, that's a completely different feeling than being in a chat room where you can't see anything.
Jon: No, it's true. Setting aside all the 3 D modeling, it does seem to be the notion of what you just said. Here I am and to my left is this person and to my right is that person. There is something kind of deep and fundamental about that, that is a little mysterious, I think, but obviously, powerful.
Professor Bradley: Yeah, and if the person next to you is dressed up as a Goth that tells you a lot about them. You can have a conversation with them that would be totally non existent in the chat room and, you can actually be quiet. So, you can approach a group and everyone will know that you're there, so if they want, they can turn to you and talk to you. And again, that's something that you can't replicate with a traditional chat room.

So, there are a lot of good things you can do. I guess I didn't mention that I've run a couple of conferences using poster presentations in Second Life, and that works really well in terms of having the avatar stand in front of the poster and people come and ask questions.

You can click on the poster to see different slides. And that's something, from a technological standpoint, that's very nice because you can take a PowerPoint and very quickly export the images and upload them in Second Life pretty quickly. So, that's something that I think, is one of the most useful things that you can do with this technology.
Jon: Yeah, that makes a lot of sense because at that level the telepresence is a really effective replacement for taking the plane trip to be at the place. Let's put it this way, on the one hand, it replaces the part where you're standing around looking at the poster and discussing it with the presenter, and that's actually a reasonable substitution. And then, to what extent it substitutes for the conversation that you had in the bar afterwards, your mileage will vary in a whole lot of ways, depending on who you are and who the other person is, and what the environment is.
Professor Bradley: And, what their experience is because if they have a slow video card, you have to realize that they're just spending all their time being frustrated. They're turning right and there are delays. So, those are some of the things that we talk about with new people, and if they're unhappy, we just try to figure out what's going on here. And, if they're computer doesn't have a good video card, there's no point in continuing because it's just too frustrating.
Jon: It's good to hear your thoughts on this because I always like to revisit my prejudices and my biases.
Professor Bradley: I know that feeling.
Jon: You're inviting me to reconsider how I have been thinking about the uses of Second Life.
Professor Bradley: Yeah, let me know if you want a little tour, I'd be happy to give you one. I could show you Drexel Island, certainly, and Nature Island has a lot of good things in terms of science.
Jon: You know, it might be fun to do that and make the movie of it.
Professor Bradley: Yeah.
Jon: Actually, for me, one of the coolest things about Second Life was the camera control, and that there really is this camera there that you can independently move around, point at anything, zoom in or out, and pan. The cinematic graphic possibilities of Second Life are pretty amazing, and I've done a little bit of that, and it would be fun actually to do this.
Professor Bradley: Where did you go?
Jon: Where did I go? Well, actually I was invited to an IBM press conference on Second Life. This is actually what gave me the sense that I still have, which is that a lot of this reminds me of the early days of the web when people would say, breathlessly, come visit my page on the World Wide Web and you're like when?

Corporations were hiring design firms to make their all important home page on the web. And so, when I started, like 10 years later, to hear about companies hiring design firms to build out their Second Life islands, I thought this is just a replay of that and I think, honestly, in some ways, it is.

Actually the movie that I made is probably the funniest thing I've ever done. It's me at this IBM press conference where basically I get there and some guy's showing a PowerPoint that I'm not interested in, and there's a bunch of people I don't know, so I wind up wandering around looking at the fish tank, and eventually I get bored and fly around.
Professor Bradley: You have to have a good reason for going in. Have someone give you a tour. I think, you'll find it much more satisfying.
Jon: Let's do that.
Professor Bradley: Now, what software are you using for recording these days?
Jon: Well, you can do it right in Second Life.
Professor Bradley: The Screencast?
Jon: Yeah, you can do a screen cap right inside of Second Life. Did you know this? It's one of the coolest things.
Professor Bradley: It's built in?
Jon: Yeah, it's built in.
Professor Bradley: I didn't know that.
Jon: You just turn on the recorder.
Professor Bradley: I'll have to check that out.
Jon: Yeah, that part is great.
Professor Bradley: I was using Camtasia.
Jon: No, you don't need to. You can save directly, or you used to be able to. I haven't looked at this in a couple of years.
Professor Bradley: I wonder why I never came across that. That's weird.
Jon: Yeah, you hit the record button.
Professor Bradley: I will definitely check that out. It just records with the camera?
Jon: It records the view.
Professor Bradley: Does it show your little avatar in there?
Jon: It does.
Professor Bradley: Behind your head?
Jon: Yeah.
Professor Bradley: OK, cool.
Jon: That would be kind of cool actually. There are precious few actually I would have to say no examples that I know of where somebody can just go, without the overhead of getting into the environment, and learn how to fly the avatar around. But, somebody can just go and see a nice crystal clear example of how this stuff is being used in an educational context, and can take away a sense of what that mode is doing and what the value of it is.

Well, it's been a pleasure to speak with you. I've been hearing about what you do from all sorts of different people who keep on saying that you should talk to Jean Claude.
Professor Bradley: Well, thank you very much. Actually you're one of the first names that I saw. This is when you did "Umlaut".
Jon: Oh, the Wikipedia movie.
Professor Bradley: That was pretty cool. And then, look at what's happened after a few years.
Jon: Which, of course, was not new almost nothing is really new. But, the idea that these representations of what happens in computer screens can be canned and replayed has become how all kinds of software are explained to people now.
Professor Bradley: Yeah, it's a no brainer once you know how to do it.
Jon: Yeah.
Professor Bradley: OK, thanks.
Jon: Thanks a lot.
Professor Bradley: Bye.

[music]
Announcer: You've been listening to Interviews with Innovators with host, Jon Udell. By joining as a paid member, you'll not only help keep the Conversations Network on the air, you'll also have access to our premium edition programs without promotional messages. Just click on the 'Join Now' button on our website to learn more.

Our audio files are delivered by Limelight Networks, the high performance content delivery network for digital media. The post production audio engineer for this program was Jon Udell. Our website was editor Niels Makel. The series producer is Niels Makel.
Phil: This is Phil Windley. I hope you'll join me next time for another great edition of Interviews with Innovators on IT Conversation.

LISE08 talk on Second Life in the Chemistry Classroom

2008-05-16T08:40:00.002-04:00

LISE08 talk on Second Life in the Chemistry Classroom screencast

Jean-Claude Bradley: OK. So, thanks very much for the invitation. I think this is a fantastic conference. We've seen many different technologies being used for science education and specifically for chemistry. So I'd like to actually show you in detail how it is that I have been using Second Life to teach chemistry.

Now before I do that, I always like to remind the audience that there is a purpose to these things. As we get new technologies, as we evaluate these new technologies, we have to remember that we are still teachers and there are things that we are trying to do with them. Right?

In terms of chemistry, I want to have students who are competent to understand and generate new chemistry. So keep that in mind whenever you look at these different applications.

The story starts actually a little bit before. I'm going to talk about Second Life but I think it's really important to show how it actually evolved to that. A couple of years ago, I started to record my lectures as I am now actually.

This talk will be made available. I do this in the form of a screen cast. So everything that appears on the screen, in addition to my voice gets recorded.

I would give that to my students after the class so they could review material. I could put these on iTunes or I could put them on a server. There are many, many different ways. We've heard about podcasting, so that is one way that you can deliver this content.

You can see from this small image, I use a tablet PC so I can draw molecules. In organic chemistry it is especially important to not just see the final answer, but see how you arrive to that final answer; how you push the arrows and all that.

So what happened is I started to track the attendance in my class as I made these available. You can see here, this yellow line is the attendance from the first day of class until the end.

[laughter]

The same thing in this class. It starts off here and ends up here. So, by the last lecture there are only 10 to 20% of students that are still showing up. Now what is interesting about that is that I look to the performance in both these classes, between those two groups of students and the performance was the same.

So, in other words, if they just watched my lectures and never came to class, they did just as well as the small minority of students who still came.

So, I started to re-think what it means for me to be a teacher. Does it necessarily mean for me to repeat myself term after term with exactly the same material? We have a lot of stuff to go through and if I am going to be lecturing, there is only a certain amount of time I have left to do other things.

So, I started to just actually assign the recorded lectures. I started to do other things with my class time. So for a couple of terms now I've been basically using the class time as workshops.

The kinds of things that we do here is a lot of what we saw here today in terms of games, in terms of Second Life. You have students who are watching the lectures with headphones and then when they come to a problem that they are having difficulty with, they come up and join the group.

It's either one-on-one attention or if there are several students, it may be group work. Whatever it is, I am spending the same amount of time teaching, but I'm doing something completely different. I'm actually being a learning catalyst as opposed to a parakeet. I think it actually is better for the students, I think.

The other thing that is really useful by having these workshops, and don't underestimate this, the technical implementation for these software packages. Don't believe that all the students are already on YouTube, that they know how to use Second Life. In my experience that's not true. It's actually pretty unusual that a student will already have been in Second Life. It requires me to show them how to create an account and how to get on.

There is all kind of issues with that. For example, a lot of student's computers don't have a good enough video card. So their experience is quite poor in Second Life. They think, "Why is everybody going on this thing? It's so lousy." It's just simply they don't know what to expect.

So having the face-to-face workshop is extremely useful for just taking five to ten minutes in helping them create an account.

I'm going to show a couple of different technologies. Last year I talked in much more detail about this. I'm just going to gloss over it. I have used blogging. Were my students to write something about imine formation for example. They would write a blog. They would upload pictures.

Each one of these technologies has its advantages and disadvantages. I'm going to try to point those out as I go through. The advantage of a blog is that it is really easy to create one, especially with Blogger. So it doesn't take that much time for me to set it up.

The disadvantage is when the student corrects their mistakes; there is no track of that. So I can't actually follow how they have actually arrived at the final presentation. So it has some uses. It is very simple.

If I'm going to be doing student assignments and I want to see basically that interchange between me and the student or between the student and other students, I will probably want to use a Wiki. A Wiki, is again, very simple to set up. It's a little bit more complicated for the student to edit, but really not that much more. It has advantages that I could look at the different versions.

Now here is an example of a Wiki project where a student went into my lab notebook. I have an open laboratory notebook. I do anti-malarial research. So we make compounds of the synthetic organic group. She went in and looked at actual and our spectra of an on-going project.

This is an NMR, it is not really that important to go into details. But in the class material, this would have been predicted to be a single peak. But it turns out, when you blow it up, it's actually a triplet. That's something I learned actually, from looking at these things more closely.

This is the kind of thing where the student is learning something. The teacher is learning something. The graduate student is doing the work of learning something. By using a Wiki, everyone can actually watch in real-time.

Some of the other things I've done using tablet PCs. This game here I call Wheel of Wargo. You put a starting material like benzene in this case and put a final product. The students will take turns trying to come up with either a step from a starting material to anything, any reaction that we saw in class. Or try to write a step that goes toward the product.

The idea was to connect one of the trees with the other tree. Students will get a point for having the right reagents for example. A student might get three points for completing the synthesis. I found this to be actually very useful for organic synthesis.

The difficulty with this is that a lot of students are shy. So it is actually a big deal for some students to come up and write on the tablet PC. So all these have pluses and minuses. That would be the minus when it comes to this. But it certainly was very effective for students who didn't have a problem with it.

So now we're going to move towards the world of more classical games. How many of you have heard of "Un-rule Tournaments." It's a first-person shooter, kind of like Halo. There are a lot of these games where you walk around in a virtual world. You can actually get a version that doesn't have any weapons.

There's a commercial version that has it. I used more extensively the version that didn't have any weapons. It was free. It was easy for the students to download it. It would basically consist of these rooms where there would be pictures of some chemical concept.

Here we're looking at a hybridization, plus a Lewis structure. Here we're looking at a chirality with a Fischer projection. There are actually four walls here, and three of the images are incorrect somehow and only one of the images is correct.

What I would have the students do is a race. If you went through a door that was correct, you ended up in the second room, and then as long as you kept picking the right answers, you would keep progressing through the maze. If you got any of them wrong, you had to start over.

So it was a pretty easy way for me to do races, actually a game. I didn't give out any points for this, but I did give out prizes, like a molecular model kit or something like that. So there was definitely motivation for the students to do it. I thought this went pretty well.

Sometimes, we actually did it with the weapons. This was with the commercial game, but it was all the same content. So I could reuse all these images, just put them in a different context. In the weapons version the idea is to survive, right?

So if you get through a correct door, you might get some more ammunition or help or something like that. So it was another way of engaging. Again, pluses and minuses. You may not want to have weapons in your games [audience laughter] but some students do find that more engaging.

Now I would probably still be using "Unreal Term" or some sort of game like that if I hadn't come across Second Life. Second Life has a whole other dimension that hopefully I will give you a taste of today in my talk. It turns out that you can do exactly the same kind of game, but instead of having rooms that you move through, we created these little obelisks.

By the way, this is the shot of Second Life. The avatar here, that's going to be me. So whenever there's a picture and you see the back of the head, that's me moving through the world. When you click on these obelisks, again four images pop up, and three of them are incorrect; one of them is correct.

Instead of going to another room you just get another set of questions. So I do the same thing. I still do races. I still give out prizes like that. I think that it works pretty well.

The advantage is that students can come from around the world at any time and they can actually take the same quizzes and they can interact with my students. So for me, the huge advantage of Second Life is really this ability to network.

I want my students to network with educators, other students. What you find in Second Life is that the content on the islands is what governs the type of person that visits it. So it's like a chat room. Basically, if you're on Nature Island or you're on Drexel Island or any kind of educational island like that, we really haven't had any negative experiences. But if you go out in the real world there's all kinds of things out there and you have to be aware of that.

So that's how I started with Second Life. After awhile I actually met people that I started to collaborate with. Andrew Lang is a very close collaborator and we've done a lot of stuff together. I put his name up on relevant slides here.

That's a perfect example of why as an educator you'd want to use Second Life. It's actually not so much teaching the students; it's just tapping into this huge reservoir of very intelligent people who are very skilled at doing things. Andy is very skilled at writing script or making buildings in Second Life, and he's a mathematician.

So when we come together I have my chemical knowledge, and we couple that to his skill in terms of rendering objects. We can do some things that we can be comfortable that are actually scientifically accurate.

Here's an example of a student project that was done in Second Life. The student is actually trying to show the concept of chirality using camphor because it's a particularly difficult molecule to visualize in 2D. This is the size of the avatar here. You can see that the molecules are actually much bigger than the avatars. So this is a completely different way of interacting with molecules.

Normally, if you make a molecule set, you hold it in your hand or you draw it on a piece of paper. Here you can actually go all around it, you can sit on it, you can do all kinds of things that you can't otherwise do. It's very interesting to see learning chemical concepts this way.

Now the reason this is possible is because with Andy you manage to create rezors that don't require any computing skill whatsoever. In terms of doing things on Second Life, what's becoming exciting now is not so much the stuff you can do as how easy it is to do it. With very minimal training. anyone could actually make these molecules.

I'll show you that in a little bit here. So students can have fun with this. You can actually sit on the molecule and fly around with it. You can try to simulate docking. There are so many things you can do if you let students play with it. We have a Bucky Ball here, which is pretty popular.

In terms of how you actually teach students to do this, I don't want to be sitting there showing them how to code. It's a chemistry class; it should be about organic chemistry. So what we've done, Andy has basically written these scripts that will take as input smiles, inchies or inchiekeys, and will actually hit a bunch of web services, one in Indiana, one in North Carolina, will actually do a minimization so that the molecule has a realistic shape, and then will actually build the molecule in 3D right in front of you.

So as a student, and more importantly as a teacher, I only have to teach students how to find the smiles code. Luckily, there are some great services out there, like ChemSpider. The student simply typed in camphor in the search box, and camphor pops up and here's the smiles.

You copy it, paste it into Second Life, and it just pops up. It becomes quite feasible then to have students doing projects at a pretty high level of sophistication because it doesn't require a lot of my time.

Some other things we've done more recently, is try to correlate molecules with NMR spectra. So again, this molecule here see the acetylphenone, this was created using the same rezor just the student found the smiles code, dumped it in, and it created it. And here's the NMR spectrum.

And then the student explains how each proton corresponds to each peak in the spectrum. Now this particular spectrum is just an image. The student went on the web, took a picture of an NMR and then put it in Second Life. What we've managed to do quite recently, actually, just a few days ago, is actually interact with the spectra.

So this is an NMR spectrum and I can actually talk to it, and I can tell it to zoom between 2.1 and 2.3 ppm, and the spectrum will actually respond and zoom to any region. So again, this is very simple, right? To interact with it, you just have to type in the chat box.

I think this is going to make it very easy to bring a whole bunch of people together: students, teachers, whatever, and be able to discuss pretty sophisticated chemical concepts. If we want to look at an NMR, we can just pull it up and we can just zoom it in and talk about it.

So a few other things that we've been able to do in Second Life. We've been able to demonstrate docking. As I think I mentioned, my lab focuses on making antimalarial compounds. This is one of those compounds that we've made. This here is actually the receptor site of enoyl reductase. It's a malarial enzyme that we've been trying to inhibit.

This is set up in such a way that if you click on the molecule, you will see it drift down and connect into the receptor site. So this is actually, you're there and you're watching this thing in 3D come down. There's actually four hydrogen-bonding points. It turns out that its actually really tricky to see that.

This is a very interesting way to understand what does it mean when you have a drug molecule interacting with an enzyme. Its just another way to do it, it doesn't replace the paper, it doesn't replace all the other software programs, but its one more way of visualizing it.

There's all kinds of things that you can do in terms of the chemistry, you can display the entire enzyme. Peter Miller has done quite a bit work. This is the same enzyme, it's the whole thing instead of just the receptor site.

And again recently with Andy Lang, we can actually go from a file in PDB and actually go to a fully rendered protein, using up only one prim in Second Life. If you're not familiar with Second Life, everything comes down to prims. You only get so many of them per island, so right now Drexel island is about 90 percent saturated so we couldn't actually do a massive project because there's not enough prims.

This here is the 3D structure of the Avidin and it only took one prim to make this. So you can imagine you could have much larger projects than you could with the other way of rendering, so this thing is very detailed and it uses up a lot of prims.

So again, I don't have to know how to code in Second Life, all I have to do is show my students this is where you get PDB files, this is what you use to make this. And then have them go and actually do their projects. Some other things that we've done, we can actually show reactions taking place.

So this is a reaction between an aldehyde and an amine, to make an imine and there are actually three steps, at least with this mechanism. You can see here this is the blue nitrogen and here's the carbonyl.

And you actually talk to these molecules, you say "Next, Next or Back" and it will actually go to the intermediate, now what's special about that is that each intermediate has actually been minimized so that it's realistic. It has a realistic shape, which is something that you don't often get when you look at these reactions on paper. On paper everything is flat.

But actually these intermediates are not flat at all, they're twisted, the hybridization changes, so there's tremendous changes in the angle. That's something that you get a really good feeling for when you're in Second Life doing it.

We're accumulating this information. Right now there's not a search engine that will actually go into objects in Second Life in the way that you might think Google would do it. One of the things I've set up is this Second Life molecules Wiki, where if we do create new molecules, we can just create a new page. Those pages will be indexed by Google. So if someone searching for this particular molecule, they will find this page, and then there will be a link.

They are called "SLURL's" Second Life URLs, where people can click on it and end up at a specific location in Second Life. This is another way, very simple thing to do, but very effective in terms of indexing.

Again, with Andy we've made a 3D periodic table. So, each one of these atoms, if you click on them it will actually show you more information about each element. And this is freely available. It's on American Chemical Society Island, if any one of you want to see that.

We can also have offices. So, this is how I'd like to look in real life, but I can't. So, I have to do that as an avatar. But, here's a picture of myself and this is an area where you can meet student's or, you know if students are visiting and want to find out more about the Drexel Chemistry Department. They can look it up.

I can put information about my lab. So, here are pictures of my student's, pictures of our equipment, chemicals, things like that.

And something that works very well in Second Life are posters. So, there are posters on Natures Island. The Nature publishing group has actually three islands called Second Nature. And there are these areas that have a whole bunch of posters. In this particular area this is an example of someone that I me...I think she's from the Netherlands, and she works on Crohn's disease.

We met at Second Life and I found out she was going to a conference and she was interested in putting her poster here. This is actually a whole PowerPoint presentation. If you click on it, it will walk you through the entire presentation and there is a little bell here that you can click it and it will summon the presenter. So, if she's in Second Life, she'll get an instant message saying, "come on over."

If she's not in Second Life, she'll get an email. Then if it's convenient, she can actually go in. And I've actually met quite a few people that way, from these bells. In fact, the posters are so effective that we've actually run entire conferences using them.

On Second Nature, there's actually a whole area called Sci Foo lives on, which is an extension of the Sci Foo conference that happens every summer over at Google. And, basically, this is an example of what happens at a conference.

We put up posters and the speaker will go up and talk. You can use voice in Second Life or you can chat. The advantage to chatting is that you can get a transcript really easily. So, we generally have used more of the chat than the voice. But people have done either. Then you basically get to meet all these people.

So, these are all people who are interested in whatever topic that you happen to be talking about. And in this particular case, this is about open science. It's about new ways of doing science. So, those are the people precisely that I want to meet. OK. So again, that networking concept in Second Life.

So, because this is Chemical Heritage Foundation, I'm going to focus more on the chemistry. There's a lot of other stuff in terms of biology, there's Genome islands.

All kinds of things that are wonderful. But in terms of chemistry, I'd just like to point to you this recent project that I was a part of that Kate Seller at American Chemicals Society spearheaded over there, to get an actual island for A.C.S. Maybe you guys will be next? Right?

This island actually has the shape of the Phoenix icon. So, this stuff here in green is land and the blue here is water. I'll just give you a few screen shots. If you're interested, you can contact me and I can show you how to get to all these.

There is actually a headquarters building where you can download some free stuff. You can get this rezor that will let you make molecules that I have my student's use. You can actually get a copy of it right here in the A.C.S. headquarters. Very convenient.

There's a section...I don't know if you guys are familiar with this A.C.S. Landmarks Program, American Chemical Society. I get one or two per year. Pick parts of chemistry that particularly important like purification of aluminum or chemical abstracts. There's this little museum area where those landmarks are located. If you click on these obelisks it will go to the web and give you more information about these. So that's another part.

For the first time, I helped them out with this with actually having a poster area for the Sci-mix session. If you have ever been to an American Chemical Society meeting, there is a Sci-mix where it's a varied group of people. They give posters.

Twenty people out of that group agree to put their poster on Second Life. So there is this whole area where all these posters are still there and still will be there for several months to come.

Some of them have on-line indicators, so you can see if the presenter is on-line. Again, it's that whole fostering, that networking. What we tried to do for this is if there was some molecule that was particularly interesting, we would put it next to the poster. So it is not just a question of replicating what you can do in real life, but to do things that are quite specific to this new technology.

Some fun things, too. It is kind of nice to be able to see a nano-tube in 3-D. You can go in the middle of it. You can see what it actually looks like. Then there are some interesting things like this molecule here is called Felasene. It actually looks like a cat.

It was part of this talk from ACS that basically, they were picking interesting molecules or interesting findings from their database. I thought this was a perfect molecule to represent this collection of molecules. You can not only put the molecule but you can add eyes. There are all kinds of things you can do.

The ACS also has a resident chemist program. What that means is that there are areas that are dedicated. If you have a chemistry lab and would like to share what you are doing, you can go on this platform and you can put different things on it.

The Anastrozol Lab, for example, has posters that they've given at various talks. Gus Rosania has a pretty interesting area. He actually does a lot of fluorescence microscopy. He has lots and lots of these little images in a cube.

So you're in the middle of this cube and you can actually try to see patterns in the data. For him, it's a way to visualize his lab information in a way that he simply can't do in real life.

If any of you are interested, there will be a little party going on at 1:30, May 6th at the Geodesic Dome at the American Chemical Society. It's always nice to pick a time and place to meet people, because often times you're interested in the island and you go there.

Maybe there is one person there or there is nobody there and you don't get to interact.

Sometimes if we can set a specific time and if anyone is interested in that, let me know. I'll make sure that you're set up and you can explore it.

Really, that pretty much covers what I wanted to say. In terms of what technology to use, I get these emails from my friends. Sometimes you get these articles that say, "Your learning doesn't work." Like a big conclusion. Or Second Life can't be used for education and it's pretty annoying because it can not be boiled down to that. It all depends on the details of how you use it.

So if you are using Second Life and you want to record hour-long lectures and you want to display them, it's not going to work well. But, if you wanted to have a poster or if you want to have students make 3-D molecules, well, now we can do that. We couldn't do that easily a year ago but now we can do that really easily.

So, it all depends on what you're trying to do. I would recommend, the easiest way to do it, is find someone who is already doing something close to what you are interested in and have them bring you into the world. Have them show you how to do it simply.

A big mistake people want to learn about Second Life, they just dive in. You end up on this place called Orientation Island, which is kind of like a purgatory.

[laughter]

You can't leave. They sort of rig it so that you have to go through certain tasks. I understand the concept, but the reality is most people just get really annoyed. It takes them two hours to finish it. You don't really need that. For our purposes, I want students to be able to fly around, to walk, to teleport and to chat.

That takes two minutes to show someone how to do that. Yeah, you can learn how to write code and all these kinds of things, but it's really not necessary for the kind of applications that we are doing.

Again, if you are interested in this, talk to somebody who is already doing it. You can use things like Wikis and blogs to interact with students. Second Life, yes, there are some specific chemical things that I showed, but I can't overemphasize this, the major benefit of Second Life is the networking.

If I have a student that does a project on Second Life, fine. They'll learn how a molecule looks in 3-D. That's great. But if they get to meet someone for their next co-op or if they get to meet someone that is going to hire them someday or they get to make a friend that is also a chemist; that actually is the greatest reward.

That is something that you will not find on sites that are closed in. There are other sites that have a virtual world but there is not a lot of interaction.

Second Life on average has 50, 000 people on it at any given point in time. So the odds are you are going to find someone pretty quickly that is like-minded, that you guys have the same objectives.

The other thing that I have done here to ensure my success is I have not made this mandatory. That is another big difference. This is not for everyone. Some students definitely get it and enjoy it. But typically, I only have about 10% of students that do the races for example.

I use multiple channels. I'm a big believer in this. So I care if you've learned the material. I use quizzes. I use tests, objective tests to make sure that students know stuff but I don't really care if you use the screen casts or if you meet me at the workshop or if you are in Second Life or if you are in Second Life next to me or if you are in Second Life in the dorm.

I'm not concerned with that. Do what makes sense for you. If you do that, you should do OK in my class. If you don't, you probably won't, but it's not mandatory. I don't think it is applicable to all students. If you do these things on a voluntary basis, I think you'll find the experience to be pleasant. It's not going to be a big stress.

The worse thing that will happen, if it's not for points, it it's not for grades, it just may not work, but it's not going to have very many consequences. So I would just suggest starting slowly.

Yes, everything I've talked about here is essentially free. In Second Life we bought an island. Drexel has bought an entire island. The American Chemical Society has an entire island. But if you just want to play around, there are plenty of places that will let you, give you a little area for educators and will let you experiment.

That's how I started. I started on Nature Island. They invited scientists to participate. I thought, "Why not?" I tested it out one term with my students and I started to use these quiz objects and it worked out. We eventually got an island. But to get started you don't need an entire island. You can actually just start with some friends. Then have them put up some stuff that you'd like to see.

And I guess that's it.

[applause]

ACS Talk on Cheminformatics in Open Notebook Science

2008-04-13T21:29:00.000-04:00

link to ACS Talk on Cheminformatics in Open Notebook Science

Jean-Claude Bradley: ...so yes, I'd like to talk to you about Open Notebook Science, specifically, the role of cheminformatics in terms of storing information and in terms of retrieving it. So first of all, a little definition, what do I mean by Open Notebook Science? Well, if you look in the past couple of years, there's been a movement towards making the scientific process more open. I'd like to use this little chart here to show where we've come from and where we're going to.

In the traditional lab notebook, for example, everything is unpublished unless somebody makes an effort to put the date together and then send it for publication. But if they don't do that, everything including the failed results are not going to make it to anybody. All right, so as we move along this area here, we have traditional journal article, so in that case, it's less closed and that more people can have access to the information. But again, it doesn't include a lot of the elements such as the failed experiments or the view of all of the experiments that have been ran in a given project.

Something has come up lately, a lot has been open access journal articles and here, we're talking about articles that could be access for free by anyone and, typically, the author or a third party will pay the cost of that. That's good, it's making things even more open, but again, these still have the traditional journal article format. So what we're talking about here in Open Notebook Science is full transparency in the scientific process where, actually, the lab notebook of my research group is made available in real time using a few different technologies which I will discuss.

OK, so to give you sort of background of where we are, my group at Drexel--we're Synthetic Organic Group--and by doing these things openly, we need collaborators, obviously. One of the greatest benefits of doing Open Notebook Science has been to find some great collaborators. Rajarshi here has been a very active collaborator of ours; he's been doing docking for us. We've had people who've tested our compounds. Lately, Phil Rosenthal has been testing our compounds for anti-malarial activity. So most of what I'll be talking about today is in the context of anti-malarial agents. We're also tested a few compounds for anti-tumor activity.

What I'm going to do in the later part of my talk is give you screenshots of the various tools that we use and how they fit together. So we have a blog, we have a wiki, we use Google Docs, mailing lists, we use ChemSpider, and we use CDD and all of these talk to each other. You'll notice that all of these are free-hosted services and that's really important for me. If we have people who think that what we're doing is a good idea, they should be able to replicate it for no cost and with minimal effort and because the services are free-hosted, you can in fact do that.

I'd like to start the story with the blog and the blog, we typically report things such as milestones or larger problems that we've been having. There are not any hard core experiments in the blog because that would be very monotonous and that you wouldn't read it. So we put things that are more interesting to a broader audience.

Here, we're targeting this enzyme falcipain-2 which Phil Rosenthal is testing for us, malarial enzyme, and I'm talking about all kinds of things. Here, I'm linking to EXP150. Now, this is actually a link to the wiki that is the lab notebook of how those compounds are actually made. So what I'm talking about this compound here from this Ugi reaction and here's a nice picture of the crystal of it.

So when I click on that link, it takes me to a pretty long page, I'm going to look at different sections of it and show you where information come from and I'll try to focus more on the Cheminformatics aspects of this. Essentially, if you're going to this page, you should be able to link to the summary post that sort of explains the bigger picture of why we're doing this. Someone might have fall on this page just by doing a Google search. It has a whole explanation of everything including the molecules.

So if you want to click on this link, this Ugi [indecipherable], it will actually take you to the ChemSpider entry for that compound. Tony has already been through how great ChemSpider is and it is and it's got all kinds of information that his [indecipherable] catalates that I don't have to and that's a huge benefit for group like mine that doesn't really have a lot of computer science people. I mean, we're Synthetic Organic chemists.

So we can also link to the Experimental Plan of the experiment and we can link to the docking procedure. Rajarshi was talking about storing the procedure in such a way that other people would be able to reproduce it and that's where we try to use as much as possible. Again, this is just as a wiki page so we're linking to the library; we're linking to information on the enzyme that we're docking against. Rajarshi actually wrote this and these are the results.

If we click on these results links, we end up with a Google Doc that has just the list of SMILES in the order in which they were docked with the enzyme. So this is still falcipain-2 that we're looking at and Rajarshi is saying these are the top ten compounds that we should probably think about making. That's what we're going to do and we've been getting feedback from the people doing calculations to decide which compounds to make next from our virtual libraries.

We also have a Procedure Section, OK, so they're somewhere done around here. The idea here is to write up the information in such a way that it could be quickly copied and pasted when we submit some of these works for publication in a traditional article. What I'm talking about here is not a way of bypassing the traditional system; it's just the way of getting the information out there much more quickly. We're still following that plan of submitting to traditional articles and this is, of course, what the format would look like.

Again, part of that page, there's a Results Section and here, instead of just linking to the NMRs as PDF, we actually link to them in JCAMP format and we use JSpecView written by Robert Lancashire. It's a fantastic free program that allows you to do an NMR spectra or any spectra in JCAMP format in a browser in a way that can be expanded very easily. So this here is what the spectra might look like in a PDF in a supplementary Information Section.

I know a lot of you probably know it, you want to find out what the NMR look like and you get this PDF that was scanned and you can't tell what the picture look like. But if you have actually the raw data in JCAMP format, you can easily expand this little peak and see that yes, it is a triplet and you can measure the [indecipherable], you can do whatever you want with it. That's really, really important if you're making a statements about things, people has to be able to verify your raw data, they have to be able to make the same conclusions based on the same information.

JCAMP is really a nice little format to use; we've done a couple of things with it. I had a [indecipherable] student last year write Excel VBA, where we basically monitor reactions. We would basically give the start time of the experiment and then Excel VBA will be able to run and it will calculate all of the different concentrations over time.

Of course, you had this on the peaks, you had to tell which peaks correspond to which compound. But if you've done automatically print out a kinetics-run for the disappearance of some compounds and for the appearance of other compounds. So those are some of the neat things that you actually cannot do wit.pdf of an NMR. So it's very, very useful to keep it in that format.

And as you saw Tony talk about, we've also been using ChemSpider to characterize compounds. So the difference here is that these are spectra that I approved of; these are final isolated compounds. But of course in research, you take monitoring runs, you take impure compounds, you're in the process of purification. And so all of those NMRs and spectra have to be accounted for as well. So right now, we're only using ChemSpider to store the best stuff, the stuff that we would send to a paper.

And the next thing that we're about to do - we've almost got this done - I'm working with Andy Lang, and we're using Second Life to actually display NMR data. And this will read JCAMP, and it will do so in a way where you can actually expand the spectrum. So right now, this is actually working, but for a spectrum of a fixed X-axis.

We're working so that you can talk to the spectrum and tell it to expand. And we've almost got that done, and I think it's just going to expand the capabilities of Second Life. I'll be talking about Second Life tomorrow. Actually ACS Island is going live tomorrow at the SciMix, so hopefully I'll see some of you there.

Another section of this page - again, I'm going through this long, long page that's one experiment - is that there has to be a log. So we can actually construct the rest of the experiment based on the log, but without the log, we can't do anything because you can't remember what you did, exactly when you added things, exactly the way you measured them.

This is something that I try to reemphasize to my students: It's absolutely critical that you keep a proper log because later on, you can do whatever you need to do. So when I say that our experiments are in real-time, what it means is that the log has to be up by the end of the day. The other sections of the experiment can take weeks to actually get uploaded.

So finally, when you come to the conclusion section of this article, it says that the CD product was obtaining 59% yield. You don't have to take our word for it at all; you can go back and reinvestigate every single aspect and the arguments that we made.

OK, so now comes storing and retrieving information and this is where the Cheminformatics comes in. So in order for us to retrieve compounds in experiments, it's been a challenge. We've used a tag section, so at the very bottom of each blog or Wiki page, there will be tags. And we can use a number of things for this: We can use SMILES, for example. But we chose not to do that because there are multiple SMILES for a given compound.

So we've been using InChIs and that's worked well for small molecules, but the reality is that for very large molecules, like our Ugi products, the InChIs are not indexed properly by Google. So what we've started to do in the past couple of months is use these InChIKeys. And we use ChemSpider to provide the service to generate those InChIKeys based on either the InChI or the SMILES that are submitted to it. And these links here of the common names, those are for human readability, and when you click on them it takes you to ChemSpider.

So that's how everything is connected together, so that when you do a Google search with this partial InChIKey, it will come up with all of the different experiments where we used that compound. And if you're going to do this, you'll have to remember to click this 'Repeat Search with Omitted Results' because Google will assume that you're not interested in results if it comes from the same domain name - but we are because that's the point of this, we want to get all the experiments.

Now you can do a lot of tricks with Google. For example, if you're familiar with the Google Co-op, also called Google Custom Search, you can take all of our blogs, Wikis and all the pages that we've generated and create a special Google search that will only look on our approved pages; and if you do that then you have a way of searching a very rarified part of the Internet. So all that is available, totally free and anybody can do this.

So how are people actually finding our experiments? Well I've yet to actually catch them when using an InChIKey to find an experiment, so this is something in moving forward that we're going to be doing. But I think it's very, very interesting to see how people are actually finding our experiments through Google.

It falls into four different categories: It could be specific compounds. So someone might be looking for the NMR of TFA. If they do that they're in luck, we have lots and lots of NMRs of TFA. It could be a molecular formula. They could just be searching for T-guanidine, just tell me everything that you know about it, and I'm sure they're going to find ChemSpider hits with that. But people are clicking on these links and they're finding them.

It could be experimental conditions. And this is actually really important because a lot of this stuff is like side reactions of amines. If you search in the traditional literatures, side reactions, how can stuff not work, you typically don't find that there. But of course, most of the typical lab book is almost all failures, so you're going to find lots and lots of stuff that doesn't work, and that's the point. If someone was searching for kinetics of the Bak protection, they will also be in luck; we have lots of kinetics analysis of that.

So the other thing that they can find out at a higher level is I talk a lot about educational things. So if they're looking for free downloading chemistry video, we've got that. If they're looking for 3-D periodic tables, it's something that I discuss, and people are looking for that. And also, some people are looking for bigger pictures, like zomal targets, Skinner formatics, project proposals. So I've discussed the proposals that I've put in and that's great, somebody who was looking for that would have actually found it. And of course, you can also search these experiments just by the traditional table of contents file.

OK, so now if you want to use this information in a much more meaningful way, we want to be able to compare different experiments. And as you keep doing experiments it becomes more and more difficult to keep in mind everything that's been done. So again, we're using tools as they become available to us. If somebody comes to me after my talk and volunteers to run a database with this, I'd be very happy. But right now, we're using Google Docs because it's simple and we don't have to have a lot of results to track, and so it makes sense, but of course, at some point, it should be imported into a real database.

But basically here, each one of these rows is one of these experiments of these Ugi reactions. And one of the things that we observed is that sometimes we get a precipitate and sometimes we don't. If you get a precipitate that's great because you can just filter it and you can scale it up, and you can do a lot of things. If you don't get a precipitate, you would have to run chromatography and that would really complicate things and make it very difficult to scale up.

So one of the things that we've been looking at is can we predict which Ugi product is actually going to precipitate. So in order to do this simply, everything is put into this table that is publicly available, and then people are free to run models on this. I'll talk about that a little bit later, well now actually.

Research has built models to actually predict, going forward, compounds that we have not tried to make yet. He's predicting right now - in the list of 100 compounds that we're scheduled to make - these three should be precipitates. We've also collaborated with other people, MSA Analytics. They've actually just this morning, run a model and co-predicted that this compound should precipitate.

But I predicted another compound that Rajarshi did not precipitate. So again, as he was talking about it'd be really nice to have ways of comparing models to each other and to do that in a very systematic way. As long as we're keeping this fully open, it makes it very easy for people to participate and can collaborate with us.

Now going forward, I show you that log and there are no rules for that log except that my students have to record what they do, when they do it, and what they observe, but they're not required to type any special words or anything. The problem with that is it makes it really difficult to convert that into a format that a machine could use or you couldn't readily extract that and put it into a database. One of the things that we've been doing in the past few months is actually rewriting our logs in a format that should be machine-readable.

Here, I have a series of steps, workflow actually, where you're allowed to add something, you're allowed to wait, you're allowed to vortex, you're allowed to take a picture but you can't do anything else. We have words that we've defined meanings certain things, we have parameters that we specified. For example, we specified the molecule using the InChiKey and we'll also specify with the common names so it's human readable but, essentially, that's just something that we decided to do that way for a bunch of reasons. But there's not reason that it has to be done this way.

If somebody wanted to convert this and have the SMILES, they could do that easily. They would just scrape the information and then convert it. So this, I think going forward, is going to be very important especially as we start to gather more and more information.

So looking at these results, we can also compare them. This is all the different than the table that I show you earlier where we're looking for precipitates or no precipitates. These are actually individual results from experiments that are stripped out and left to stand on their own. So we would mix compounds together and then wait four hours and take a picture. That's not the whole experiment, that's just the first data point. Then we will take an eight hours, we will take a 12 hours.

Now, if something bad happens on the 12th hour, let's say the student drops the sample, well, we will call that an aborted experiment. Everything in that experiment probably wouldn't be worth going through and digging through it. But if we extract every individual result as something that's addressable and minable, then it really doesn't matter what happens down the road.

If somebody who may not be interested in the Ugi reaction whatsoever, may not just be interested in all the reactions where an amino has reacted with an Aldehyde, they would find that here. They would not get any interpreted information; they would just get a picture of what that looks like. What does this look like I mix it together and wait four hours? So that's a strategy that I've been using to get a lot more information that's going to be much more machine-readable and machine-friendly.

A few things about a wiki, when we first started to do this project, we used the blog actually to record experiments. Then it turns out the blog is really not a great tool for this because if you change an entry, you have no record of it. You can't tell if it was changed, you don't even know who changed it. With the wiki, you can see all the recent changes in it; you can look at a specific page. So this is EXP150 that we've been looking at through all this time. I can see all the different versions and I can see who made the changes. I can compare any two versions and using wiki spaces, the new stuff shows up in green and the stuff that was deleted shows up in red.

I can use the wiki as a way to organize results, to explain something that is extremely difficult to publish - failures. So here's a little story about the synthesis of DOPAL and we tried to make this compound. We eventually did make it but we failed trying to make it in some really interesting way. This is just the story of that and it's got links to the papers we tried to use that had wrong information. It's just basically explaining all of that and I think that that can be useful for synthetic organic chemists. It's typically not something that you make public.

We also use a mailing list which turns out to be really handy for collaboration between groups. My group would use the wiki almost exclusively, we'll only collaborate with people who do docking, with people who do testing, the mailing list appears to work pretty well.

The other piece of this that we've just started to tap into is CED collaborative drug discovery. Drexel University now has users on here and this is a way for us to basically store or retrieve or ask a results. It turns out that two of our compounds and active against falcipain-2 and are active to prevent the infection of malaria. They're not terribly active, nor are they less active than chloroquine or the best agents that they have, but it's a start, so those results are stored here.

Something really neat that actually has happened just last week or two--so what's the point of making all of these stuff towards the public? Well, you get contacted by people that you totally don't expect. Brent Friesen at Dominican University, he runs the Sophomore Teaching Lab and he was interested in having his students do something more interesting than just repeating experiments that they've been repeating for 20 years that everybody knows the answer to. He thought maybe the Ugi reaction might be useful for that, so he contacted me and we talked for a little while and we determined, "Yes, this will make sense."

So he just wrote his manual for the spring for Chem 254 and it is the Ugi reaction and his students are going to be doing new reactions that we haven't done yet and we're going to be testing those compounds against malaria. That would be really neat to be able to include students taking regular teaching labs; it's a whole untapped resource. It requires some more time, it requires some more dedication from people who run the teaching sections, but this could be very, very interesting and it could be very motivating for the students.

There have been some other people doing Open Notebook Science, students from Gus Rosania's group was here earlier. He's a collaborator with us; he's going to be studying the drug transport [indecipherable] for our compounds in the parasite and the red blood cells. Cameron Neylon over at Southampton has also been doing Open Notebook Science. He doesn't use a traditional Wiki; he used a modified blog for this.

I just like to end on this slide where I think Science is headed. We've been living in a world where Science has the only point of communicating it was really for other humans to understand it. We're getting into this really interesting time now where we can have actually human beings collaborating with machines if the human beings choose to make information available to them. I think that's how we're going to get to this point where we can have machines actually doing real science, formulating hypotheses, testing them, analyzing the results, and then planning the next experiment.

I think to get to that kind of situation, we need to have free services, we need to have a possibility that anybody in the world can write a script that's going to try to process information and spit out something useful. Hopefully, this is one way that we can actually get there and, I think, it'd be very useful once we do.

So that's it.

ACS Talk on Teaching Chemistry with Second Life

2008-04-13T21:21:00.001-04:00

link to ACS Talk on Teaching Chemistry with Second Life

Jean-Claude Bradley: OK. Thank you for the opportunity to talk about Second Life and teaching chemistry. What I would like to do first is step back a little bit. You know, we've been talking about using a lot of different technologies. And sometimes, we have to remember what we are trying to achieve with these technologies. Right? That lets us know whether or not we're wasting our time.

So, I'm just going to take a few minutes to go over what is the roll of the technology teacher. I think that as technology changes, we have to remember that we still have to make chemists. That's our job ultimately, right?

And what does this mean? Well, for me, it means that we are trying to make individuals who are chemically literate at the undergraduate level and competent to create new useful chemical knowledge at the graduate level.

So, any tools that enable us to do that, we should use. Any tools that we are currently using that are no longer effective we shouldn't use. So, what does this mean in terms of actual activities from the teacher? So, how do we actually teach?

We have to do three things. First, we have to select and build our content, then we have to assess and validate the skills and knowledge of the students to know if they learned it or not and third we can help catalyze the learning process.

This is the third one here that I have basically put Second Life into. This is the stuff that you can only do if you have enough time to do it. So, I need to explain how the rest of my course operates to show you how it is possible for me to spend time on this.

So, very quickly, I'm not going to talk at all, or very, very minimally about blogs or wikis or things like that here. I just wanted to give you an idea of the evolution of my course over the past several years.

I teach undergraduate organic chemistry. I started off with, of course, face to face lectures using paper hand outs. Then graduated to using optional screencasts of lectures, which I'm recording this a s a screencast. Then I went to audio podcasting, video podcasting. I started using blogs, wikis, Google video, You Tube, Google co-op.

Finally now, I'm really not even using podcasting in my class because everything's already archived. So, it turns out its far easier to just give the students a zip file and just have them unpack it, because I'm not currently recording lectures. Let me show you why I'm not currently recording my lectures.

This is what a screencast looks like, if you're curious. There's several different formats. You can have flash, this happens to be the m4v format or mp4 on iTunes. The students just basically click this of they can expand the screen and they click play and they can hear me explain the chemistry.

So, it's very, very similar to being in class and watching me doing what I'm doing here, right, just presenting. So, what happened is I actually plotted the attendance in my class over time and observed that in all of my classes the attendance by the end was between 10 to 20 percent.

So, when it ended and I looked at the performance of the students who were still coming to class versus the students who were getting the class material exclusively through screencasts and it was identical. So, that's one of the things that I've stopped doing then is actually lecturing.

Now, instead I just assign the recorded lectures and I do other things with the time, which I'll get into in a second here. OK, so while all this is going on in terms of content and delivery, I'm also changing the way that I'm assessing students.

Obviously, I started with manual grading, then moved on to using WebCT quizzes, voluntary, then making the exams and the tests all mandatory on WebCT. Then, I moved on to doing extra credit assignments using blogs and wikis. Quizzes in first person shooter games like Unreal tournament, quizzes in Second Life, and finally student's assignments in Second Life.

I will obviously focus on the last two, but I will show you a little bit of what these things look like on the way. So, this third part that I was talking about earlier, this learning catalysis what does that mean? Well, sort of by default it's your office hours and email and the time that you're not in class.

Because I now assign my recorded lectures I have time to do things like be present while students do problems, while they watch lectures, while they play games, while they use Second Life. We can talk about the extra credit assignment. I can spend more time on that. I can address technical issues very, very important where they bring their laptop to me and I can actually see what the problem is.

You don't want a situation where you're assigning archived lectures and the student has some kind of technical glitch and they can't do it. That would be a nightmare.

This is what I end up spending my time doing in my workshops.

OK. Student assignments: So, starting with blogging, I don't do blogging anymore, but that's how I started. Basically, I just had them pick something relevant to the class and blog about it, all right, so this was a couple of years ago.

I then moved on to using the wiki. I think, it's a little more useful because you can modify the text and you can see all the different versions. What I do here is I basically have them do an assignment based on my research wiki. We are making anti-malaria compounds. So, they can actually see our lab notebook and they have to make some kind of comments on that on their projects.

We're using J-camp formats for the NMRs, using J-spec to view the NMRs and everything. I obviously, don't have enough time to get into full details about but if you ask me, can wikis be used for education? I think yes, and I've got some pretty good examples I think of having students use them in assignments.

Let's talk about games a little bit. I've been using games for many years, even before WebCT and everything. This is a game that I played a long time ago called Wheel of Orgo, where I start with a starting material and I put a final product and then students take turns trying to come up with steps.

So, they have to put the reagents and they have to put the intermediate. And they get points for having that correct. The idea is, of course, to find a path from the beginning to the end. That's an example of a game. Something where it's the same material, it's just delivered in a different maybe more entertaining format.

Another kind of game that I've used is Unreal Tournament. If you're familiar with that, it's a first person shooter game. There actually is an educational version of the game that doesn't have any weapons.

The way that this one works is you've got these doors and they're just images and they're either correct or they're incorrect. So, if you walk through a correct door, you make it to the next room, if you walk through an incorrect one, you have to start over. You could do races like that.

So there's no injuring or anything like that. Of course on the full version with weapons, there's lots of blood going on. We didn't use that one too, too much, but it certainly was available.

Now, I would probably still be using Unreal Tournament if I hadn't come across Second Life. Second Life actually is a much better infrastructure for doing this kind of thing. Here instead of having rooms, we basically have obelisks. So, if you go on Second Life, and you're going to see lots of pictures here, so you'll get the idea.

This is me, by the way, and this is what I see as I'm moving through the landscape. So, what happens is students click on this obelisk and the same four images pop up that I had in Unreal Tournament. And when they click on it if it's correct they get another set of four questions. If it's incorrect they have to start over.

So, I can actually have many obelisks in a room and I can have many students competing against each other. That's what I refer to as my races, which I do a couple of times per term and I give out prizes. So there's no grades here, it's basically just additional stuff the students can do.

Now that's the stuff that I did. What about if my students are doing anything in Second Life. So, I have had students do some extra-credit work, and one of the things that we have the ability to do now is to actually create molecules, starting from smiles or inchies, and we just talk in Second Life, using the chat box, to these little rezzers that are built to do that.

And here's an example of camphor, showing a pretty complicated example of chirality. So, these molecules are actually much bigger than the size of our Avatars. And you can walk around the molecule, you can fly around it, you can see it in a way that's completely different than you would in a small model, which you're limited to in real life. So, that was a pretty good assignment.

And we can have fun with it here. You can actually fly around on the camphor molecule, and the students can engage in that way. So, this is actually on Nature's Island, called Second Nature.

Right now, what we're doing is we're trying to work on displaying spectra, especially NMR spectra, in Second Life. And I'm working with Andy Lang, and we've almost got it to the point where we can actually talk to the spectrum and have it expand. Again, we're using JCAMP format, and if we can get it to work with JCAMP, we can get it to work for NMR, or IR, or whatever. Because a lot of the equipment can add spectra in those formats.

Other educational things that you can do. Well, you can actually demonstrate docking. So here this is actually the receptor site of enoyl reductase, which is one of the malarial enzymes that we're trying to inhibit. And you just walk up to this molecule, you click it, and it slowly meanders down and fits right into the docking site. And you can walk around it and you can see what's going on. It's actually a little bit hard to see where the hydrogen bonds are, but it's a good exercise nonetheless to try to see it.

Now, if we put the entire enzyme here, we would run out of prims, which are the fundamental units. So, we only put the pocket. But if you want to simplify the enzyme, you can actually create the entire enzyme, but you don't have every atom here. Right? You're just showing it in a simplified mode. Peter Miller has actually been very active with the constructions of proteins in Second Life, and you can go right from the PDB file to this 3D format. All right?

So, things are getting a lot easier for chemists in Second Life. There are more tools, and again, if you can get the PDB, or the inchie, or the smiles, you're in really good shape now for actually just doing these projects.

Other things we can do. Well, we can actually see how chemical reactions happen in 3D. So, here's an example of an amine formation. I've got an aldehide, I have an amine. So you can see the aldehide here, the red oxygen, here's the nitrogen amine. And you actually talk to the chemicals. So you come right up to them and you say, "Next." And you'll see every intermediate pop up.

So, the next one here would be like this, where the nitrogen has moved over and now it's connected to this carbon, and you have a carbinol intermediate. And you can actually see the entire shift. And these are actually chemically realistic, so they minimize so that that's really what they probably do look like. And it looks very different than it does on a piece of paper, right? Where everything's flat. So, I think this is a pretty good exercise. And there's every step. So, there's a couple of intermediates in that amine formation, and if you keep saying, "Next," it will keep going.

Now, as we've been putting molecules on Second Life we've been worried about how people are going to find them. And one of the things that I set up is a wiki: secondlifemolecules.wikispaces.com. And here we basically just put the scriptors, we put the uses, and we put the slurls. The slurl is a link that when you click on it, it will take you to Second Life to that specific location. So, that's a way for Google to index it.

We've got three Periodic Table, again working with Andy Lang for the ACS, we actually did this. You can have faculty offices. This is sort of what my office looks like on Drexel Island. You can put whatever you want there. Here's an example of my lab. So, these are just pictures of my students, there's pictures of our chemicals, you have pictures of the equipment. There are all kinds of things that you can do to explain what you're doing.

But, the one thing that works extremely well on Second Life is posters-and you're going to see some of that at the Sci-Mix Session tonight, if you come. And because you can do some really nice things - you can take your PowerPoint and you can just dump it into this viewer in Second Life. And when you click on it, it changes slides. So, from the standpoint of a learning curve, there's really not much to it. You just give your PowerPoint, boom, you're done. Right? And then you could put these little bells where when you click on it, it will summon the presenter. So, that's what we're going to do tonight at Sci-Mix. We're going to make sure that all the presenters have their little bells working.

We've had conferences. Here's an example of a conference that I organized. The SciFoo Lives On Conference on Nature's Island. And you can see there's lots of people hanging around talking to each other, and we're using the poster boards to give the presentations.

This is ACS Island, if you're not familiar. It actually has the shape of the ACS logo. So, this is the land, and the water here gives it the outline. So, if you see lots of moats and you follow them, that's the reason. It's to have this look.

So, there are just a few screenshots of ACS Island. Here's the headquarters. You can go inside here and get some freebees. Get some lab coats, goggles, whatever. There's an ACS Landmarks. I wasn't familiar with the Landmarks before I started this project, but every year or every couple of years ACS gives these Landmarks, like the foundation of the chemical abstracts, or the discovery of helium, things like that. So, these are pretty neat, you can visit this, click on it, and it will take you to the website.

And here's what the virtual poster area looks like. So, tonight at 8:00 you can come around. So, the posters look pretty familiar, and we've put some molecules here that represent most of the posters. So, for example, the forensics lab talks about methamphetamines, so guess what? There's a molecule there to attract people to come over and look at it.

[laughter]

There's also nanotubes, and Cass actually has a really interesting presentation. Hopefully, you'll be able to attend. This little molecule here I put is called felicene. It actually looks like a cat, and we put in some eyes and some whiskers so you can see it here, but the ears are actually on the top. So, again, very, very interesting what you can do in Second Life.

ACS Island has a resident chemist program where scientists can put up some of their work. In our [indecipherable] lab at Cornell is there. The Rosania Lab-that's Rosania from Michigan-is there. And he basically, put up images from his microscope. So he uses that to have meetings with his students and talk about scientific data. And there's also a geodesic dome, so when ACS does run parties, that's where it will happen. And that's a good place to meet. I don't know if anything tonight is going to happen there, but you can check it out.

And so basically, that's it. I mean, if you want to use wikis, it's a pretty good way to organize content and to interact with students. I didn't have time to go through that, but because of the versioning, you can actually tell students to do things on the wiki and then when they correct it they can remove you comment, but it's all in the versions. So that's a good way to interact. And you can use Second Life to stretch student and teacher imagination.

So, what I'm showing you is just what I thought was interesting and cool to do. There's many things we can do in chemistry and if you have any ideas, just let me know and I can tell you if it's realistic or not. And I guess the bottom line is really, we're not trying to replace one means by another, it's just additional channels. We're communicating the same basic chemistry; it's just, to make it interesting and to get students engaged. That's really the point of it.

And that's it. Thank you.

Albright Talk on Educational Technology

2008-04-10T14:42:00.003-04:00

Transcript of Albright Talk on Educational Technology.

Jean Claude-Bradley: All right. Thanks very much for having me. What I'd like to do today is to give you sort of my journey with trying to use technology to better my teaching. I teach Organic Chemistry at Drexel and so a lot of the things that I'll be talking about are Chemistry-specific. I'll be showing molecules and reactions and things like that. But you know want to think in terms of your own fields, how that can map especially when I talk about things in Second Life. So those are just specific examples but this will be completely general.

So again, I'm going to focus on Chemistry here. It's not really about the technology, it's really about the teaching and what we're trying to do as teachers. We're not trying to do anything else except produce people who are going to be competent in their field. I think people lose that a little bit when they start to think it's about the technology, but it really isn't. If you make it above the technology, then it's not going to work because people are not going to be using it for actually doing what they were hired to do.

So if we focus on that and keep remembering that, we can keep adopting as new technologies come on board. You have to think about--again, from the Chemistry perspective, if I'm trying to make chemists, what does it actually mean? I think that it really boils down to having somebody who's chemically literate at the end of the undergraduate level and someone who's competent to create new useful chemical knowledge at the graduate level. I'll be showing you tools that can operate at both those levels and they might not necessarily be exactly the same tools so I'll show you that by example.

As teachers, how do we actually do this? How do we make chemists in the case of Chemistry? We have to do three things pretty well. We have to select and do our contents. That's our choice. We have to assess and validate the skills and knowledge of the students. So we can give content all we want but if we don't evaluate the students, we don't know if they've learned it or not. The third thing is we can actually operate by catalyzing the learning process, which is something that most teachers don't have time to do because they're very busy trying to deliver the content and trying to assess their students. That for me is probably one of the most important advantages of this new technology is that if you use it in the right way, you can generate this time that you can use in a way that you couldn't previously.

So I'll be talking about specifically Organic Chemistry courses, sort of a journey, like I said. I'm going to be starting with--this is what I started with in '96 when I came to Drexel. Traditional lecture-based course, of course, done face-to-face, all the grading is completely manual. There was really--sure, I had office hours, we have all office hours and we use email but that's just really not enough time for doing a lot of the in-depth work that I am now able to do with my students but this is our starting point.

So I'll be going through each one of those three. The first one is assessment. What actually happen over the course of time? As I just mentioned, initially we had manual grading and then I started to use WebCT, so I think you guys here use Blackboard which is they're not merged so it's basically the same concept. Any of you here uses the Quizzes feature? A few people.

Basically, my classes start to get larger and larger and it seemed to be something that was worth investigating, it isn't investment in time. Some of the things I'll be talking to you about are quick fixes or quick to implement. This is not necessarily one of them because you do have to set up your question base and you have to learn how to use the system but I was very happy with the kind of things that I was getting out of the system. First time that I implemented them, it was not grading the students, I was just experimenting with the system. When I saw that yes, this could be used for grading that I moved on to do all my tests and exams with automated grading. I use the video surveillance system that's already at Drexel, it's already built under the public safety. So that's an option depending on what level of security you want, that's something that you might consider.

I started to get in to using blogs and wikis for different reasons, but I saw the potential for teaching. So I will give you some screenshots and some examples of the types of things that you can do with that. By then, I got involved with gaming and so I used Unreal Tournament which is a First Person Shooter game, kind of like Halo, that kind of style. You'll see the evolution of that whether or not weapons make a difference and all that kind of thing and at the end, I actually settled on Second Life. So I actually don't use the First Person Shooter game anymore because I think Second Life is a lot richer and it has more potential, actually.

OK. The other component - the content delivery, again, evolution over about 10 years. So first, of course, face-to-face with paper handouts and then face-to-face with online PDF. A lot of people use the Blackboard, the WebCT systems initially to upload their syllabi and that's a no brainer. It's very, very simple to do, it's something that all the students can find very easily, it's very little work, so that's sort of a no brainer.

Next here, I started to record my lectures. I'm using Camtasia, but I hear some of you guys are using CamStudio. Anybody here using the CamStudio? So George was telling me of his use of that. It will record whatever is on the screen, so I'm actually recording the stock now. Then if you wanted to review it, you can give a link to somebody and it will be a pretty similar experience. But these were optional in the sense that I'm still giving both the lecture in class but I'm recording it and then making it available to the students and there's no penalty for them not following it.

A little bit later, actually, this whole podcasting phenomenon started to get going and, actually, a student asked me, he had a slow connection at home and he said you have just the audio of the class. I hadn't considered it before and I started to look into it. I learned the tools for how to podcast and, basically, it was helpful. But again, I didn't replace the screencast recording, because it was just another channel, and also providing PDFs over iTunes and things like that.

Then I started to get more heavily involved using blogs to deliver content. All right, and I'll definitely show a lot of examples of that. Video podcasting through iTunes, and I did start near the end to use a wiki and you'll see that it's a completely different function than a blog. The wiki is really to organize things as to make it easy to find and it's a very, very quick for anyone to learn how to do it. So that's one of those quick and dirty things that actually does a work.

I will then talk about my use of YouTube and Google Video, these also turned out to be very, very handy for certain types of problems. YouTube, for example, you can't really upload anything more than 10 minutes so you wouldn't necessarily put a whole lecture on there but you could put quick solutions to problems and I find that to be very useful. And because it's so public, you get contacts from people around the world to other Organic Chemistry students who either like what you did or point out a problem. I think that's extremely useful as a teacher.

I won't talk too much about Google Co-op, but I'll show you that there's a search bar. Google is, of course, a wonderful company, and there's a lot of things that they enable you to do for free. One of these things is called Google Co-op, where you can actually specify a whole list of authorized links for your class. If there's an online textbook you like, if you want to use Wikipedia you can include it; if you don't want to use Wikipedia you can exclude it.

So when a student types their search term, it won't search the whole Internet. It will just search the resources that you've approved. That's a really nice little trick. Again, nice quick and dirty thing you can do. I'll show you right now, I'm not using podcasting in the way that I did initially, because now I have archives. It turns out that if you already have a full archive, it's a lot easier to just give it in a whol.ZIP file for the student than showing them how to use iTunes. Showing that.

You notice here that I went from recorded lectures, making it optional, and then eventually I completely replaced the live lecture. For one of the terms I actually studied the attendance of the students. Again, this is video, so it's not just audio podcasts. This is the whole experience, everything goes on the screen, all of my recordings. The attendance drops until the end of the term and goes to 10-20% in both classes. This gave me a great opportunity to evaluate the performance of students who were actually still coming to class versus those that weren't.

The performance was identical. I realized that I was wasting my time repeating myself term after term, and from that point on I assign the recorded lectures in the same way that I would assign a book chapter, and I would do workshops with my students. They'll come in and we'll work on specific problems. I have time to work with them one-on-one, we can do all kinds of things, we can get into Second Life. Basically, that frees up the class time for me to be more involved with my students.

This is what we're talking about here. This whole Learning Catalysis concept, which I think is absolutely critical as a teacher. You have to have time to do this kind of stuff. It's not enough just to put the content out there and to test the students. You don't, honestly, need a teacher to do that. The University could fire all the teachers if that's all it came down to. Teaching is about interacting with students and its about taking your knowledge base; evaluating the knowledge of the student and trying to customize your interaction with them.

Of course it requires the participation of the student, and that's their prerogative. If they don't want to attend those sessions, that's OK, but they're not going to get as much out of the class as the students that do come. It's just a teaching philosophy that I have that I think works. We're almost up to the screenshots, I want to show you how this is all laid out. I do still use a course management system, we use WebCT. It's not the center of the class.

The center of the class is actually the wiki, and this is public. I try to make as much as possible, all of my class material public. The assessment of course is not. Well actually a part of it is, there's a demo account where you can take my quizzes. But in terms of the tests that my students take you have to be registered in the class so there's a whole security thing.

But otherwise, the wiki is a central thing. We've got the content as available as possible. I have the interaction of my students. I'll show you some of that. I already talked about the workshops. I have students doing blog assignments sometimes, wiki assignments, and I can show you examples of that; but everything starts at the wiki. This is a little slide; don't take it too seriously when I say the unhappy old person here. All of the tools have their uses, but it is kind of nice when you discover these new tools.

Instead of pushing on your students, emailing them or contacting them in some direct way like with a phone, most of these new technologies rely on a pool system. You put yourself out there, and the receiver is actually the one that goes and subscribes to your stuff. You can't force anybody to read your material. Yeah, it's great in many ways in that you can get more subscribers. It's not as forceful. Some of that is a disadvantage. You do have to assume that the students are going to be subscribed to your stuff.

It's not necessarily happy and bad, but I think once you've experience both you can then allocate which tool you want to use for which purpose. All right, so these are the screen shots. Again, this is for Chemistry, but they can apply to any field. This is the website that the students get when they're first introduced to my course. Here is the Google co-op search. It's the first thing on the wiki page. If they want to search for a concept in the class, they can put their search term in there. That will search all of the online textbooks that I mentioned, but it will also search all of the transcripts of my lectures. It'll search any content that I have that is in text form. This is actually a really convenient tool.

I record the first lecture. I put it in Flash, I put it in MP3, whatever; and if a student misses the first lecture, which is the only live lecture of the class, then I can point them here. That's actually pretty handy. Really, it's just a little explanation of the class.

On the bottom of this front page are links to all of the resources of the class. I'm not going to go through all of these today, I just took screenshots because I don't rely on the Web. You never know when it's not actually going to work when you need it. Of course, all of these are what they say.

The idea of the wiki is that anyone that has permission can go in on it, can hit an edit button, and can add a link or can add content. So this didn't develop by anyone writing HTML or anything like that. It didn't develop by any plan, actually. It's just, "Oh, I have to give my syllabus, I'll put it here." As you keep getting the same questions I should probably have a FAQ page, so you add it there. The wiki develops.

Again if you remember this "push-pull" system, anyone in the world can subscribe to this wiki for changes. You can either get it through a blog reader or through email with wiki spaces. That's also nice, which you don't get with a regular web page. That's just part of the benefits.

These things are new here. I've just found if you already have an archive of lectures, there's no point in messing around with podcasting. Just give the whole thing; it's about a gig and a half; and then they're done for the term. They can access everything.

Student: That's with the audio? That can't be video, can it? It can?

Jean-Claude: Yeah, m4v files. So the m4v files will play on their video iPods as well. Yeah it's not that big actually if you put the settings right.

Student: You're just capturing the screen.

Jean-Claude: Yeah I'm just capturing the screen. I think they're like 50 megs per hour, it's really quite reasonable. And at the bottom here is a site meter. And what this does basically is it's a free service that sees how people are finding your site. So if they're using Google with certain search terms you can look at that. And it's a thing that I like to put on all my websites, whether they be blogs or wikis. First of all it's free, secondly it's pretty interesting, actually, you can make that stuff public. So people should know what kind website it is. And you can get a really good idea by looking at recent hits.

OK, so the blog. So the first time that I taught this class and recorded it I used the blog, which made a lot of sense because, with the blog it's chronological. So you have a class and then you go and blog about it. So you write some things, you upload your files, you can link to the PDF, you can link to the flash recording, you can link to the audio.

And there's a way of doing this with blogger that enables you to do podcasting really easy. So if some of you want to talk to me about that afterwards I'd be happy to discuss it. So what happens if this isn't a live class, it makes a lot of sense because you get new posts after every class. But once the class is all recorded, and I'm not going to be redoing that class live anymore, the blog, it's not necessarily the best way to contain the information because it's not live anymore. So this one, it hasn't changed since 2005, but it still already has all of the text for all of my classes so I still use it. But if I were to redo this I would probably put this in a wiki because it's a static document basically at this point.

Do any of you have blogs, maintain blogs? OK. So with a blog again it's just, it's a web page that has chronological postings. So if you want to follow it you can use different feed readers. I used to use Bloglines I now use the Google reader. I think it's pretty good. It comes with your Gmail account. And whenever there is a new post, it will show you that you have so many posts. So if you're following a lot of blogs at the same time, it's better to have a reader because there's just one place to go. If you're only following one blog then it makes no sense to have a reader you might as well just go to the website. Right, so a reader would be to manage multiple sites. So again I used to teach my students how to do this, but the reality is now that since I don't have any new posts, there's no point. I just give them the zip archive.

Of course, one advantage of having it in a podcast format is you can put your stuff on iTunes. So that people can find you like that, they just click on subscribe. And then you know this will sync up with your video iPod. iTunes can also handle PDFs. So if you want to distribute material like that. It won't play on the video iPod I don't think. But it will certainly play on their computer. And this is just to show what the interface looks like for the student.

So you've got the PDFs show up with a little book next to it and then you have these other recordings. There's none like this here. If it were video then it would have a little television set and if it doesn't have anything then it's just audio by default. Again the video iPod, you would convert your file to an m4v4 format, and that's not very difficult to do. And that will also play using QuickTime, so they don't need a video iPod to look at the m4v4 format, or the mp4, same thing.

So I've used the blog in a number of other ways. And again this is an evolution, so before I learned about wikis I used a blog to record these FAQs. This is the big limitation. If you have a change here, you can certainly change a blog post. But blog posts are not really meant to be constantly changing. They're meant to publish once, then you archive them. And you can access them at any time. But there's always changes right in a class.

So the FAQ now I actually run on the wiki but initially I would just run it like this on a blog. So basically what's nice when you make these things available to the rest of the world you find actually that there's a lot of interest. I know that there's a lot of premed students that contact me about my classes. And when I was first doing this I don't think that there any other organic chemistry video recordings. But now there's a lot -- Berkeley has them -- there's a lot of different places you can get them now. But especially in the beginning, a lot of students are really appreciative to be able to access that, because they may be in a course where they'd like another interpretation of the material. So having the lecture recordings is really useful if you want to have open coursework.

OK, now going to the assessment part, so student blogging. Well it is not mandatory in my class. I have like between 150 to 200 students usually and you don't want a blog with 200 students. Because this is one of these things, it will require more time. You cannot assume that first of all students are familiar at all with the technology, most are not. And so you have to really start at the beginning. So I do this as an extra credit work. I'll offer up like up to 2% of their final grade will be on a Second Life assignment, a blog assignment, or a wiki assignment. And that's worked pretty well for me, where I might get maybe five students out of the class who will really take me up on this and the actual work for it. But this nice for them as well because they have a record of their class that's open to the public and they can use as a link, sort of their e-portfolio.

Now I didn't talk about this at all but in my laboratory I actually have a wiki that's used as the lab notebook. So my undergrad students and my grad students working in my lab will actually post new pages for all the experiments they're doing. And what's nice about that is it's public and I can use that as an example of real active research to show my undergrads what research is actually like.

And so I've been doing that for the past couple years, where these students -- remember this is the introductory organic chemistry -- so they're just learning about this stuff. But as they see concepts they have to try to relate it to something in the lab notebook. And, of course, that's messy because students are posting to it all the time, they're updating. So it is kind of nice to give them that other view, where you know how everything works perfectly in your textbook? Of course real life isn't like that. So you can show them a little bit of that flavor.

An example is this. We use NMRs, which are basically just plots which we use to analyze chemical data. I don't want to talk about chemistry very much, but this is something we did not cover in class, the fact that this line here is split into three. It was something that the student came across, and she talked to me and said "Why doesn't this match what we learned in class?" We had a chance to discuss this, and she was able to put this up as a wiki post.

She was able to show the data and then link back to the actual experiment from the lab. So this I really like a lot. The way that we teach things is always too simplistic and it's nice to show them the exceptions; it's nice to show them how it actually works.

So why a wiki? Well a wiki is very different from a blog in that a blog; you're going to be posting chronologically. So if you make a blog post today, it will be March 17th. For the rest of time you'll be able to link back to this entry. You can change a blog post, but you should really, really try not to. People don't expect them to be changed so they're not really looking for that.

A wiki is exactly the opposite. People expect the wiki to change constantly. So you can have a wiki page that could go through 30 different versions. That's OK because you can always go back in time and see what all the previous versions were. Here, for example, is a page of one of these wiki assignments that my students did. You can see every version here. This is my undergrad, this is me, this is my grad student, and you can see everybody's contribution to that page. Unless you're the organizer, you can't really delete the page. If somebody were to come and just put blanks everywhere, you could just revert to a prior version. A wiki is pretty safe in that regard, and it's extremely nice to be able to see all the different versions in a project.

The way these show up -- I use Wiki Spaces, which is a free and hosted service. If any of you are interested in starting a wiki, you can do that 100% for free with this service. This is a nice feature here; when you compare two versions, it will show you in red the stuff that got deleted, and it will show you in green the stuff that got added. You don't have to look very much for the different versions of the pages. If you ask a question of a student, and then there's a change, all you do is look at the two versions. You'll see, in green it will be their new stuff. Sometimes students will go and delete your comments without making any changes, so you can catch that really easily with this feature.

This is the site meter that I told you earlier about today. Not only does it tell you how many visitors you get and what their search terms are, it will also show you where they are coming from. I'm just showing this as an example of the kind of world that we're in today. This is a course that's only taken for credit by students at Drexel. But, yet, there's people from around the world that are somehow finding it and making use of it. I would encourage any of you; if you are interested in sharing more of what you do, if you can; this is definitely a good time in the Internet era to do so.

I want to talk about a few other different things you can do with technology. This is a little game that I did with my students -- more upper level organic, maybe Organic III -- that I call "Wheel of Orgo". The idea is I will use a Tablet PC; you can also use a Smartboard but I prefer the Tablet PC because you can write on it.

I will put the starting material, and I will put the product we're trying to make. We'll go in turn, where the students will put one step. A student might try this, and then they'll write something. If they're correct they get a point, if it's not correct then I can correct them and then they can go get their turn around again.

The idea is to complete. The idea is to either put an arrow going forward here, or put an arrow going to the product. At some point the two will connect and, by definition, you have a chemical synthesis. This is something where, "What's the investment in time here?" It's really nothing. If you already have time to spend with your students, that catalysis time I was telling you about, this is a perfect way to implement the boring stuff that you teach through your content delivery mechanisms.

All right, a little bit more about games. I told you about the first-person shooter game Unreal Tournament. There's actually two different versions of that game. There's the popular version with the weapons, but there's actually a free version that doesn't have any weapons. You can build mazes, castles, whatever you want, and people can walk through them. I basically set up a system where you've got these doors. Say a room has four doors. On it is going to be an image that's either correct or incorrect. So three of these images will somehow be incorrect and one of the images will be correct. The idea is they walk through the door that's correct. If they do walk through the correct one, they go to the next level in the maze. If walk through an incorrect one, they have to start over.

I was able to have a system where I could do races with my students. They would all start at the same time and the first one to make it to the 20th level would win a prize. I would give them a molecular model kit or a book or something like that. [laughter]

This is something else that works with some students. Not everybody wants to do it so I never make this mandatory. I think you run into problems with these things when you start to make them mandatory.

I'm not teaching new material here. This is the same material that's in my lectures, the same material that's in my quizzes. It's just another way for students to do it differently. Now I did actually use the weapons version. The disadvantage with that is that it's a commercial game, so you actually have to figure out how to buy it. We had a couple copies installed in the libraries and things like that. I think if Second Life had not come along I would probably still be doing this.

But Second Life did come along. It's just so much richer in terms of the things that you can do. Second Life is not a game; Second Life is just an environment. Just to orient you here, these are the avatars. This is actually me in this particular role and this is how I view the world. I'll try to go on after; I think I can connect to the Internet and I'll walk you around.

So what I used here are obelisks instead of the mazes in Unreal Tournament. So when you click on the obelisk these four images come up. These are either JPEGs or bitmaps. I didn't need to create any new content. I was able to take all of my content from Unreal Tournament and just port it into Second Life. It's the same deal and I can have many obelisks in an area. Students can all come and they can compete against each other, or they can come any time and practice for the tests. So the only difference here is when you click on an incorrect one, you've got to start over. When you click on a correct one it gives you a new set of questions.

Now there's a lot you can do with Second Life; and again, this is going to be pretty chemistry-specific. Of course molecules are important. Working with Andrew Lang, one of my collaborators, have this thing we call a rezzer. It's an object in Second Life that enables you to do something. This particular rezzer allows you to create molecules. So, you feed it information about the molecule and it will create it in 3D. You can see, this is the size of our avatars, you can make a huge molecule. It's a way of looking at chemistry in a way that's completely impractical in real life. You could buy a model kit that would be gigantic but that's not very convenient or practical. You can do these kinds of things in Second Life.

You can do things like fly around on your molecule. Once you've made it, you can wear it and run around. This is actually on Nature Island. There's a lot of educational areas on Second Life and I'd be happy to give you links to that if you're interested.

This is a Buckyball, if you've heard of these. There is some chemistry there. The really nice thing about Second Life is not so much what you can do there, it's the people you can meet. If you're in an area that all it has is science and molecules, you're likely to meet some interesting people from around the world -- whether they be teachers, or students, you're going to meet people that have some interest in that area. If you go to other areas in Second Life that you may have heard a lot more about, then you'll find other kinds of people. So Second Life is much like the Internet. You need to find the locations where the type of content is of interest. If you hang around there, you will definitely have a good experience and meet people.

3D periodic table. Again, we did this for the American Chemicals Society. You can walk around this periodic table, you can click on these atoms and it will give you information about each element. So many things you can do; again, you've got 3D here. You can use your imagination in ways that you simply can't in a traditional website.

Another thing that works extremely well in Second Life are posters. So if you have a PowerPoint, there are tools that we have. Actually, Drexel has an island called Drexel Island, and there's a store there. There's these boards that you can get for free, if any of you are interested. You basically just export your PowerPoint in the JPEG format, and then just dump it into the board. It will show your PowerPoint. If you click on this it will actually change the slides.

The really nice thing about this is you can see; so this is me and I'm talking to two people. This is Loly's poster actually. You can, either with a voice; talk to them; or you can type so you can chat with them. There's a little bell here that you can summon the presenter. If the presenter's online, the text will be in green, you can IM them and you can invite them over. If they're not online it will actually go to their email account, and if they happen to be online somewhere they can quickly log into Second Life and come talk to you.

So I really like posters for Second Life. I think it's a no-brainer basically because it's easy to do, everybody gets it. There's not very much training with it. You don't need to learn to do all kinds of tricky things.

In fact, I've organized conferences in Second Life. There's the Scifoo conference that Nature and Google and O'Reilly organized last summer. I extended some of the sessions on Nature Island by having a lot of posters and people presenting. We'd have maybe 3-6 speakers. Most of these people have never been on Second Life, yet they were able to present in very quick time. And of course this is the social aspect of it. You meet a lot of people in conferences in Second Life, they're going to be attracted to the content. A lot of this content was about Open Science, so if you had any interest in that you could certainly meet people.

And you can have faculty offices. This is really completely up to you. Here I have a little area with a real picture of me, some molecules. This is actually the chemistry department. It's a little pod area. Again, a lot of these things are very simple. Any images, that's very simple to do in Second Life. I think the big problem is people getting too ambitious with it. You have an idea, and you want to do that particular thing for your class, but it's not a realistic idea.

Now there are people in Second Life who are developers who can definitely help you if you pay them. There's a lot of people who will do it for free. What you need to do is talk to somebody who is already doing it and ask them how realistic your idea is. Most of the time, all people really want to do is they want to put up a presentation or a couple of posters. In Chemistry, of course, I want to put molecules up. If you're in Bio, maybe you have other needs and so that would be something you would discuss with people. I could certainly talk with you guys about that if you had any ideas.

So, in summary, you can use blogs for creating podcasts or for storing static, sequential content. Transcripts also are a very quick and dirty thing. If you buy transcripts, you can quickly create a blog. Just dump them in there, and they will get indexed by Google pretty quickly, and you can link them back to your recordings. That's one of the things that I've done.

You can use wikis to organize contact and interact with students on assignments. Again; very, very useful. There's a versioning system in the wiki were you can actually see all the past actions. You can use Second Life to stretch student/teacher imagination. Again, one of the things that people tend to discount is this networking aspect. I think that's very, very important. If your students can meet a couple of people from around the world, you never know who you're going to meet that can help your student down the road.

Use multiple channels to deliver content. This is not about using one of these tools versus another. What it is, it's about giving multiple channels to your students so that they will find the path that makes the most sense to them. Some of the students will like Second Life. Some of them won't. Some of them will like the WebCT quizzes, others won't. As much as you possibly can, try to give it in different versions. Most of these technologies are simple, free and hosted. So you really don't need anything for most of these.

Second Life you do need a place to build, but I can talk to you about that if you want to experiment. We can probably find a little place for you. Ultimately, if you want to buy an island, then that would be done at the Institution level. I've gone through that proccess, I can also advise. But certainly you don't need to buy an island to get involved with Second Life. So that's it for my talk. Let me try to log on and we'll see-- we have a few more minutes?

Open Notebook Science and Cheminformatics

2008-04-10T14:32:00.003-04:00

Transcript of Open Notebook Science and Cheminformatics presented at Indiana University.

Jean-Claude Bradley: ...OK. So thank you very much for the invitation to speak to your Cheminformatics class this morning. I would, basically, like to show in detail how we're using Cheminformatics concepts in my lab. But in order to really show its place, I'm going to give a little bit of an overview of the big picture. In other words, where Open Notebook Science, how its actually done on a high level and how that trickles down to the smallest details of SMILES, InChIs, and all of that.

So, in the very beginning, let me just introduce the concept of Open Notebook Science. You want to think of it as, basically, being at the end of a continuum here. There is recently been a lot of effort done to try to make Science in research and teaching--although we're talking mainly of our research here--more open. If we look at the traditional lab notebook, typically, it's an unpublished document. The only person who has access to it is typically the student and their supervisors, of course. But, when they leave the lab, all of that information is typically not readily accessible to other people. You may have other people around the world repeating their experiments when they could very well make use of that information.

Of course, a step above that is the traditional journal article. Here, this is the typical article format where you have your Introduction, you have your results, your discussions, and it's all one little story. That's great in that it helps communicate some science but a lot of what's missing in there is often all the failed experiments, a lot of the ambiguous results that are probably more common than not in a typical or organic chemistry lab. That's more open, but it's still not completely open because not everyone in the world can access it. Usually, you have to get a subscription to the journal.

So there's a new wave coming out to make journal articles open access. There, typically, the fee is paid by the author although not all of these, but those articles are available for free to anyone in the world. But again here, the format is the same as the traditional journal article, so a lot of the failed experiments and things like that are not included. What we're doing in my lab is what I call "Open Notebook Science," which is where we're trying to achieve full transparency so the actual lab notebook is a public document and it's on a wiki, actually.

Now, to show you how all this connects together, we have various vehicles in the lab. We have wikis, blogs, mailing lists, things like that. They all have their place. Usually, when I get this talk, I like to start at the blog level because that's really the public interface. That's where things get discussed that most people--scientists or possibly people who are not scientists--can actually figure out a lot of what's going on. So I'm going to give you a few examples of what goes on there and I'm going to show how that's connected to our laboratory notebook.

Some of the things that are discussed on my UsefulChem blog are funding. Again, this is something that's not typically public, but I think there's a tremendous advantage to making these things public. One of the things is you can find new collaborators. You can have people try to understand what's going on in their field, what people are trying to do. I think that, overall, even though there's some hesitations about scooping--and we can discuss that later--I think, overall, it's very positive to make things as public as possible.

The other thing on my blog that I've done recently--this is just examples from the past couple of months--supporting funding initiatives. My friend, Cameron Neylon at Southampton University, he was writing a proposal to help people travel to an Open Science talk. He put out a request out there for support and with my blog, I was able to do that in a small way. Whenever we had media coverage--I like to report on that-high light peer-reviewed coverage. Lab notebooks that I'll be showing you are not the traditional peer-reviewed publication.

It doesn't mean that we're not interested in that> In fact, we're very much interested in publishing our work using traditional channels. But, if you want to be able to cite these things, people don't necessarily believe that you can do that, that you can actually cite lab notebook page. So I always like to point out specifically when people in peer-reviewed articles, actually, cite our work. So that's just one example of that happening in the past few months.

I like very much to announce new collaborators. Rajarshi, of course, has been a long time collaborator, but in the past few months, we've had some recent one's. Gus Rosania, University of Michigan, talked a little bit more about what he's doing drug transport and collaborating with us. Matthias Zeller, he is an expert crystallographer, who's actually done crystal structures for our compounds, which Rajarshi and I was talking about a few minutes ago. So he's the guy, actually, who's responsible for that.

Again, another collaborator who is very generous with his time to be able to provide us this information. We have another collaborator, at University of California in San Francisco - Phil Rosenthal. He's the person who has been testing our compounds for anti-malarial activity.

The other thing I like to talk about are presentations, so what I'm doing here, I'll most likely blog about and link to the recording. Presentations in Second Life, so you'll see a few slides here about Second Life, which is a virtual world where people exist in the form of avatars. This would be me, for example, and these were all the people at the meeting, then we can interact this way.

We can have presentations here and these are just basically PowerPoint slides in Second Life, so that's something else that I discuss. I can also discuss Science in new media, so here's an example of a protein in Second Life. I can talk about how I use it in teaching, so here's a student of mine flying around on a camphor molecule and here's a buckyball.

These are all things are related somehow to the work that we're doing in my lab. As you know, we're doing malaria work, so we're trying to make anti-malarial compounds. Part of the advantage of having a blog is once people know that they can ask you for support for other related initiatives, here is a "Run for Malaria" in Philly and it's to collect money for nets in Africa. A perfect example of people who would be following our work here, there's a good overlap of people who might be interested in participating in things like this.

Finally, I talked about more general science philosophies, so not necessarily just organic chemistry or the services or anti-malarial compounds but a lot of the fundamental issues about how science gets done and the opportunities of Web 2.0 technologies to facilitate that.

OK. So those are just really quickly some examples of things that I discuss. The one thing that I didn't show in those blog posts is a lot of them, actually, have links to back up some of the statements that I'm making. I'll be linking to specific experiments on our laboratory wiki. Basically, here I make an announcement that the falcipain-2, which is an enzyme discovered by Phil Rosenthal that degrades hemoglobin. So it's an enzyme that belongs to the malarial parasite. We just talked about that we just shift a couple of compounds.

Now, there's a link here, it says "See Experiment 150." So this is where the beef is. Basically, there's no reason for you to believe anything that I'm saying, and you really shouldn't if you're really applying the scientific criteria. I'm going to be linking to the original data and you can make up your own mind as to whether or not what I'm saying is reasonable.

So if we click on this link, we'll end up on the Lab Notebook page, which is on a wiki, so this is an example of a Ugi reaction. We're just mixing four components together and we're getting a precipitate, which is this Ugi product.

There's no need to really go into the chemistry here, just to say that we're using these compounds so we want to index them in some way and I'll get into that. We're making this compound and if we're trying to find which experiment was this compound made, there are ways of, basically, finding that using some cheminformatics tools. But right now, I'm just going to break down this Lab Notebook page and show you how you can gain access to all of the raw data.

The first part, this is actually a pretty long page, so I'm going to take it section by section. The first part is, of course, the Objective, and we're trying to make this particular compound. I'm going to click on this on the next slide and I'll show you that it's going to link to an entry in ChemSpider, which hopefully you're familiar with. It's a pretty large database of chemicals, I think, it has almost 20 million compounds now. We've been using ChemSpider to archive our results to a large extent.

The other thing you'll notice on the Objective here is that it has links to all kinds of things including a Summary Post. The reason that I really want to make sure that there's some sort of link like this in every experiment page is, if you're Googling and you find this lab note page, I think it's very important for people to be able to know what the bigger picture is.

If you read this, and OK, you do understand the chemistry but you don't understand why we're doing it, you would click on the Summary post. This will take you, typically, to a blog post that explains, in a lot more detail, at a much higher level what--first of all--anti-malarial compound are trying to make. It will also explain the reason why we're attacking falcipain-2 as target enzyme and the docking results that Rajarshi ran for us. All of that, basically, is traceable and linkable from here.

So I'm now going to click on this Ugi Add It link to show you what the ChemSpider looks like. So ChemSpider has a bunch of pages and here they have the molecule. There's a little bit of a rendering problem here, you all know this bond, it looks kind of weird. That's actually been resolved for the most part. ChemSpider has been around for about a year and they're in constant development. One of the things is that if you're working with new technology, sometimes these things will happen.

But the people there are extremely responsive. That's the advantage that a lot of things that we want to do, they can actually implement for us. Whereas, if we're a more traditional kind of archive, it might be more difficult for them to customize what we want to do. But this service, actually provides a lot of useful stuff. They provide the SMILES, they provide the InChI, and they provide the InChIKey automatically.

So I'll be using these for various purposes. The SMILES, of course, is pretty handy for searching in online databases. If you can search by any way, usually, the SMILES is going to be always included. The InChI is starting more and more to be included on online databases but it's not always the case. The advantage of the InChI is that there should be only one unique InChI per molecule. Whereas with the SMILES, oftentimes, there are multiple SMILES for the same molecule, so that's a big advantage of using InChI.

One of the disadvantages of InChI is that for large molecules--and this would be considered actually, a pretty large molecule for InChI. The InChI is so long that it doesn't properly get indexed by search engines like Google. So we've started to use a lot more the InChIKey, which is basically, just look up table from the InChIs. The advantage of the InChiKey is it's very short, and it's just a bunch of letters that should not recur accidentally very easily. So if you actually do a Google search for the InChiKey, you're pretty likely to find what you're looking for and your not going to get a lot of junk, in addition.

InChiKey here has two components and that's also a pretty useful thing. One of the components, the first part here, actually, tells you the connectivity of the atoms. So if you're not interested--like here we have a trans-double bond, so if I didn't care for the cis or trans, I could just search for the first part of the InChiKey and it would pull up all cis and trans, all the various stereoisomers. But if I wanted to specify this particular isomer, there is this additional information in the InChiKey that does that specification. So this is handy as well, this way of making InChiKeys.

OK. So the other thing that we can link to is the experimental plan. Before the students start the experiment, they typically, are going to follow some sort of plan. This is something that you can look up or anybody can look up. We also want to link to the docking procedure. You may not be a synthetic organic chemist; you may, actually, be more from the docking side.

If you want to see exactly what was done--Rajarshi, in this case, actually, did this run for us--and so here's the library, if you wanted to see the list of all the compounds that he used to dock, you can see that. Here's a link to falcipain-2 and it explains more about this enzyme.

The procedure--this basically Rajarshi wrote--and he's explaining how he used the PDB file and he's explaining the two docking sites on that particular enzyme that he thought would be a good starting point and here are the actual results. So these are the list of compounds that we're trying to make. If you want to see what they look like, you click on one of these links and you'll see that these are just tables of SMILES.

Once again, SMILES is a pretty convenient format to store lists of molecules and that's what we've done in this particular case. Someone could actually, if they were interested in all of the first 1500 hits; they could easily come here and copy and paste.

We also have a procedure section. This is supposed to look like more the kind of thing that you'll find in a traditional journal article. These are written in such a way to make it easy for us to send out our papers. We just have to basically copy and paste these sections in the "experimental" section. In order to actually verify the observations and conclusions of the InChI experiment, we provide all of the raw data for the spectrum. In this particular case, again, we're looking at the same Experiment 150.

A compound was isolated, and the proton NMR and the carbon NMR were uploaded. They're uploaded using JCAMP-DX format. This is a pretty convenient format for all kinds of spectroscopy. This is NMR; you could have carbon NMR, proton NMR, IR, Mass Spec; all of these different experiments, equipment can usually save the results as JCAMP-DX format. The advantage in that is that there are free open-source viewers such as JSpecView that will enable you to view the data in an interactive format.

So if you were to come onto the website and click this proton NMR link, it would pop this up. If you wanted to zoom into any region, all you have to do is drag with your mouse across and it will expand all of these little peaks. If you're familiar with NMR, you'll know that that's actually really critical. That's the only way to get J-Constants, for example. Also, it can reveal a lot about the phasing. On this unexpanded view I can see peaks but it is unclear what the quality of the peaks are.

When I expand them, I can see that this is a triplet, but there's some phasing issue going on. It's a way of looking for the details of impurities and things like that. In the supplementary section of most journals, they don't typically give you all of the expansions for the NMRs. They will give you the expansions that the researcher wants you to see, but sometimes that can be a little misleading. That's why I'm a big fan of using JSpecView. This also does not require the person viewing the information to download any software.

This is just using Java, so they're using a common browser and they can just click on it and view the information right away. I'm a big fan of that. Finally, when you get to the conclusion of the experiment, in this case the UV product was obtaining 59% yield; you really don't have to trust that. You can drill down to any part of this experiment and you can see if you agree with that conclusion, based on all the evidence provided.

That's really what Open Notebook Science is all about. It's about making all of your results public, so that if you're making a statement you can truly back it up with real support. OK, the last section on that page is typically a tags page. Here, we're listing all of the molecules that were used in this experiment. There are three or four formats that we're using right now. The common name. When I say the common name of course, that is the problem with common names.

There's more than one name for a molecule, so the common name is just a handy thing for us to keep track of. What is this entry? Really, what we're interested in is to put the InChI, and to put the InChIKey for each one of the molecules that was used.

These are actually linking to Google, so if you were to click on one of these links, it would give you a Google search for this InChIKey. It would show, most likely, mainly the results from UsefulChem, but it would also show other people who've used this compound and have indexed it with InChIKey. So right now I think this is the best way for tagging molecules. Now we're going to be looking at comparing experiments. I just showed you one experiment there; we've actually done a whole bunch of experiments.

We'd like to have convenient ways of comparing them. There's a few ways of doing that, one is with a simple table. We're using Google Docs, again because it's something that's easy. It's hosted, we can actually make it public very easily. Remember, the point of this is to make things as public, as quickly as possible. I'm a big fan of Google Docs. You can see here that we are keeping track of things, not only with the common name, but also using SMILES.

We've also used InChIKeys in this case as well. InChI not so much, again, because a lot of the InChIs for the larger molecules are just unmanageably long. I will put InChIs for small molecules but I tend to stay away from it for the big ones. The most important section of every experiment is of course the log. If you don't have the log or if the log is incomplete, you really can't do anything with that experiment. We have a log, which is just basically the student recording what they did and what they observed at different times.

You can actually construct all of the results from this. You can construct your discussion, and ultimately, of course, your conclusion. But if this is missing, you really don't have much proof for what you did. I do consider it the most important section. The problem with the log written in this way is that this is written in freeform. I know that Rajarshi and I have talked a lot about trying to automate things a little bit more. If you have a log in a freehand format, that makes it very difficult.

If a machine were to look at this, it might be able to pull a few things out. It would know that benzylamine was used, but it wouldn't know very much more precisely what it actually did. One of the things that we're doing now is converting all of these logs, that are written in a freehand form, and converting it to a machine-readable format. Here's one example of how we're doing that. I'm taking that log and I am now breaking it down into a series of steps in a workflow.

These words here; add, weight, vortex, take picture; all of these are terms that we agreed that we would use to specify certain kinds of actions. If I use the term "vortex" every time I vortex, I'm going to be using this exact way of representing that. These are represented in steps. This actually could be read by a machine fairly easily. When I say "Add Compound," I specify with a common name. This is mainly for human use so we can tell roughly what's going on.

I'm using the InChIKey for the machine to read. The InChIKey, again, I prefer this to the InChI because it's always going to be the same length no matter how large the molecule. It's a really convenient way of keeping things concise. This is one of the ways in which we are trying to automate things, or make them available for people who are interested in automating it.

So we can take these workflows as well and we can represent them in some more tables.Here, what we're doing, just to clarify the difference between the first table I showed you and this one. On the first table, I was looking at entire experiments. Here, I'm actually breaking down each experiment in to each individual result that was obtained.

In Experiment 150, for example, I took pictures multiple times and each one of these is a self-contained result. This is a self-contained result that--let's say the experiment, I drop the flask on the fifth day. That doesn't mean that everything that I did in days 1, 2, 3, and four are not helpful.

This certainly can be helpful but not if I think of them in terms of an experiment. If I drop the flask on the fifth day, the typical thing to do would be to just abort the experiment and move on. But if we're breaking things down into each individual result, we can actually use that information to plan further experiments. The key here is to represent it in such a way that it's systematic and that other people can use it easily.

So just a couple of different organizing ways, there is a table here on one of the wiki pages that is just a table of contents, so the list of all experiments. If you, as a human being, are looking for information and you know the experiment number, this is probably the easiest way to do it. You can also see the person who did the experiment. You can see a brief title, but in order to really see what's going on, you'd have to click in but it is probably the most common way of starting.

Now, I would like to talk briefly about why it is that we're using a wiki in Open Notebook Science. One of the things is wikis, it's very easy to tell what's going on in the lab. So if I click on the recent changes button here, it will tell me in the past few minutes, hours, and days who did something. It'll tell me exactly when and it'll tell me which page was modified. So if I'm interested in either what Emily is doing or if I'm interested in Experiment 158, I would then click on this and then see exactly what the addition was.

So if I do click on one of the experiments, there's a history button on every page of the wiki and I can see every single modification of that page over time. Now, we're using Wiki Spaces to do this which is a free-hosted service. The big advantage of that is that these date-time stamps are third party generated. So if I were running this on my own server, someone could argue, "How do I know that the time is correct?" Since we're using a third party time stamp, I think, it's pretty objective that if I look at anyone of these versions, I'm able to prove that I knew what I knew at this particular time.

So even though things might change, anyone can go back in time and see what exactly we knew and what we talked about. If there are mistakes made, we can see what those mistakes were and how long it took to correct them, all kinds of things like that.

Comparing two pages on a wiki is very simple, you just compare and anything that's new will show up in green and anything that's deleted will show up in red. So if you're making comments and the students are responding, this is actually a really convenient way of doing that and keeping track of it.

I also use on every blog and wiki page this little service called Site Meter. Again, it's another free-hosted service that tells you how people are finding the various pages. So this is something that I check pretty regularly because it tells me how the information that's on our wiki and blogs is actually being used. This is very interesting because you see people, for example, searching for the NMR of butylamine. That's the kind of search that is a little bit harder to do on a traditional journal article.

Whereas if I'm looking for oxidation of catechol or if I'm looking for immine chemistry, these are things where there's a lot of discussion about troubleshooting. There's discussion about things that don't typically show up in a traditional article. This gives me good feedback that we're actually accomplishing what we set out to do in terms of making the information usable.

Another nice thing about having Open Notebook Science is that you can actually tell the story of the failure, something very difficult to do in a traditional journal. We did manage to make this compound, for example, [inaudible] and we ran into a lot of problems. It took actually a long time to do this. Although you can discuss a little bit of this in a traditional article, here, I can go into great detail and talk about exactly why it is that we fail, why it is that it took so long. I can link to the original experiments. Maybe we save somebody sometime if they're trying to do a similar thing.

So we use additional vehicles besides the wiki and the blog, we use a mailing list. I find mailing lists to be very useful for other groups. The wiki is good for my group and I certainly welcome people to contribute to it. But a lot of times, it's easier for people that are different institutions to just hit Reply in their mail. So we use a UsefulChem mailing list for that purpose. We're working out a lot of little details that are not important enough to make it into the blog.

So if I just step back and look at the very big picture here, my group at Drexel--we are synthetic organic chemistry group. In terms of the information flow, so we have Rajarshi doing the docking. We also had, although not recently, Tsu-Soo Tan from Nanyang Institute who's also done some docking work for us.

What we'll do is take that information from Rajarshi and we will then decide what compounds to make. Once we've made the compounds, we then ship them out to either the Phil Rosenthal group if we're doing an anti-malarial test, or we'll shoot them out to NCI, where they've actually done anti-tumor testing on our products.

So once we get feedback from that, we can go back to Rajarshi and we can say, this is working, this is not working, then we can alter the model. This is nice to have so many great people that are willing to donate their time and expertise to actually do something constructive, do a whole loop here. So what I call it "Closing the Science Loop." Once we get information, then we can then start over again and get more information from the docking group and just make more compounds until we make a better and better agents.

A couple of other people that started to collaborate with us, I talked earlier about Gus Rosania. He's actually building red blood cell model in a malarial parasite model, so that we can try to simulate the transport of the various drugs that we're making to see if we can make them better by changing their transport properties.

Other people who are very involved with Open Notebook Science: Cameron Neylon from South Hampton University. He's also recording his experiments in great detail, but he's not using the wiki. He's actually using blogging software that is modified to keep track of versions.

There's not one way to do this, I'm just showing that you can use wikis and blogs to do it this way. There are other people and they have other reasons for doing things in a different way. So it's nice to see different examples like that.

In the next few minutes here, I'd just like to talk about some more detail on the Cheminformatics side of this. What we want to do, by exploring the information about compounds, InChIs, SMILES, whatever; is we want to be able to have machines process it as much as possible.

Here's something that we've done on our server, where we published information about each molecule in the format of SMILES, using a traditional blog. One post would correspond to one molecule on the blog. We're no longer using that because we have too many molecules now, but at first we were doing this. There are a few advantages to this; we can actually read the feed from that blog, and we can then calculate the InChI and we can calculate the molecular weight.

We can look up suppliers; we can make all of that available as separate web pages. We can also show the appearance of the molecule in 3D using JML. All of this stuff here is generated automatically. It only requires people to dump the SMILES in a blog post. OK, so that's one example. The other thing that we can do, is we can take that same feed and we can convert it to a CML RSS feed. We're not doing a lot of this, but we did it just to demonstrate that it was possible.

We can take that CMLRSS feed and we can read it in readers like BioClips. Very briefly, BioClips enables you to read CML RSS and then each entry here would be a different molecule; you can associate spectra and things like that. If anyone as more interest in that, feel free to contact me. There are people that are still working on this. This hasn't made it to part of our routine workflow, but it is something that we have experimented with.

Now I talked a little bit earlier about looking at spectral information using JSpecView and the JCAMP format. If you remember, the reason that this is really nice is you can expand any peak. This is showing on the browser how it looks, and that I can expand the peak. Now if we want machines to be able to make use of this JCAMP format, we can actually use Excel DBA. If I have Excel DBA reading the information from the JCAMP files, I can do something pretty interesting.

I can specify different regions in Excel as to the peak locations, and I can attribute each one of those peak locations with what I think is the corresponding chemical group. If I run that, it will read each individual spectrum and it will take out all the XY data and all the metadata. It will automatically give me a reaction profile where I can determine kinetics from. This is neat because all I'm starting with here is.

I'm monitoring an experiment using NMR. I'm dumping those NMRs in JCAMP format, in a folder. I specify the start time of the experiment, I click on the Excel DDA and it spits out this reaction profile.

We don't do reaction profiling much lately, but about a year ago we did a lot of this. This is just another example of how you can leverage automation if you have the broad data in a usable format. A last thing here, what's the next step with what we're doing?

I showed you a little bit about Second Life, how we can actually create molecules. We have a rezzer in Second Life that Andrew Lang built for us. All that means is it's a little bit of software where instead of figuring out how to connect all these bonds, you dump either the SMILES or the InChI or the InChIKey in the chat box.

It will create a 3D version of the molecule in Second Life. This is using some of the scripts that Rajarshi wrote. It's hitting ChemSpider, web services for converting InChIKeys into InChIs. It's using all kinds of different things, and it is very conveniently giving you the molecule. One of the advantages of these SMILES and InChIs and all this, if you can minimize how much the user has to worry about transforming things; you can get people who are not familiar with Cheminformatics to do some pretty powerful things.

This is an example where I have my students do assignments in Second Life. All they have to do is figure out how to grab that SMILES or InChI and they can do this stuff. In the background here, this particular student assignment is looking at acetylphenone. He is trying to explain how the spectrum supports the assignment of the molecule. Now, it's a little fuzzy here in the back, but this is basically a screenshot from JSpecView. What we're currently working on with Andy is we want to make this interactive.

We want to be able to read JCAMP files directly into Second Life, and to have an interactive way to do expansions. This is something that I think is going to be really neat to meet up with students, and we can talk about the molecule with is here in 3D. We can interact with the spectrum and we can try to figure out all of the different regions of the spectrum; whether or not they support the assignment. In order to do that, we need something better than this, which is just an image. We need to interact with the spectrum.

The bottom line with all of this is these Cheminformatics tools that we've been talking about; yes they're great for communicating between human beings, but I think ultimately where the real power is going to be is to go from human-human interaction to human-machine interaction; and eventually to machine-machine interaction over the free web, to design experiments, execute experiments and analyze them.

A big motivation for us, at least, is to start to use these Cheminformatics tools in a way that is easy for people who do like to do coding for them to be able to write programs that will analyze what we've done in the lab. Without having to interact with human beings to figure that out. That's the much bigger picture, and that's where we're headed. That's all I have for today.

The Role of Blogging in Open Notebook Science

2008-02-07T15:18:00.000-05:00

Transcript of "The Role of Blogging in Open Notebook Science" at the North Carolina Science Blogging Conference January 2008.

Jean-Claude Bradley: OK. So I'd like to talk to you about what we're doing in my lab at Drexel University in recording the raw data from the experiments that my students are performing.

I'll be referring to this term "open notebook science." What that means is basically everything that we do is put up in real time -- and we use a number of tools to do that, wikis are one but there's a number of other ones -- and I'll show you how all of that is sort of interconnected.

So just one slide to give you the big picture of why we're doing this. If you notice, in the past couple of years, there's been a trend from closed information sources to open information sources. Your traditional closed research would be a traditional lab notebook.

Basically, no one ever gets to see that. It's not published after the student leaves, all the field experiments are not usually reported to anyone; so it basically stays there -- if part of it never gets converted to a traditional journal article.

Of course, one level off from that is the traditional journal article. That's still not completely open because you have all the failed experiments. You also have selected data sets that the researcher put together to write this specific article to make a point.

The problem here in terms of the closed/open is that, of course, the traditional journal articles are not free, typically. We discussed that extensively this morning -- how open access journal articles are even more open.

But I'd like to focus here this afternoon on this open notebook science concept, which is where we're aiming for full transparency in the research process.

So how does a researcher use Web 2.0 tools to also do science? Well, I will basically start with the blog aspect -- because this is the Scientific Blogging Conference after all -- and I will show you how the rest of it connects with the blogging. We will see wikis, Google Docs and [indecipherable].

What I tried to do is look, for the past couple of months, at the things that I'd actually recorded in my blog, to show you what it is that I'm thinking about and what's relevant to my lab. So of course, recently I'm looking for funding, so I put this blog post and uploaded the proposal up on "Nature Proceedings" which is a fantastic source if you haven't come across it to basically pre-publish pretty much any document that you want.

Another thing that's happened here is I supported another researcher in his efforts for getting funding -- this is actually Cameron Neylon, I'll show you his blog a little bit later -- and he's trying to get some funding to have people travel to talk about open science.

But it's kind of neat -- the way that we all have these blogs and we can support each other, really with minimal efforts.

Some other things that I blog about is if we get some media coverage, or there's somebody who talks about Science 2.0 stuff. So there's a recent "Scientific American" article which is really interesting.

The other thing that I can blog about is when we get referred to from the peer review literature. I see basically the Peer Review Literature being paralleled with this open source initiatives but there's going to be a lot of cross-talk. So I try to make a point of it, that when I do see that cross talk...

And of course how do I know? Because I see all of a sudden the link someone has referred to me -- through, in this case, Chemistry Central. So I think that that's going to be more and more important as we move on.

Man: I have a question. This goes back to where [indecipherable] back from one source to another source. In your experience, [indecipherable] people linking to you and finding those links and what they've taken so that the link connectivity between blogs and other sources [indecipherable].

Jean-Claude: OK. I think that the idea to try to quantify the importance or the relevance of a particular post through citation I think is very misleading. I think though what you can say is, "will you find a link somewhere in your blog, somewhere in your wiki that leads you to meet somebody?" I think that's pretty solid.

Man: [indecipherable] finding someone.

Jean-Claude: Then here's a case right here. Gus Rosania, he's a faculty who basically went on my blog and was interested in open notebook science and thought, "Hey, I should put my lab online!"

He has, in fact. In the past few weeks he's created wikis; all of the students are uploading stuff. So that's exactly how it happens, and it only takes one event for that to actually transpire.

So people ask me, "Why do you bother doing all this?" The bottom line is it produces results. And the main result is collaborators. I managed to find some people who are willing to work openly as well. There are not a lot of people who are willing to do that, but there's enough that we can actually do constructive science.

We have an x-ray crystallographer, Matthew Zeller; he has a nice crystal structure he did for [indecipherable].

It's also a way for me just to announce all these collaborative. Phil Rosenthal is a researcher who's [indecipherable] enzyme. I work in malaria, trying to make anti-malaria compounds, and basically he is willing to test our compounds to tell us if they're active or not. So that's how his collaborations actually happen.

What else do I use my blog for? To discuss presentations in real life. So I'm talking here obviously. And as will most of you, we're going to blog about this event. I'm also recording it and I will put it on this separate blog here that has links to the PowerPoints and the recordings and all of that.

The other thing that I discuss is presentations that are not in real life. I think I recognize a few of you who were at this Sci-Foo Lives On meeting. This was on Second Life, and there was a session in October on science blogging.

I don't have a lot of time here. But just to give you a rough idea, Second Life is a virtual world where you have an avatar. This is me here with the blue cap, and some of you probably recognize yourselves here. So we got posters here, and we've been talking about open science, and all of the transcripts for these meetings are actually on a wiki. So if you're interested in looking it up, I can point you to that.

What else can I do as a scientist? I can basically showcase science in new media. Here's an example of... I was talking to you about the enzymes that we're trying to inhibit with our anti-malarial work. This is Peter Miller's work, this is an enzyme represented in Second Life, and the enzyme is much bigger than you are. You can climb it, you can sit on it, go can go through the receptor site, you can do all kinds of things that you can't do with a lot of other software. So when I see stuff like that I'd like to blog about it.

In Chemistry last term I had my students do so much credit work in Second Life, so this is one of my students sitting on the molecule of camphor and you'd become the molecule and actually fly around. I'm actually also here flying one. So basically, this is not enough for me to write a full paper and send it out to tell the world. This is a blog post, "Hey, this is what I do with my students; maybe you want to do something similar. If so, here's the information to do it and contact me." So that's really what a blog can be use for.

Other things I'd never even anticipated, people contact me because they know I work in malaria and here's a Run for Malaria in Philly where it was very simple for me to simply put that announcement on my blog and maybe they put a track to put a bit more interest. Sometimes I like to talk about science's philosophy, so yes, I do talk about my actual research in malaria. But I also think that some of the things that I'm doing have broader applications and I do like to talk about that occasionally as well.

Now this is really the bottom-line as far as I'm concern in terms of doing the science. Here's a post about the fact that we just shift these targets to Phil Rosenthal and it goes into some detail. This is about this molecule that we will make, that's quite beautiful, it crystallizes like a snowflake and [indecipherable] in the flask, and this is all well and good, but the thing is why would you trust me? You have no reason to.

So what we do is we link here to the actual experiment where this compound was made. That's just the link if you click on it; it takes you to the lab notebook page of this particular experiment. So this is an actual lab notebook page and it looks very similar to what on it would on paper. I can't show the whole thing here on PowerPoint because there was not enough room so I'm going to show it in sections.

The top part is the objective, so this tells you what we're doing, this year it tells you why we're doing it, and see you've got a link here to a compound, you've got links to an experimental plan, you've got links to libraries of compounds. So let me take you through each one of those links to show you how much you can draw a [indecipherable] each of this information.

So if I click on that first molecule link, you end up in ChemSpider. ChemSpider is a company that basically--there's about 20 million molecules that they're currently managing. They predict all kinds of properties of that film and what they enable me to do is to upload my molecules there and manage the searches, manage the archiving so I don't have to worry about it.

So most of the things that I'm showing you, if I can at all I'm going to get it off my server, put it into the cloud, have other people worry about it and optimally, do it in a redundant way. So if something goes wrong, I still have access to it. So this is a perfect example, ChemSpider, I can link to it and now if you want to know the molecular weights, whatever, there's also a bunch of information underneath here.

Now, there was one of these little links to an experimental plan, so there are pages on Useful Chem where this is me basically outlining a protocol for my students to follow. Now it may turn out that they won't follow it exactly and that's why they have to recall a log every single time you do it. But this is a way of streamlining that so I can ask them to do something.

Then there was a link to the molecules that we're trying to make. So why are we trying to make them? Because we have a collaborator and in this case, Rajarshi Guha at Indiana and he did docking studies. So he tries to take some of our molecules and fit them in the enzyme of the malarial parasite, and then he told us which molecules are most likely to be active. So he returned the list back to us.

Well, why should we trust him? We have no reason to. So here's the procedure he's using and there's further links you can keep digging down to see the receptor areas that he used, why he used them. Over here, you see these links; these are links to the actual molecules. All right, in some way your Chemistry recognizes your molecule codes. This enable you to represent a molecule and you're just using text, so you don't have to draw it out.

So you can see here, molecule 1, this is what Rajarshi thought was the most useful molecule for us to make. So you can draw down and access the information as deeply as you wish. There's a procedure section which looks like what you would paper. And you can link to our data that there are spectrum. All right, so in Chemistry we take [indecipherable] which is basically a spectrum that helps you identify the molecule and helps you identify your [indecipherable].

All we do is we put a link here and the person really doesn't even need to have a software installed, this is all browser-based. You click this link, it pops up the spectrum and then you can expand any of these areas to look for the fine detail.

That's something that's actually been a little bit annoying if you're trying to repeat something, you may on the supplementary section of the paper actually get--this is a PDF. But it's kind of convenient because if you were to expand it, you'd see that there's a lot more [indecipherable] there than it shows in the full picture. So that finally, when you see this conclusion--that the [indecipherable] product is obtained with 39% yield--you can actually see what evidence I'm bringing forth to make that statement. You can see all the way.

All right. The other thing that we do is we indexed the experiments with the molecules using different kinds of tags. There's something called an InChi which is a way of representing a molecule. There's also something called InChiki which for a number of reasons, I'm going to be switching more and more towards than--I can discuss that with a chemist at some of the time--but the point is that all these tags are indexed in Google, so if somebody is searching for that molecule they will show up the experiments that where we've used it.

OK, comparing experiments. So a bunch of pages is not really that handy to compare experiments. So one of the things that we started to do is to put similar experiments in a master table and this was using Google Docks which you saw earlier on, very convenient. You can share this Google Dock to anybody, it's a spreadsheet, you can collaborate, you can make it public, you can make it not public, you can have some people be able to edit it and some people not.

What we're basically recording here is whether or not we get a precipitate from this reaction. So if we get a precipitate, it means that it's really easy to do the reaction so we're trying to find a reactions where we do get a precipitate and actually, this table is a lot wider than I'm able to show you here. But you can try to find patterns in here and that's another collaboration we're having with people who are trying to plan models to this data to predict which compounds will precipitate. So everything here is up for grabs in terms of contributing to this project.

The most important section is the lab section because if you don't have this, you can't really be completely certain that you really did all the things that you were claiming you did in the other sections. So that's something that I try to really reiterate with my students, have to have this. Now, the lab the way that it looks right here certainly a human being can read this, but if we're going to be doing lots and lots of these experiments in order to be really searchable in an intelligent way, it'd be nice to represent it in a better way as we're mentioning.

So a number of ways, I'll show you two right here, one of them is to basically define a series of actions and to write a script with parameters for each one of these actions. So instead of having all the stuff typed out in a narrative, you basically have a list of actions where you're allowed to add a compound, your allowed to weights, you're allowed to vortex, you're allowed to centrifuge. There are about 10 actions that you can take and these you certainly could have a machine read this and you can have them imported into whatever database that was available. So we can do the same thing but do it in a table format.

OK, so here what we're doing is we're taking the experiment and we're stripping out each individual result. So let's say we did an experiment and after the first day we take a picture. Now, we wait another day and we take another picture. And then on the third day, you drop the vial and you lose the compound. OK, so normally you would just x-ed out that whole experiment. But by recording each individual result, every result that was obtained up to the point of failure is usable if it's represented properly. So that's why we're taking a result-centric view here, and also table content is very familiar than you want [indecipherable] have a lab notebook.

Just a couple of things on why we're using the Wiki to do all these. For one thing, I can just hit the Recent Changes button on the Wiki and I can see exactly who's been contributing, which experiments they've been working on, exactly what they've done, and I can compare any two versions. So if I'm looking at an experiment, these experiments can last for months and months and months as new information comes in and so I can basically compare two versions.

The stuff that's new will appear in green and the stuff that got deleted will appear in red in these version comparisons. So in terms of proving that you that knew something at a specific point in time or you changed your mind into that something, you can prove that in a [indecipherable] usually using a Wiki.

We use other free services like site meter to tell how people are finding these experiments. So I have some idea basically what people are using this information for. A lot of it is for debugging their reactions. They're looking for problems of reactions, stuff that you wouldn't necessarily find in a journal article from a traditional search. Of course, this enables me to tell the story of our failures.

If I were to write a paper that was all about how we failed, it'll be very difficult to get it accepted. But here, I can actually lay this out which I'm writing from a chemist to another chemist and saying, "Look, this is what we're trying to do and it took us these 50 attempts but this is why, this is where we went into problems." We also use mailing lists, that's useful for lots and lots of small activities that you need to go back and forth. You wouldn't use a block for that, you wouldn't necessarily use a Wiki and it's just that other component that works well.

So when you look at the whole story, together basically, we're using all of these tools and my lab is right here in the middle, Drexel [indecipherable] Chemistry Group, so we know how to make compounds. But we need help from people who can do [indecipherable] so who could do theoretical studies to tell us which compounds to make and we definitely need help with testing. So right now, I have Phil Rosenthal who's testing for malaria and National Cancer Institute's Dan Zaharevitz who's testing for anti-tumor activity.

So this was another very nice development, basically Dan was seeing the kinds of things we were doing online and he said, "Why don't you send me a couple of compounds and we'll test them for anti-tumor activity?" So this is what's happening and this is what's possible, and until you actually do it, you won't know what kind of people you actually find that will agree to collaborate with you.

And I guess sort of to lead you with the big picture here, I've shown you mainly--this is about communicating what's done in my lab to a fellow chemist and certainly that's our first priority. But as you see that at the end, we're trying to format these results in such a way that machines will be able to read them. Ultimately, I see we're going to go towards a world where it will be machines talking to machines basically formulating hypothesis, executing experiments, and having other machines analyze them.

I think a way to get to that is to take the lab notebook to go down to the absolute fundamental unit of action in a lab and make sure that we can record those in a way that can be read by anyone who needs that access.

I think that's it. This is a blog of another person, Cameron and I, who basically put his lab fully open recently. So there are a couple of examples of people who try to do this.

Cameron Neylon's Talk on Open Notebook Science

2007-12-20T06:00:00.000-05:00

Watch or listen to recorded talk here

Jean‑Claude Bradley: Well I'm very pleased today to have a special guest from overseas, Cameron Neylon. He received his bachelor's at University of Western Australia, a PhD at Australia National University ‑ Research School of Chemistry in protein chemistry doing some work on ribosomes, and then he did a post‑doc at University of Bath ‑ Wellcome Trust Fellowship. In 2001, he became a lecturer in the Department of Chemistry at the University of Southampton working on protein chemistry. He has a joint appointment at the Rutherford Appleton Laboratory's Neutron Scattering Facility, and he's going to tell us about that.What makes his visit very special is that Cameron is working on Open Notebook Science, which is something that my lab is also working on. It's really a pleasure to have people come and share their experiences and to talk about how we can do science in that way. So Cameron, please.
Cameron Neylon: Thanks Jean‑Claude for the introduction. It's a great pleasure to come here and talk about what we've been doing in the area of Open Notebook Sciences, Jean‑Claude being the person who really kicked this off as an idea, and was the inspiration for what we're doing to make our work open as well. I titled the talks, slightly tongue in cheek, 'Beginner's Guide to Open Science', not necessarily because I'm trying to downplay what we're doing as unimportant, but because I think we are beginners when it comes to figuring out how to do these things.I'm going to try and make the talk quite interactive. I'm going to show you a bunch of things that are live on the web ‑ that's the whole point of what we do in this area. Some of these things may not work and they may break, but that goes with the territory. But if you've got any queries along the way, please ask questions if you want to. I'll be quite happy to discuss things as we go along.So where I started in this area was with a problem. I have a group, mainly made up of graduate students, who work in a lab and generate data. That data is collected in lab books and computers. Some of these computers are ancient and are running Windows 3.1 because we can't get the cards to run the instruments.A lot of people outside chemistry and biochemistry as well, possibly still think of this as the way laboratories look. And while in many cases, the infrastructure and the benches maybe the same, as when these pictures were taken, that's not what a modern laboratory actually looks like. This is actually a picture of McGill Biochemistry Department in 1921. This is my laboratory, incidentally, from pictures ripped off the web in the usual fashion.The modern laboratory is full of instruments and lots of computers, some of these are legacy computers, but some of them are up to date. But there are a lot of separate computers and that's the core of our problem. We have our data spread out over two many different computers, some of which are network, and some of which are not. Many were not allowed to have networks because again, we're running old versions of our program systems and we can't get automatic virus updates.The data is almost usually not accessible or indexed in any useful fashion. And what's critical is the data gets lost, as both the computers get retired, whether those computers are in a write‑up area or computers in the lab, or people leave and you don't have their passwords anymore. All these things are problems that I'm sure are very familiar to a lot of academics.So that's where we started. We started with the aim of developing some sort of laboratory notebook system ‑ we were very open‑minded about what that might look like ‑ that would solve some of these problems. So our starting objectives, in priority order, were to have a system that would actually store the data in one place, is backed up and reasonably safe so I can find it. Students can usually find their own data given a day and a half to pull it out of some computer somewhere. But I want to be able to find it, even if I don't know what their email address is anymore.A lot of what we do is quite 'high throughput' where we're developing 'high throughput' systems. It would be very nice if we could embed into this a system that would track samples, so that we'd know which sample is what, and when you go to the 'frig and the label is some obscure number in rather poor handwriting, we can actually tell what it is ‑ that would be quite nice.As Jean‑Claude said, I work in two different places and I'll come back to that point a little later. It's really important for me to be able to actually track what my students are doing. I may not see them for a week or two weeks. I've been there for 10 days now, so I haven't seen them for two weeks. So actually being able to keep track of what they're doing, making sure they're on track, that things are happening and any problems have been dealt with is quite important as well.Number four is the dream of where we'd like to be. We'd like all this data to be in a form that can be processed, possibly not by us but other people. We want to be able to go back and understand, if we got this result, and that feeds back to some material that we bought from some supplier two years ago, can we link those things together? Is this particular primer, chemical or whatever bad for whatever reason and can we figure those things out? Or, as I'll come back to a bit later, can I tell who used up the last of my buffer? Little things like that can be quite useful. So those are our objectives and starting point.There are lots of systems out there. I'm going to take you through what we've done. This was built out of a blog‑based system. The system we're using is being built in‑house by my collaborators. It's based on a blog format and it's fundamentally an open source engine, which has been modified. So it's not a publicly hosted service or a freely available system, but that means we can make changes to it and adjust the way the system works.I've said something that's jargon, 'a fully flexible system with arbitrary meta‑data'. What this means is the system itself has no idea about semantics. There's no presupposed structure of the data that's going in. Any instructions that you put in, you're completely free to do, and that causes problems but it's also very powerful. An important point, if you're going to use something as a notebook, is that there is a full record of the changes. This is not like for blogs on publicly available systems where you can actually change the date on a post after the event. Obviously, this is totally unacceptable for a lab book.So we have a full record of changes. Changes can be made, though it's not terribly easy, and deliberately so. But at the moment, we don't have the nice feature that you have in wiki, where you can track back through something that will be developed, but at least the systems are there.So the sites down at the bottom are the URLs for the lab books we have, and I'll show you those in a second. Also I have another blog discussing how this is progressing. I'll put those links back up at the end as well, if anyone wants them.What does this thing look like in practice? If I go over here‑‑so this is the lab book that's been set up for a collaborator. This is a project that hasn't started yet. This is what it looks like before anything goes into it. Conventional looking log type of thing, I mean this looks like possibly something you get out of a default version of WordPress or something like that.Fairly conventional looking kind of thing, there's some sections down the side. There's a search box. Unfortunately, that doesn't actually work at the moment, but that's something we'll work towards. If I go to where we started with what we're doing here, I go right back to the beginning.This is a blog. The reason why we used a blog is because a lab book is essentially a journal. It makes sense. Your first thought is, "It's a journal. That's what a lab book is, so we can use it that way. That's fine." That's what we did. Essentially, it was just a process of typing in some of the stuff that was going on.At this stage, actually, we weren't able to make changes. That's a point I'll come back to. These are the very first posts that went in. This was halfway through an experiment, as it happens. So Stevens described an experiment down here. In this very first experiment here, you'll notice one thing down the bottom here. There are 10 comments.Our first thought was, "Well, you describe what you're going to do. Then, if anything changes, you make comments on it." If anything happens, make comments on that.A lot of this is actually about the mechanics of the system. As you go down, one thing that comes across quite a lot is that tables are fairly awful. In fact, this has got some problems down here, obviously. This is the kind of thing we had. The results of the posts were going into comments.So a couple of things came up fairly quickly. There's a couple of things we can do here. The student whose lab book this is was working on two different experiments in parallel. So she categorized those as Î²‑galactosidase and Î²‑[inaudible], just two different enzymes that we were essentially doing the same things to. And he brought immediately, the first step beyond a piece of paper. I can now click on one of these and see all the stuff that relates to that particular project.But something that became quite clear early on is that we've got a lot of text here. It's very difficult to figure out what's going on. How different posts relate to each other.You see that there are a lot of these numbers around the place? Those are actually references to the student's paper lab book. The student was still using both in parallel at this point. Partly for political and safety reasons we were obliged to use paper, and partly because she wasn't comfortable with trusting the system at this stage. So she tended to be writing stuff in the lab book‑‑in the paper lab book‑‑and then transferring it to the notebook.She's got a series of references here‑‑this again shows you you can put in any type of method data the whole way. The problem was, we didn't know‑‑so if we do an experiment‑‑we want to say we used a material to generate another material. We do something to it. We want to link those two things together. How do we know what was the material that went into an experiment?The easy way to do that, we thought, was to have this thing called a sample parent. This is a method data that's attached to each post. If I click on this, and go through to that particular post, we have a procedure here. This happens to be restriction digestion of a piece of DNA. You can see this is the lab book reference where she's done this thing. This is a reference‑‑happens to be on the same page for some reason‑‑but on the same page of the paper lab book was where she made the material that went in.I think you probably immediately see what the problem here is. As soon as you've got a reaction where you put in two things, then you're in trouble. We ended up‑‑you can see if you track down here. We had sample parent, sample parent 2, sample parent 3. This was just starting to get a little bit ridiculous.If I just show you‑‑oh, I'm not allowed to edit this one. We had this problem. We want to link products; materials being used through to the materials they came from, through the materials go into. I don't know. It may seem obvious to you, but it took us a long time to realize this, that if we want to link something to something else, then the easiest way to do that is to put a link in, as in a hypertext link. I certainly have come to realize that in this field that you often come to the situation, there's something that's blindingly obvious once you've thought of it.At this point, we realized that we had‑‑we'd been actually doing this entirely‑‑not in a wrong way, but in a way that wasn't going to help us. So what we did at that stage‑‑what Steven did‑‑was actually start it again, from scratch. We reorganized the system.If I now go into the lab book, which is using "at the moment", this is an experiment done‑‑is that today or yesterday? I've lost track of what the date is now. It's the second today, isn't it? Obviously she hasn't done anything yet today. But this is right up to date. Actually, it's probably it's that she's been in the lab in the morning, and she hasn't got round to putting it in. She tends to do things‑‑put things into the lab book afterwards.What we have now‑‑I'll just track down the right hand side again, show a few things. We've now divided these posts up, so one piece of method data‑‑actually what I should show you is‑‑I'll just show you what that method data looks like. Oh! Oh, I know what that is. I'm not allowed to edit her posts. Again, there are obvious reasons for that.I'll duck out of this one, and actually go into my lab book so I know I can edit things. If I edit this post‑‑I just want to show you what this method data thing looks like when you're dealing with it. We have a group that each post falls into. At the moment I'm using this thing called "post type." I'll show you why that's not a terribly good idea in a second.I can type anything into here. The category nine can be anything. Then, what the attribute is can be anything. You can add as many of these as you like. Let's back out of that. Oops.We have these sections now. We have materials, stuff we've brought in basically, notes, just anything that doesn't fit into any other category really, descriptions. Procedure, where we've done something. Product, something we've made. Software issues are software issues, unsurprisingly. I'll come back to the templates in a second.What I can do is, if I just go into the middle of a process‑‑back out of this. I'll go to‑‑this is just a category post. If I run down‑‑oh come on, go into that post. OK, so‑‑oh there's no data in it. I'm not actually operating on my own rules. I've actually put the gel in there, which is a bad thing to do. Nevertheless, this is a gel I ran sometime ago.Basically, what I am doing here is an analysis on a set of samples. This is a calibration standard that goes into that analysis and these are my products that I am doing an analysis on. So where do these things come from? Well, let's click on that. This takes me back to a product post. This is the post that refers to a material, a tube, of something.If I wanted to generate a label for this, I can do that because each post has a unique ID number. We automatically have a system of labeling each and everything we make. I can press print and it will print on a label printer in Southampton which is not going to be helpful to anybody.It will print out this label. It's got the date, time, a nice little code and the post number and that bar code refers to the code for the number. So I have actually got a quite powerful system here for identifying samples already built‑in.I can track back to where I made this. This is now the thing where I have made this product... where I have gone on to analysis that this is a PCR reaction. I can clink through to all the material that went into that. I can click backwards and forwards, the machine can do this as well ‑‑ track back through the entire history of the sample. What we have is a standard build out system that is quite powerful for tracking data and samples.I just want to show one more thing. This is a blog. The idea you can put anything in you like, you can type anything you want. The problem is ‑‑ as with most wikis and blogs ‑‑ we really like to organize things in tables.Tables are a nice way to represent stuff particularly when you are doing things in parallel. If I show you the codes for this post, all of that nonsense is what created that nice table. This is not something your average grad student is prepared to do ‑ figure out how to get this coding working.Another problem is, because you can type anything into the metadata sets, it is quite easy to make a target mistake because we are doing the linking manually. It is relatively easy to get the link wrong. This is why we actually needed to put in the ability to edit the posts actually because we are just making too many typos and that was a complete disaster.Is anyone here a microbiologist by any chance?[pause]
Man: You mind if I ask you a question?
Cameron: Yes.
Man: The last thing you clicked on was for something from a gel... a gel is somehow in the table.
Cameron: Yes.
Man: Is the gel [inaudible]?
Cameron: I should have. One of the reasons why I find this good is because actually it does force you to raise your standards. Not just the student's, it's also me. I actually keep one of the worst lab books I've ever seen.
Man: Another dimension to having to do the things with different computers... the gel is just the same as a spectrum that is [inaudible]
Cameron: If I go back to Jenny's lab book, I'll try to find you an example of a gel. The trouble is that she is now running through the system so fast, she doesn't actually run the gels that often.I can show you some pictures. There you go; there's a gel image.The result of the analysis is a picture. It's not the physical object. That is a JPEG, rather than, perhaps, a higher quality image, too. That's another issue.A lot of what we generate is images, but we're also doing analyses on the enzymes we're generating, so that the Excel files come out of the product analysis there, as well.The intention is that any data that we would record should be in there, in whatever its raw form is.
Man: Like you said, though, it's hard to find a grad student who has the enthusiasm to write the code for that table. This grad student, for probably very good reasons, didn't want to go to the trouble of making a better gel image, so that later on, you'd be [inaudible].
Cameron: The problem there is the gel, not the gel image, actually. And to be fair, for what she's done here, that's actually for this type of low melting gel purification. They don't actually get a lot better than that, to be fair.That's actually not terrible. Actually, the light's not terribly good, either, is it?It's better now.
Man: You can see it better now.
Cameron: Yes, sorry. As I said, this is a JPEG, which is a bad way to do it. The reason why the students prefer the JPEGs is because the system automatically displays them.The technical reason is that no one has written a plug‑in to display the TIFF. No one has imported the plug‑in to display the TIFF here, yet.
Man: I think the JPEG was a very good way of doing it.
Cameron: Where was I? We're getting to the right lab book.There's actually an interesting question whether we should have one lab book for the whole lab, or one lab book per person. That starts really interesting issues, as well.We can crosslink, but we can't do what I'm about to show you.The classic problem with recording data in any form, whether it's a LIMS system, a data base, or anything, is actually persuading people that it's worth putting any metadata in. Unless it's very, very easy, there's an issue with that.Additionally, we've got this problem with creating tables. We've got just the problem of doing the linking, and all these things that are just a little bit difficult. All we want is to make all of that easy, so that people do it automatically.We have an advantage in molecular biology in that a lot of the things we do are quite stereotyped. The procedures we use are very similar, each time we do them. There is quite a large set of procedures. Nonetheless, each time you do any one of them, they tend to be about the same thing.There is an obvious answer to that, which is that you have a template procedure which you work from, and then you just put in the material. You don't just want to have a template which you need to fill in, even. You can do slightly better than that.I showed you the gel. This is the template. For that gel post that I showed you in my lab book, where I hadn't put in the image, this is the template, or is very similar to the template, that made that post.I'll show you what these little codes do, in a little while, but basically, the templates are exactly the same as a normal post. They just have little place markers in them. Those place markers say what is supposed to go in that place.Up here, the system will look for anything that has been labeled as DNA. The percentage symbol is a wild card, so it's looking for any post for which the metadata DNA is not empty, because those are the types of things you want to run, or gel.The box, unsurprisingly, creates a little box that you can type into.Down here, we have the procedure so that you know what you are supposed to be doing. Then down here this actually will tell it what other method data to enter the post when I use the template.So, when you do something that is stereotyped, that is a common procedure, which is precisely the ones when you want to track the flow through things is it's all handled automatically. So if I then use that template...what it comes up, it just renders that in a slightly different way so that a title up here, I can change the title as appropriate.I can select anything that's in the blog that has the appropriate metadata. It comes up as nice drop down menus. So, let's say, we'll run our standard again. These are some products from an earlier demo, but I'll probably want about five micro liters of that, five micro liters of that, say. I can change these things at the bottom if I want to, but I shouldn't really need to. Pop that in. It then goes into an edit windows if you want to make any other changes to the thing you can. This post now is actually now the post‑it so if I just open it up again that's come up.Now, there is one problem we haven't dealt with here which is that I have pulled down a product that had been created previously. We're still creating those posts manually. Then we actually have to do some linking backwards and forwards to tie all the ends together. So, we still have an automation process that we need to solve.My feeling is that once we've got that process of generating these product posts sorted out, we actually have a very powerful system here, but semi‑automated collection of metadata. We have got a system relatively easy to use. People really don't need to get down to the level of putting the formatting in to posts.We're making some sort of significant progress toward what our goals were. So, is that the right one? Nope, that's not. This is kind of where we are at the moment. We have this one post per item approach. I think this is actually our real breakthrough. Doing that really creates an information framework where a lot can happen.Templates are really very important, and I'll come back to this issue. We want to develop this web service interface that other things can link into it. So, in terms of what we set out to do, we've actually got a pretty good system of storing and recording the data.I can stand here; I can go back into the system; and I can track bits of data. I can pull that data out, and the only person who is really falling down on the job of putting data in the first place appears to be me. So, I've only got myself to blame for that. Actually, the students are quite good at this, primarily because they are aware that I might be watching.We have one post per sample. Every sample, every thing has a unique ID, so we've got a real chance to track where things, what things are and also who has been using them. So, again, this issue of someone using up the last of the buffer is covered.We can monitor researchers' progress, as I said. I'll just flip back here. If I pop over to our accessorator and Peter Murray‑Rust has been very busy again; [laughs] that surprise is there, nonetheless.So, these are a set of posts that have come up. These are the new ones that Jenny has put in since I last looked, which is quite nice. She's done a bunch of things, so I can follow this wherever I am; pull this down and see what's going on. It's really quite a robust system for tracking what's happening, and I'll show you how I aggregate that whole set of things in a little while.So what we've not done...we think this system is broadly speaking in a theoretical sense, machine rateable. We know we've got a fair bit of work to do on what the best way to organize the metadata into really make it work. But, we've not done any work on really showing whether that's true yet.That's the direction we'd like to go, and it's really beyond the scope of the grant funding we've currently got to do this. So, it's kind of the next stage of development to really try and do that, seriously. But, we've made some progress.I've put open sides to the title. I've actually not talked at all about open sides. So, what has this got to do with it? I have to admit when I started this project I wasn't really thinking about the process of making this readily available.I live in Bath which is the left hand drawing pin on that map. I also work at the Rutherford Appleton Laboratory which is the one at the top right and at the Southampton Chemistry Department. That is a map of the entirety of the UK. That's a triangle that is about 80 miles a side. So, I do a bit of commuting.But, putting that aside, there's this real serious issue of being able to find out what's going on. Now, I showed you that I can pull that through on an RSS data, but there's a problem with getting access into the system. The people at the Rutherford Lab run a really quite irritating firewall, and so essentially we couldn't find any way of me getting an authenticated log‑in into the lab book at Southampton from Rutherford.I just got sick of this. I thought, "Right, let's just make it wide open." That was easy. I had access to it. There's the first real benefit of actually making things open. Not so much that anyone else can get at it, it's that you can get at it.[laughter]People tend to skip over that as a benefit, but it's actually really quite an important one. At about the same time I was beginning to become aware of what other people were doing. I started looking around once we made it, and I saw a particularly good video by a guy called Deepak, I think. He actually had been doing this amazing five minute presentation at a conference in Seattle which really inspired me; as what Jean‑Claude was doing here at Drexel.So, the background information and the community that was really building around making these things available and the potential for doing that. And that got us really excited about what we could do. That's where we really bought into this, this open notebook science approach. There's a lot of benefits here, a lot of potential benefits. There's also a lot of confusion.Open science means more things to more people probably than open access does. We have adopted this terminology "open notebook science" which was created by Jean‑Claude to really try and describe the process where really you do your absolute utmost to try and make everything available ideally as it happens. I use the term "as fast as practicable".You can't make things instantly available. In reality, you can never make absolutely everything available. There's always something that doesn't get recorded. There's always some information that's just sort of between the neurons of the people involved, but you do your best to take that as far as you possibly can. That's really the key.So, there are lots of potential issues with making the material completely open. The thing that everyone starts to disassociate is: Isn't someone going to steal your results? Answer, probably not, realistically. Yes, people feel that this has happened to them, but I think in most cases and speaking as someone who has been scooped by papers now twice in the last four months. Most of the time even when people have become aware of results because they're already doing it, they move to publish faster.Now that's a problem, obviously, if you're beaten to publication. In many cases, you possibly would have been beaten to publication anyway. But if someone was really coming in and looking at your results and then going away to publish faster, you've got a record of them being there.What's more, you've already disclosed and reported it. You have a rigid date stamp saying that you've done this. It's not peer reviewed and that's an important distinction to make, but it's out there and you have reported on it. We've actually got a case of this now in my group, where we have disclosed a particular technique for fluorescent labeling of protein about three weeks before the paper that scooped us came out. It's going to be interesting to see how that flows through when we try and publish it.There's a real potential to be embarrassed, to put your foot in it and look really stupid. The flipside of that is if you want to get help from people, you've got to ask. I think this actually is what's scaring people a lot, particularly the grad students that you're asking to do this. Someone's going to see what you're doing. We're all stupid, really. There's always someone smarter and we all make mistakes. So that's a real issue.It does require a bit more effort than putting together a paper notebook. I suspect the reason it requires a bit more effort is because most of us don't keep terribly good paper notebooks. Again, this creates a bit of an emphasis to push you into doing better, and I think that's a really important aspect of it.There are potential legal issues. In fact, if someone were to take a particularly rigid interpretation of my employment contract at the University of Southampton, by doing this I could be in violation of it. I'm supposed to report anything through our technology transfer office, just so they can find out whether it's potentially commercially‑viable.That's not really a major issue in most cases because in practice, you don't send in every paper to the technology transfer office, for most people in most places. I was talking to someone in Oak Ridge, yesterday, and they actually have to do that. Every paper, every poster and every note has to be approved by the technology transfer office. It's a nightmare.One area where I am a little bit more worried is safety information. Now in the UK safety information is very strongly tied to the lab book. We weren't putting this in, and arguably, this was information on how the experiment was done, so we should have been putting it in. I had a post‑doc come in the door to do a few weeks work on a project, and she said, "It's a lab book. It has to have the safety information", so it all went up.And I saw this going up 15‑30 minutes after it happened; I was offsite that day. I thought what if someone looks at this, uses it and manages to injure themselves? This safety information is totally inappropriate for anyone working here. You have a different regulatory framework, different legal framework and different working approaches. Yet the other side of that is it's very difficult to get good safety information. MSDSs are usually useless because they tell you that salt is a carcinogen and that you should wear a full respirator to do anything with it. This is actually a serious problem.And there are ethical and political issues. If you're working on animals, some particular stem cells and these kinds of things, you possibly don't want those to be made public. The question then is if you don't want it to be made public should you be doing the work. There are lots of issues here that are not clear. But there are lots of benefits as well, and I think that's where we're going to go.I wanted to talk briefly about the differences between the different groups doing open notebook science. Obviously there is Jean Claude's group here using a wiki‑based system which is shown up there on the left.The other person who is really doing this in a really notebook‑centric manner is [inaudible] student called Jeremiah Fife at the University of Boston and he uses a PDF document that he creates each day. The difference between wikis and blogs, I think, is not per say a central issue. It is just a different way of looking at a day device of posts. People think differently about how they interact with wikis and blogs, but I think what is more interesting is the difference in how Jean Claude's group and my group lay things out.So, up here we have ‑‑ what is that? ‑‑ experiment, that is 135. So I think I've got experiment 918 here. This is an experiment from UsefulChem Wiki. This is the final version. So there are a couple of interesting things that I take from this. This is a version where it is now described in sort of a complete, finalized approach. This is the experiment after all the analyses have been done, after everything has been explained. We can go back and look at the history of this, being a wiki, obviously. There is a history going back over several months, I think this actually was done over. When there are various things going on, the experiment going on in the first couple of posts, then some comments between Jean Claude and a colleague on what these experiments mean to how the interpretation should go.Now, if I pop across here ‑‑ I've actually tried to replicate some of this in our system in a way that I think I would go about it. Now, some obvious differences, one page on UsefulChem ‑‑ There is the first set of posts, there are the second set of posts, there is the third page of posts. Somewhere down here we actually get to the description of where something happens. Now, you see a lot of these are written in math so the experiment was based on an end‑amount time costs, taking a series of analyses over time and I wanted to separate those out because each piece of data ‑‑ so you can upload the end amount data for each of those things. Now I actually have put those in there in fact.To associate a particular product with a particular piece of data, so a computer can tell which one was necessary, I felt, creates a separate post for each of those end‑amount samples. So arguably I've made it easier for a machine to pass this, but I've also made it fairly horrible to read. Now we can take all those product posts out and just look at the procedures. That's one option, but I can go back through these, go back to the top policy ‑‑ again just because of the way the different systems work, I've put a slightly different picture at the bottom.I think the really essential difference between the way Jean Claude's group worked and the way my group is working, really in fact one student is working, is that we sort of try and log the whole process in the visible final form. It's more like a traditional lab book in the sense that the record of what's happened is immediately available.In Jean Claude's group's case, the final product is actually a finalized description and to go back through the process, it is not immediately visible, you have to go back to the history. I am slightly uncomfortable with that, but that is just because I think of a lab book as a log of what has happened and I think it is a question of what these things are being used for. So the object of UsefulChem Wiki is to provide information so you can come to that and realize how they should do the experiment.That is less true of our system because they have to track back through a series of things to figure out how they ought to do it, but they can see the process that has happened. I think what we are finding out is actually that the notion of the notebook ‑‑ we have a lot of biases and obsessions about notebooks, and properly said because record keeping is important, but a lot of those things don't matter when you are using an electronic system. We've got to figure out which ones do matter and which ones don't ‑ different things will matter to different people. OK, I'll come back to the right one at some point.Interestingly, again, this is a more traditional written record of a notebook. There's less obsession with linking backwards and forwards and keeping the connection between things. A lot of people like this because they feel comfortable with it; it looks like a lab book and feels like a lab book, if you print it out.I think the differences between Jean‑Claude's approach and our approach largely comes from where we started. I started from the perspective of wanting to manage the information, and Jean‑Claude started from the perspective of wanting to make that information available. That's what is actually driving a lot of the differences, rather than the difference in the science we're doing.For most laboratory research, there are electronic lab notebook systems out there, and there are Win systems out there. But as soon as you actually do the research, those systems are going to break. With any sort of structure that you try to impose on the data in advance of the experiment, you're almost instantly going to break.It's very important to realize that different viewers of the system have different needs. The supervisor has different needs and the student has different needs to the visitor, and we're trying to work through ways of making those different views available to people.Most people start this with a simple journal approach. They have some sort of online presence and keep a journal, and that's actually quite good. It has a lot of advantages; you can do text searching and all these kinds of things. It also has 'ease advantages'.There's an issue here of getting people to do things where you've got to get them over a barrier, and if there are disadvantages, then they're not always going to see the advantages. I'm not sure that keeping a simple journal provides enough advantages to keep people involved. I might be wrong about that but we'll have to see how it evolves.Flexible meta‑data is critical. If you're going to keep meta‑data, you need good ways of getting in there, and you desperately need to be able to play with it and change it at will, if it needs to be changed. I think this method of templating things is a very powerful way of bridging the gap between structured systems, where you can impose some structure in advance, versus systems where you really want to be able to type some random stuff that says "I did this, it made this or it turned green", things that don't necessarily fit into any straightforward structure.So where are we going with this? I think I've got my slides in the wrong order. We want to take our system and do a couple of things in terms of usability; but the next big step for us is to try and make the system a web service. There are packages out there that don't work terribly well at the moment, but they let people manage workflows.So you can grab some stuff from here, put it over there and combine it with something, which is called all sorts of different things. You've got to make the system available to a computer to do something with that. For instance, this is our workflow engine at the top, which is being described as 'MySpace for Scientists', but it's not quite there yet. It's a thing that holds workflows, lets people share workflows and will ultimately allow people to execute them as well.I've got to show you one other thing that we're doing, which is what we do when there is a data structure. We're actually using an online, freely available web‑based data system. It's a lovely graphical system called Dabble DB, and it's really worth looking at if you're interested in these things. We're actually making all of our lab stocks available through a proper database. You can see these things are publicly viewable on a public page, and they're accessible by Jason, RSS and various other approaches.So we can set off something that might go to our lab book and then comes back and reports something, maybe a data file or a sequence file. That workflow can then go off to the database that could be stored and maintained by a facility of some sort so that we can go on to do some experiments. Then you might want to combine those sets of data and send them off to query another database. I'm showing germ bank here, but it could be any sort of data analysis, which pumps it back into your workflow engine. And because all of this has to be put back into the lab book, you've got a record of how this thing is run.The problem with these workflow engines is that they're written by computer scientists, and that's a problem in and of itself. They don't have the concept of letting you know how this was run, when it was run and what exact parameters you used to run it ‑ they don't pass that concept at all. So we need to keep a record of instantiations and particular runs of data analysis, which is critical from our perspective.So where are we? I think there are small groups in terms of people who are doing Open Notebook Science, as Jean‑Claude originally defined it. There are really three groups doing it. There are a variety of other projects that use a variety of other names and approaches that have some sort of similarities, but it's a relatively small group of people.I think we're seeing benefits to the community, but in terms of the science community, we're seeing less benefits in terms of driving the science, at the moment. But as the community size grows and the activity grows between those groups, I think we're going to start see some real advantages.I think a lot of the tools we have at the moment don't really provide clear wins and real advantages that are really going to drive adoption by a wide range of people. I think we're still at a relatively early stage. We're a bit hesitant to suggest people start using our system, unless they really have a specific need, which it can serve, compared to trying to persuade them to make their results more open.If we're going to communicate in this way, we need to think about how we provide tools, and in a wider sense, how people are going to find it. In the chemistry world, a series of tags that describe molecules can be searched. You can pick those things up in Google, but that's less true for what we're doing. You might think that with biology and biochemistry it would be very clear; you just link back to the database.The problem is that the database doesn't actually refer to what I'm working with and it doesn't describe what I'm doing. We need to think a little bit about how we're going to use some of the tools that are already out there, and perhaps, do a little tagging. The whole Web 2.0 thing is really based on picking something, going with it and seeing whether other people adopt it.I think we need to figure out how to do this in an integrated way. But I think overall, Open Notebook Science is a great term in terms of its ability to get people excited, though I don't think we understand what it means, in terms of the terminology. It really is quite a different approach to put your stuff directly out in the full glare of the two or three people who might look at it.It is a very different way of thinking. There are a lot of subtleties that I think ‑‑ or we're certainly still trying to figure out what they really ‑‑ where they're going. I think there's also a desperate need here to deal with the problem that you cannot simply, in this day and age, evaluate people on the basis of how many papers they've got in a particular journal.It's not the way we're working anymore. Traditional publishing is broken anyway. e also need a way to try and figure out what people's contribution is in a much wider sense.So, I need to acknowledge a few people, a few very important people. I don't do any of the technical development of the work. I just say, "I'd like this." Andrew Milstead is a PhD student in Jeremy Fray's group that goes away and does it sometimes, when he has enough time. The development of all of this has essentially been Andrew's work. He's only actually months into his PhD so it's really quite impressive.The people who've used the system and helped to evolve it. My PhD students Jennifer Hale, Wendy Smith is a post doc who came in for a few weeks on this project. Justin Shay is another PhD who's been involved in recording some stuff along the way.We have some funding from not quite our equivalent of the NIH, but broadly speaking that kind of thing to develop this specific system. And also Jeremy Fray is a much bigger eScience. He's got a platform grant which provides a five year reasonable long term funding to develop these things in general.If you want to look at some of these things, then go to the web sites and I think I've probably gone over time, but thank you for your attention.[applause]
Jean‑Claude: Questions?
Man: I thought when you put up a few slides back. I can't remember the title, but it was like the five dimensions. You had the one before that where you show, for example, a flow diagram and some vents coming out of the right hand side. Vents on the left hand side, and you jumped around.I suppose in a way that's what I was looking for. The database is... The management systems from the [inaudible] really go without saying. They kind of... Literally a window. But I'm always trying to do like this, to open the window to see what's there that I could grab onto. I mean, that workflow...Not the workflow per se but the kind of logic diagram that the example finds is really a great thing because what if you could do... If you could click on a part of that, and continue on so you could have the gel runs, the compounds that went in and out of the box. The air mask connected behind those in some way.Even if you anticipate a net [inaudible] visible, it's best for your potential.
Cameron: That certainly where we're trying to get to with the idea of making it available as a web service, and it links also to this concept that different people want to view things in different ways. Let me show you one or two examples of that. Why don't we talk what we forgot to do on the way through it?This is a very simple example. Basically, there are five blogs operating in my group, and I post to those as well. I don't want to look at those in five different places. I don't want to look at the stuff that I've already seen. So, there's some really quite cool tools out there.This is Yahoo Pipes for anyone who hasn't seen it. Basically, this allows you... It's essentially made to manipulate RSS feeds. It's essentially a way for doing graphical programming for mashups. This is simple enough that I can use it, though I have been known to swear at the screen when I can't figure out how to make something work.What this is doing and this was wired up in five minutes or less, is it just takes all of the feeds from the web that I'm interested in and it aggregates them into one and filters out anything I've written.There's a relatively simple example, but nonetheless it shows you the kind of thing we're working towards ‑ If I show you just one other thing, which I think you might find ‑ These are examples. They're not quite what you're looking for, but they are quite nice examples.This wasn't working this morning. I hope it's been fixed.So, there's more than one way to look at a lab book. There's certainly more than one way to look at an electronic lab book. And ‑It was working this morning. Ah, here we go.So, one way you might want to look at it is: what's happened over the last, sort of, period of time. This is being generated by a ‑ This is a viewing product which is freely available, again, developed by a group at MIT. And what this does is it takes XML data with some time information and generates a timeline. So this is that timeline.Posts that categorize colored by the category, by the section. The red ones are products; green ones are procedures. Some things are student key always generates the products first and then adds the procedures. It's interesting. One of those little issues that comes up and how you think about how these things work.But we can either track back on a large scale at the bottom here ‑ the screen size isn't brilliant here, I'm afraid ‑ either track back on a large scale, or get more into the data. We are tracking slowly here.What we'd love to be able to do is impose on this the links. Or to have the network impose, to understand how things are linked in together. No one seems to have quite generated the visualization tools that will do that for us yet. I'm going to Boston on Sunday talking to the people there who develop this and have done some similar stuff, and hopefully we'll see what we can put together there.Absolutely, we need ways of getting in there and letting people manipulate the data in what ever way they want, because that's where the real power is going to come out of this. We're working on it.
Man 2: I have a question about your data. Is there data available to the general analysis or some other analysis?
Cameron: It's available to them if they wanted to do something with it. The principle we generally work on here ‑
Man 2: Because if scientists bring their instruments, and they are not linking them to your website, they are not using the information for their research.
Cameron: So there are two approaches to this. Jean Claude has looked at how people come to him, and what sort of Google searches bring people there. We haven't done that. And partly, we haven't the right tracking thing set up.
Man 2: Are you indexed on Google?
Cameron: We are indexed.
Man 2: Not Google Scholar?
Cameron: Not Google Scholar. [laughs] This is a mini discussion. This is part of this whole cultural shift. Google Scholar is about peer review literature.I just did a search on sorties, then. We're not at the top of the list ‑ hold on a second, I've got to find it. If I'd done a search on sorties cloning, which is the title of the blog, it would have been right at the top. There we are. So, the second page.If I was working on a really hot cancer gene, we'd be down on the bottom somewhere, obviously. We're not heavily linked to from outside. This is a moderately obscure system, so we're quite close to the top.It's this issue with tagging, though. How do we expose the right sort of data, so that people doing searches do find us? And I don't have the answer to that.If you put in an entry key or a smiles code, or you're exposing CML, then there's clear ways of indexing this molecule. We should put that data in where we are using specific chemicals. But how you do that for a protein or a small DNA sequence, that's the hard thing I haven't got the answer to that yet.
Woman 1: If you want to go to total electronic lab notebooks writing in everything on the projects, how do you handle it when the students are ruining the technique, when they are not doing anything new.It's not a new experiment yet, but it is what they are doing, and they need to show how long it takes. You need to go over it with them and see what they might be doing wrong if they can't duplicate a well known experiment or whatever.
Cameron: It should be in the lab book. It should go in. There's no question on that as well as experiments that don't work.
Woman 1: Do you shove that up inside in your own way?
Cameron: No, I am sorry. Perhaps, the other way to answer the question of question is, "Do we promote the exciting stuff up to a higher level?" So, we have some ideas about how to do that. One thing that it has become very clear is that you don't learn a lot by looking at most people's lab books. You need to either find the specific thing you are looking for, or you need some sort of summary of what's going on.What I've been doing personally is...I have another blog, which is a completely separate conventional blog, where I am trying to tag some of the interesting stuff that comes up. I hadn't done a great deal of that either, I have to say. Jean‑Claude points up stuff on his blog as opposed to the old useful Wikiware where interesting stuff has come up or where he's introducing an experiment that is going to start up.So, there is a series of different levels, and again it's part of this view. How do we go from this, which is basically the equivalent to scribbles in a paper notebook to something which is not a paper, perhaps, but may be a report.So, it can automatically generate a report that covers the things you are interested in and how we go about doing that is a very interesting question.The first step we want to take, and again we probably don't really have the results to do it within the current grant, is that we want to somehow create a button, where we can say...what's written in this paper is going to published, and I want to generate a supplementary information, perhaps readable, all the raw data in it and whack it out as a PDF.
Woman 1: I think that it's very appealing not to push it off to the side. How do you highlight the stuff in advance?
Cameron: Yeah. Well. Again its...I think this is on the first page here. The student has been struggling for a very long time with experiments. She's been trying to do a moderately complicated experiment, and I think it's down here. [pause] I can't find it...She's actually just got it to work at the beginning of this week. She suddenly multiplied by 10 the number of transform that she had, the number of columns she hasn't applied. That's really important to the experiment. And she says that, but I wouldn't have noticed it unless I had actually read it through in detail.So, we could just have a piece of metadata that says: Worked? Yes. Or this is a good result. Or this is something that you want to see. This person wants to see. Yeah, we don't know how to do it yet.
Man 1: Could you put some kind of tag on it?
Cameron: Absolutely, yeah.
Man 1: Whereas you could assign an experiment a certain number value. I think a wonderful example is if you've got something you are trying to do with students. You try at least 37 times to do this, and three years from now what you want to be able to do is have a new student group go back to attempt it and not bother...
Cameron: And the reason why it worked is because she used a different brand of [inaudible]. [laughs]
Woman 1: Is that true?
Cameron: No. No. It's absolutely true. She's been struggling because ‑‑ if you know anything about getting DNA into cells, in these bacterial cells, we do what's called a heat shock. So, you basically heat the cells for a very specified amount of time at a specified temperature.The width of the plastic and the shape of the plastic tube make a huge difference. I simply hadn't realized they we're using different tubes.Last week, before I went away, I said we need to get some of these tubes and test it out. I said, "That's not going to make any difference." So, these things happen. I could have told her that had I known they weren't doing it, but it's a classic thing. She wasn't writing down the brand of tube she was using ‑‑ why would you ‑‑ unless you realized it was important.
Man 2: It really does highlight the fact that you have to have different vehicles for different audiences. Someone will not read this lab notebook ‑ you don't read our lab notebook page after page. They'll do a Google search. They're looking for the boiling point of something and we happen to know [inaudible] follow that.You need to have another vehicle. I use a blog to summarize important things. Even people who are not in my field can actually get some information and then those link to specific experiments. So that does require effort, I mean, you know you have to decide.
Cameron: Again, it's this issue that my students are terrible at writing, at noting what's interesting, what's worked, what the context is. They're really actually quite bad at that. I try to encourage them to do it. It's one of these things that require extra effort. It's because we've traditionally not kept very good lab books because no one looks at them.
Man 2: Compared to what you've first started talking about getting instrument data; you know inspect all the instruments. It seems to me that one of the big problems is the format of how we save that data. There certainly are some older formats like the JCAM. There's all of this before, and there has been some attempts at coming up with 'X' and all these formats there are sometimes probably very humungous when you take a spectrum and put it into that format. Do you have any question about where those kinds of things are going? It seems to me like that's a big sticking point.
Cameron: We don't have a problem with storage space. That's not come up as a problem yet. This system will upload a file ‑ any file. It will start to chock if you try to put in something that's five gigabytes, but it'll cope with 20 megabyte GIFs, for instance. I've done that. So it will take anything.What you can then do with that is another question. But you can, again, for me this is partly the philosopher here of plug‑ins to start with someone could write a plug‑in to display or do something with it. One would particularly imagine this with DNA sequences. You automatically have a little thing that pops up and gives you a semi‑editable graphic picture of a plasmid sequence or something like that.Part of the idea of making this accessible to the web that we don't worry about the data format. Someone who is interested in using it has something that comes and grabs the data. Maybe they have to send it off to a translator to translate it into the appropriate format for their thing.A lot of these things are available as web services now. It's relatively easy if you've got a package sitting on your computer to make it either look like a web service or make it available as a web service, even if it is just to you. There are ways and means of pulling these things through. Having spent three days talking about file formats I don't have an answer. It seems to me XNL's a good thing ‑ at least it's partially self‑describing.You've got some internal information in there and it should be relatively easy for people to put together starshades and schema that can tell you, "I want to do this with it". That does seem to me to be the way forward, within reason. A lot of the time what you really want is a couple of columns of ASCII, that's the easiest part for making it ‑ figuring out where the columns are.Jean‑Claude: Well thank you very much, I appreciate it.

Tim McGee

2007-03-13T09:39:00.000-04:00

link to the screencast

Tim McGee: The title of my presentation would lead you to believe that educators are not yet prepared for multi-literacy, and that it might be a big enough job that you can't just do it in one swipe.

I myself am an intellectual bureaucrat right now; I direct a couple of graduate programs, so I'm not actually working as a teacher. But I spent about 20 years of my life defining myself as a "techno-retirition", so I've specifically engaged in trying to use technologies to try and improve the communication skills of what were usually first year college students.

What I want to do is look at a group of educators who have, up until, now been charged with the communication skills of students. The group I'm going to look at is English secondary education teachers. I'm doing that for a couple of reasons, including this is the group that is last responsible for them before they go into college or go into the workplace, and also because English secondary education teachers, their curriculum represents the response of the university to what is the perceived need for communication skills in colleges or in the workplace.

This is the abstract that I've produced to present here. Here's another version of it, slightly larger. What I want to do is just focus on a couple of parts of it, including the definition of literacy that I hope will be relatively non-controversial; that this is what literacy used to be.

The next thing is the idea that with advent of digital computers, they create multi-literacy demands. Now this one could potentially be a little more controversial, because it might look like I somehow believe in technological determinism and it turns out that I don't.

What I want to do is talk about the way technologies demand illiteracies; they don't determine them. Many people, when they talk about technology, they think, "OK, it's not just the computers, it was also the book." And some people I think don't go back far enough and realize it was also the alphabet.

The alphabet is a technology, and it's a technology that is radically different from the idiographic characters of Chinese language. Each has costs, each has benefits, each has affordances, which is one of the words that Gunther Crest uses; he's a member of the New London Group. What happens is the cost benefits and affordances of each of these technologies has implications in terms of the illiteracies that they demand.

My parents, who were excellent readers, writers, they had excellent penmanship, they were educated through college, would be illiterate in today's world because of the fact they have no understanding whatsoever about computer technologies. And part of my claim is that the digitally literate students of today, who are digitally literate in mono-model communication are going to become illiterate in the next generation if they do not become literate in multimedia illiteracies.

Later in my abstract it says, "Teachers at every level find themselves ill-prepared to teach even the decoding of multimedia and multi-model text, much less their encoding or production." And I carefully chose two words there that were intended to not raise the hackles of English faculty, who when I talk about consumption and production get all out of shape. So decoding and encoding are a couple of other terms for those. But the situation exists where people who are charged with teaching people to be literate, reading and writing, are not as well prepared to have them read and write multimedia/multi-model text as they had been for print literacy.

So, the way I'm going to go about it is to take into consideration state standards, teacher education programs and current theories of multi-literacy and multi-model discourse. This presentation suggests short and long term action plans.

Wait a minute? Where's the problem? Where's the gap? If we were using what's called the ISD model, the Instructional Systems Design Model, it says, first you find an identifiable or a measurable gap. What's the performance gap?

Well it turns out that approach isn't going to work here. Because in order to have that gap we would have to say, "Here is how the students are performing on some test, and their performance on their test is not good enough. Therefore we need to remediate the teachers and give the teachers multi-model instruction to help these students perform." But the students aren't being tested on that.

So we do not have at our disposal one of the usual methods for determining, "We have a problem, and we have to fix it." So in effect what we have here is a problem with the problem. One of the questions is, is it really a problem, or am I just another snake oil salesman who has come along with a patented solution to a problem of my invention, because I have something I want to sell you?

One of the issues has to do with standards. My question is, "Do standards really matter?" This is a graphic that came from "Improving the Quality of Literacy Education in New Jersey's Middle Grades: Report of the New Jersey Task Force on Middle Grade Literacy Education"; there's the URL where I got it from. The claim here is that state standards do matter and they matter in a couple of ways. They don't matter just in terms of "We're going to hold the students to these standards", but standards determine what is the curriculum that the college students who are going to learn to teach, then gets informed by.

So in effect, standards if you look at the second one, "Clear expectation for students and schools; motivation to work hard", the next one over "Professional development improved teaching; higher levels of learning". So the notion that what your state standards are, what they say and do, impact the teacher education curriculum, impacts what happens in the classroom, and then eventually you get the performance in the classroom that is or is not meeting those standards.

One of the questions is why did I choose New Jersey rather than Pennsylvania. We're here in Pennsylvania, I work in Pennsylvania, I happen to live in New Jersey. I chose New Jersey for the reason, even though I'm a proud native Pennsylvanian; I've spent some time comparing the language arts for Pennsylvania versus New Jersey. New Jersey is much more ready for the 21st Century than Pennsylvania if you take the state standards as a representation of what we're asking people to do in the classroom.

So there's Pennsylvania, there's New Jersey. One of the differences is Pennsylvania standards cover reading, writing, speaking and listening. The New Jersey standards: reading, writing, speaking, listening and viewing.

The inclusion of viewing in the language arts standards is in my estimation, huge. If all they did was just add the word, that's not much. But if you look at what the standards say, there will be standards in there. So viewing now doesn't just belong in the art curriculum; it's in the language arts curriculum.

Here is the cover for the academic standards for reading, writing, speaking and listening, and I would be hard pressed to describe an image that more clearly recommended that this is from a state Department of Education.

Here is the cover for the New Jersey Standards. Now, to me that's different, and then the question is, what does it signify? What it signifies, and the fact that images are open to much broader interpretation, is just one of the knotty problems that arise when we talk about what it is that the language arts teachers are doing in their classrooms. But if you go, as I have gone in detail, you will find that just as there is a difference in the covers, there's a difference in the standards. Through every grade you're going to have much more specific mention that the language arts teachers should be engaging New Jersey students in multimedia and multi-model literacy.

One of the recent standards matters is, if you look in the highlighted red portion, "Those who teach and administrate or teacher maintaining programs need to familiarize themselves with the standards for language arts literacy in this framework, which provides examples of excellent teaching and learning. Faculty should be sure that their pre-service programs promote both content and methodology that are consonant with the new standards."

Now that's all well and good; New Jersey may be doing better than Pennsylvania. There's another thing going on which has to do with standardized testing. New Jersey just sort of revised its standards. Why did it revise its standards? Why was the language arts core curriculum standards changed? The driving force was required testing in language arts each year in grades three through eight by 2005-2006. Are those standardized tests asking them to engage in the production of multimedia documents? Absolutely not!

So it's like, we have one step forward we have two steps back. Even though the standards were thinking toward the future, the imposition of "No Child Left Behind" upon it means that what is actually happening in the classroom is again preparing people to take the tests that aren't testing multimedia literacy. So it's not like everything in New Jersey is just wonderful.

This is an image of the web page from the College of New Jersey. So just like I chose New Jersey rather than Pennsylvania -- because I think Pennsylvania would actually be allowing me to get in a real strong-man argument, New Jersey is ahead of Pennsylvania I chose the College of New Jersey because it is a particularly highly regarded public college in New Jersey.

I know from having taught there for a while and the fact that my wife works as a middle school teacher in New Jersey, the graduates of the College of New Jersey are especially valued; these people are considered the gold standard in the state of New Jersey. So you graduate from English Secondary Education College of New Jersey and go on the job market and you get jobs like that.

This is the text of what it says the English Secondary Education students will take, in addition to their English requirement. Their English requirement, like many, is a literature requirement. You have lots and lots of literature courses. Yes, there's one course in structured history of the English language, etc., but here are their requirements for English Secondary Education. Nowhere in there is anything that specifically says multimedia/multi-model discourse. There is one course in there that's called "EED400: Teaching Writing". That's a course I taught while I was at the College of New Jersey. That was the one opportunity where you could get into the curriculum something that was other than writing words only and only in rows, and even there, there was only a tiny space for it.

There's this question of, what is multimedia literacy? What is media literacy? I took this one from a conference that's up at Yukon every year; it's coming up soon and is called the "Media Literacy Conference". There are a lot of definitions around, and one of the things I find is, just as traditional literacy often privileged reading over writing, the definitions of visual literacy and media literacy often privilege that over that. So the first one, which is a really nice one from PBS and is a wonderful collection for teachers of things to use in their classroom, it's really to teach your kids how to read images.

The one in the middle I like a lot better because it says, "The ability to transform thought and information into images, including thinking and communication. Visual communication takes place when people are able to construct meaning from the visual image." So that is much better, because it's not just reading, it's reading and writing. Interestingly that comes from the National Standards Essay up there, it's for South Africa. So South Africa I think is ahead of us when it comes to "let's have this literacy be a two way street."

The one from the New Media Literacy actually is nice because it says, "To not only become more careful and critical consumers of media messages, but to also become creative producers of media to more effectively communicate their thinking, ideas and priority.

Laura Blankenship

2007-03-13T09:37:00.000-04:00

Link to screencast

Laura Blankenship: I'm going to talk a little bit today about my -- I don't know if you want to call it an experiment an experiment that turned into a PhD thesis, about using a class blog in our freshman seminar classes that we teach in Bryn Mawr. A side story, if you want to hear it, is that I actually co-taught this class with my husband, and we're still married. So, it worked out all right.

Actually, to test my own multi-literacy, this is a lot of numbers. So, it's numeric literacy for me. I'm an English person by training, so I was challenged to come up with a numeric way of quantifying what happened in the classroom. So, that's what you're going to see most of today, if I can get the slides to cooperate. Here we go.

The goal in the class when we started out -- the topic of the class was blogging -- so that was sort of obvious, that we wanted them to understand blogging. I put that last, though. Mostly, we wanted to create a collaborative learning environment. We also follow what we call an emergent pedagogy, where we talk about student-centered learning. We let them guide the class a whole lot.

We didn't have a syllabus to start off with. We had the first day planned, and that was it. And then after that, we just kind of went with whatever happened in class and then we determined what was going to happen in the next class. So, we kind of just followed whatever they needed to know. Whatever they wanted to do, we did, within certain guidelines.

We also wanted them to become more aware of audience. That's a big issue in writing pedagogy. Most students have been trained to write for tests and to write for their teachers. And then, once they graduate from college, they're supposed to be able to write for real audiences in some way, even if it's in a business environment. And they have no idea how to do that most of the time.

And then we wanted to focus on writing as a conversation. That's blogging. We wanted them to gain an appreciation of all the different perspectives that are out there. Learn how to incorporate those and then deal with them, because they're going to be bombarded by them at some point.

So, the basic set-up of the class was it's a freshman seminar, so it's all freshmen. It's Bryn Mawr College, so it's also all women, which was really nice. There were two sections. I taught one section and my husband taught the other section. We had 30 students total, and they all blogged in the same place. We didn't create separate blogs for each section, because we were all reading the same material. We thought 30 students would be a nice collection, so that if we didn't get an audience from the outside, that at least would be enough to create some sort of collaboration.

We had no set assignments or topics in terms of what they could write about. We had no set requirements for how they contributed to the blog. We let that evolve out of the class.The only real requirement we had was that they had to derive their papers from their blog posts. We said, "You can write about whatever you want, but when it comes to developing your papers, it has to come from something you've written on the blog." And then they created a final portfolio out of all of those formal papers.

That created a sense of revision in the class. They wrote a blog post, they had to revise it into something a little bit more formal, and then they had to revise it again in a portfolio, although many of them revised much more than that because they just wanted to. Bryn Mawr students tend to be over-achievers, so revision became a big issue for some of them. They wrote five or six different versions.

Here's just some numbers from the blog. We wrote about 500 blog posts all together. And they wrote about 1,250 comments. That does not include comments they received from people not in the class. It's about 265,000 total words, about 700 pages. So, we wrote a giant novel, basically. About 9,000 words per student; that's about 23 pages. And that was just on the blog; that doesn't include their formal papers, their portfolios, their revisions, anything we might have done in class.

By October -- we did a really detailed analysis of what kind of traffic we were getting in October -- we got about 250-300 visits a day, and half of them were coming from outside of Bryn Mawr College.

We advertised our blog very heavily on campus. We put little table tents in the campus center, and the students all came up with the slogans that they put on all the table tents and on posters around campus. We let them to do all the advertising. A lot of them put the URL in their IM; you know, the little away messages and things like that. So, they really got into that. Here are the real numbers.

After all the blogging was over, I started looking at trying to figure out, OK, what do I want to find out what happened, and how do I figure out what happened. So, I looked at all this information and all the posts that they made, all the comments that they made, all the comments that they received and all the links that they made. I tried to figure out what was going on. And I'm just going to talk about two of these. They're all pretty highly correlated with each other.

So, typically, someone who was posting a lot was also commenting a lot and was also making a lot of links. The two highest ones were comments received and posts. So, someone who posts a lot also received a lot of comments; and then, comments made, and links, which doesn't make sense to me.

If you made a lot of comments you were also apparently making a lot of links in your posts, so you just want to look at those two a little bit more closely. So, I started looking at those two correlations and trying to figure out--what does this mean? Obviously if you make a lot of posts you're probably going to receive a lot more comments because there's just more content for someone to comment on. But when you look at and compare the top, very top, cream-of-the-crop, the top five people in the class, compared to people further down the scale, people who only made, say, nine posts over the course of the whole semester, these people received four comments per post as opposed to a lot of the people at the bottom of the scale who weren't receiving any.

So there is something about what they were writing that drew people in to comment. The biggest thing that I saw was that a lot of these people, when they received a comment, they would comment back. So they really followed that process of turning their writing into a conversation.

If someone made a comment that they disagreed with they would write back and say, "You know what? I think you're wrong." If you look at some of the longer comment threads--there was one person in this group who received something like 32 comments on a single post--and it really was a back-and-forth between her, students in the class, and people outside our class trying to comment on this, and trying to figure out what's going on. So they created that conversation, and they really tried to figure out how to deal with all those different viewpoints.

Now the comments made and linked--those with more links were more widely read and interested in adding to the conversation; that's my theory about why they made more links. So when they were making comments on other people's posts they had more information, they were armed with a lot more information to make those comments. They were able to present another viewpoint, whereas some of the people who weren't linking, they didn't really have those other viewpoints. They couldn't go into a conversation, a blog post, and say, "You know what? I think this is wrong because of 'x'." They didn't really have that information.

Some of the students told me that they actually realized that as they made more comments, they got more comments in return and that they really liked that kind of self-promotion. They wanted this whole blog project thing to work and they knew in order for it to work they had to be commenting on other people's work. So those are some of the reasons.

But the biggest thing that I found was that the linking was the key factor and that, in fact, if you linked more, you got a better grade in the class, or actually on the portfolio; so that seemed to be just the hugest thing, which we kept trying to tell people, "You have to link! You have to link!" mostly because we wanted to drive traffic to the blog, but we also wanted them to incorporate outside sources.

So here are just a few of the reasons why I think most of the people who linked got better grades. I mean, they were obviously exploring a wider range of topics; they had more models to work with, so they were reading more widely. They were gaining an audience awareness, they just had generally more practice in writing and integrating those sources and they got more feedback on that writing. I think they learned a lot more about their writing, so when it came time to put their portfolio together they had some feedback to base that on besides just me, which I think is important, because I don't know everything. I wish I did!

Here are just some quotes; I'll let you read them. I asked them, when they started writing on the blog, "Who do you think you are writing for?" Most of them said something along the lines of, "Well, I'm writing for the professor." or, "I'm writing to myself." They didn't really think--they had no concept--of anything else outside the classroom. And then, this happened totally outside of a formal interview, somebody said, "Well nothing really happened until we got an audience, and then once we got an audience it was great." This other student really took that whole idea of audience and once she got her first outside comment she really wanted to write more posts that would get more outside comments, so she was actively trying to find things to write about that she thought would appeal to not just Bryn Mawr students, but people outside of Bryn Mawr.

Then when they finally realized that other people were going to read this, they had lots of interesting things to say. They figured out that there are other people out there; that they have other ideas that might be different from my ideas, and I have to figure out what to do with that.

This is my favorite quote from all of my interviews--they all wrote self-evaluations which were really interesting, and this was really the whole point of the whole class, so I'm just going to read it out-loud even though I know you can read it yourself--"Bloggers not only passively read the news, but also write posts, make comments, and create links; they get actively involved. This vigorous participation makes the web look like a real web, a chain of connected sites. The absence of involvement makes the web look like a set of unrelated dots; you can only see the dots, you cannot see the whole picture unless the dots are connected." And that was really the point of the whole class, we wanted them to connect the dots, connect to each other, and connect to that outside world.

That's it!

Jean-Claude Bradley PAETC07

2007-03-11T12:56:00.000-04:00

link to screencast

Man: All right. I'd like to talk to you about research and teaching the blogs and wikis. Because a lot of you are involved with the teaching aspect, and we did actually discuss a lot of the teaching in the workshop yesterday, I'll be focusing on more of the research. But as I go through this, look at some applications in some of the other kinds of teaching environments where you can see that this could apply.

A big picture here is we're doing science - we're doing chemistry - and if you're not in the sciences, or you're not running a research lab, maybe you're not aware of what's going on right now. There is a transition of communication, which used to be human-to-human communication, towards a world where it's going to be machines talking to each other.

Where we are right now is somewhere in-between: people talking to each other, people talking to machines, and what that means, basically, is machines reading scientific information and doing something with it. We don't have to discuss in detail here what that is, but that's sort of the concept.

There are things like the robot scientists, that actually can form hypotheses and do reactions and test them, so this is the world that we're going to. But the question is, how is it going to happen? For this particular talk, we're going to move over here to using the blogs and wikis in answering that question.

We're trying to do science; we're trying to do science that is useful, that is relevant, and we're going to find that out by actually looking at what people are saying is important. That's how this particular project, UsefulChem, started.

We looked for phrases like "what is needed now," "what is missing is," and found that basically malaria was one of the things that was most often cited. So we did a project on malaria. We're trying to do the entire project completely transparently, using blogs and wikis. What I'll discuss is the evolution of that, and how we used each technology to meet our objective.

One of the things that we came across are other groups that are actually producing information that other people can use. Find-a-Drug is an organization that had actually tested some molecules to see whether or not they have a good chance of inhibiting one of the enzymes for the malaria parasite.

They gave us their collection of molecules, which we set out to make, because we're a synthetic organic chemistry lab. So this is one of the components that's coming together to make this project happen.

As far as the chemistry is concerned, this is not really the right place to discuss it, but the planning of the synthesis and discussing the pros and cons was all done through a blog, and that was done openly. If you're doing chemistry, you're basically having to deal with molecules.

So one of the ways that we started to use blogs is by actually having one post per molecule, where we would put information about the molecule - for example, a link to its commercial availability, a link to some of the spectroscopic properties of the molecule. And you'll see this little "SMILES" here; this is a way of representing molecules that is often used today to search in databases.

Remember I was telling you about the automation part, machines interacting with it? I think that using social software is a good way to bridge the gap that exists right now between machines and humans.

A second blog that we started - and again, we did all of this not as a big planned strategy, but basically we just created what we needed to, to reach the objectives that we had, or to overcome some of the problems. Initially, I thought that it would be good if we had an experiment blog, where every experiment was a separate post and we could link specific molecules that we used back to the molecules blog.

In fact, that was kind of interesting because we got comments from people; a few comments from people around the world. This particular comment is about this reaction that actually is not even finished yet, and he's talking about how maybe the concentration isn't good, maybe we should use a different concentration.

Normally, if you're not familiar with science publishing, this really never happens. Normally you do all your work, you completely get it done, then you submit it to a publisher, and then it goes through the peer-review process, and much, much later down the road do people even know that you've done it. So by posting our experiments directly to the web the same day that the experiment is done, we can get feedback. That's what we're trying to achieve here.

Now, that worked for a little while, but then it became obvious that the blog format, as we discussed yesterday in the workshop quite extensively, that because the blog format is really strictly chronological, it's very good for discussing time-sensitive issues, but it's not very good for organizing.

So I created this UsefulChem wiki to basically link to specific blog posts. We still use the blog for new items, but we use the wiki to organize that information. That actually worked out pretty well.

One of the very next things that we could do on the wiki, in terms of organizations, is actually talking about our failures, which is not something that is often discussed. It's pretty hard to publish things that failed, in journals. It is possible, but normally you do it in the context of a larger project, and it's not something you want to dwell upon.

We do want to dwell upon it, because the wiki is actually our laboratory notebook. Everything that is done in my lab is actually recorded, so we have to address the issues. If this didn't work, what's the reason it didn't work, or maybe there's a mistake that happened.

This a page on the UsefulChem wiki where we tried to make this compound, and it turns out that there were errors in the peer-reviewed literature that led us astray. There were issues like that, that we're actually able to document and say, "We were doing this based on this report; turns out that that wasn't actually accurate, so this is what we're finding."

And then finally, experiment 25 is when we had the whole thing working completely. This is something that any chemist can use to make the compound that we're trying to make here.

Woman in audience: What level are the students that you're working with?

Man: The students in the lab ranged from graduate to undergraduate students. This is university level.

Now, the experiments I was telling you about, where every post is a separate experiment, the problem with that is that there's no history tracking in the typical blog. So a student would write something, but then they would get a comment, and then when they would fix it there was no trace that it was ever made differently. There was no trace of how it was actually fixed.

So we found that actually having a wiki page as an actual experiment is an extremely effective way of tracking who does what, when. You can also track what we knew at a certain time. So if we're talking about precedents, I think wikis are actually far superior devices than blogs.

For example, as I was just saying, in terms of who does what, there's a "History" button, and it tells you who has done what. This is my grad student, and I can click on this to see exactly what he contributed at this specific point in time, and I can keep going back, over and over. Even though you're not doing research necessarily in chemistry, you are doing research in other areas, and this is really a good way to track and to communicate with your students.

This is an example of what it actually looks like. If you're not familiar with the wiki interface, I use Wikispaces for a number of reasons that we discussed yesterday. One of them is that it has a really nice way of representing what got changed. The red is the text that got deleted, and the green is the text that got added.

In this particular example, I had put y millimeters, z percent yield, because the student had not put the percent yield. Instead of me calculating it and putting it, I will typically ask a question or say, "Something's missing here."

So that's a good way for me to interact with my students, more as a mentor than a fact-checker. It takes a little bit longer for the information to get accurate, but I think it's worth it, because that's really my job as a teacher: to teach them how to learn and how to tell if things are right or not.

Again, a very important thing: if we're talking about science, it's a really big deal for you to say that you are the first to do something, or that you knew something at this particular point in time. And there again, the blog is not a particularly good way to do that, because on Blogger, for example, you can change the date to any date if you want to. It's pretty difficult to find out if this post actually occurred at this time.

But if you use a third-party wiki like Wikispaces, you can see exactly the date and time of that entry. So you can link not only to the wiki page, but you can link to the specific version of that page. And you can do that pretty much on any wiki, I think, and that's an excellent way of resolving debates, which are bound to happen.

So, I was showing you a specific page, you can tell the difference. In the wiki you can actually click on a button that shows you all the changes that are recent. So in this case, on a day-to-day basis, that is how my students and me interact. We check on the recent changes button. I'll see that experiment 25 got updated. I'll see what they did, and I'll respond. That's a pretty good way to interact when you don't have a lot of time to meet face-to-face every day.

The other thing that I think is very very important in terms of finding out about your audience and finding out how your work is being received. Normally when you publish something in a typically paper peer-reviewed journal, what happens is that you'll know who has cited you, but you won't know who has actually read and why they've read you.

And when they cite you you don't know if it's good or bad. They may actually be citing you because you did something stupid, and that's the reason you get a high citation.

The advantage to using social software is that you can put things like Sitemeter, which tracks how many visitors you have a day but also the keywords they are using or the websites they are using to make it to your site. So on this particular day, I can see that I got one referral from another chemistry blog site, and I can see that someone searched on Google for the chemistry of protease inhibitors, which is actually an HIV issue that we discussed at one point.

So this is something that I look at every day to see what's the impact that we are having? How are people finding our materials? Sometimes it's surprising to see - you'll see people looking for a boiling point. You would never just publish a boiling point. But because we are recording everything we do, we record it. And that's useful.

So even though it is not a complete thought, it is something that can be used by other chemists. And they do use Google. You do see people looking for boiling points on Google. So it's definitely a vehicle that I think is going to be used more and more.

[unintelligible question]

The question is about Sitemeter. It is actually a third party. And the free version lets you view the last 100 entries. You can pay like $6.95 a month if you want to get up to 4000. But all the tools I have shown so far are 100% free.

I was talking a little about the automation part. So, again, we don't have chemists in this room, but basically Ng is a way of representing a molecule that is considered to be a very good way because it is a unique way of representing a molecule. And so we have agents for example that will read our blog and will then calculate the Ngs for the compounds and publish them on another page. Every day that happens.

So if you go on Google and you search for the Ng, it will pull up our wiki pages, it's going to pull up our blog pages, wherever that particular string happens to have occurred. That's what's exciting in terms of chemistry. You can do something as a human being.

And then without even your knowledge, you can have these autonomous agents start processing, figuring out if this has been published before, if anybody has done this before. So this is pretty exciting. You can do all kinds of things by producing 3D structures that you can rotate.

There is a thing, if you are familiar with RSS, you know if you subscribe to a blog you are doing it with a blog reader. There is something called CMLRSS which is chemical markup language. The reader of course has to be able to understand chemistry, so bloglines wouldn't do it, for example.

It can actually read the text as a molecule. Then it can do things with it. That is something that is relatively new and it's going to be used more and more. Again making that human-machine bridge. If you do use bloglines, it will still work but it will just ignore the CML.

One of the things by going through this project which has been really interesting is that it is a completely bottom-up approach. There are other people around the world that are interested in doing science in an open and transparent way. We kind of meet each other naturally because there are their blogs and wikis out there.

So the organization is trying to coordinate scientists interacting with each other. One of their biggest projects is on malaria. It is actually a commercial enterprise, where they actually looked up information for us in exchange for having a link. So it's not just people who are doing it without profit. There is every motive out there; there are ways for people to interact to get things done.

The other thing that is very useful about actually having the work completely publicly available is that you can have collaborations. For example, with Beth at Lehigh Carbon Community College. She teaches English, and we have been able to do a little collaboration where her students can look at our malaria blog and be able to look at the humanities components of malaria, for example, or of the issues.

So that is something that you can only really do if you do operate transparently because it is already there. You don't have to do anything special. You don't have to add accounts. You don't have to control it. If you see some patterns here that are useful you can certainly contact me and we can show you how to do this.

I was telling you that the blog wasn't that great for recording experiments, but it is really good for recording your milestones. The main UsefulChem blog - basically, if something interesting happens that a good portion of the population can understand, I will put it.

That doesn't mean that 100% of the people will understand all of the posts. Some of them you do have to be a chemist. But some if it you can probaly figure out what's going on roughly. We are trying to make compounds, if we are having a lot of trouble, I will explain why we are having trouble. If we've made it, I'll be happy and give you a post that we made it.

So you might not even know what we've done, but at least you can see roughly where the project is going. So that is where the blog fits in really nicely. And then of course, the wiki has really evolved to be a very good laboratory notebook.

You can do raw data on here and there are other people that have other ways of communicating their raw data. That's a whole other issue. So you have other blogs like Daily which actually do publish some of their failed experiments. Not all, so it's not an actual notebook. But there is some of that going on.

You have people discussing vendor reliability. That's not something that you usually read about in the journal work. But is extremely important as a chemist to know not to order from a particular vendor.

There is open webware - I don't know if you have heard about this. This is a pretty big initiative from MIT to basically do science using wikis. But here people are pretty selective about what they will actually share. There is an example here for intragroup communication.

So that this is public, there is a diagram here and a little explanation. But you really have to be in the group to understand what this means because there are a lot of things that have not been explained here. We try to do it so that our wiki pages are very complete.

If you are a chemist and you happen to fall on that page, you can absolutely understand 100% of everything that got done. You can look up the raw data to see if it really does support the claims that we are making. You can link out to understand our motivations. So there are these components that are flying around but I think it really becomes powerful when you integrated everything.

Another blog here our research where it discusses hypotheses. She doesn't really put raw data up. But she likes to talk about "I think this is going to happen," and she gets from good feedback from her colleagues that way.

And I would say probably the greatest collaborations that we have been having lately are really from the automation part. There are people from around the world that are coding for chemistry, and we are contributing to that and we are using all of this open source stuff that is going on and these are some of our collaborators. I think that over time, this can spill over to the actual chemical research, but right now it is mainly the coders who are collaborating.

And this called, in general, "open source science." There is an article over the summer in Chemical & Engineering News which is the flagship journal for chemists. These are my two students here. This is actually really important, because the fact that open source science appears in the C&E News means that it is moving towards the mainsteam.

It means that people who are not just freaks on the border are thinking about there is something to this, there is a reason for doing it. And it can be something that is very useful. I think that that's very important.

Mike Zarro

2007-03-11T12:52:00.000-04:00

link to screencast

Mike Zarro: Hi, everyone, I'm Mike Zarro. I am on the other side -- the flip side -- of the coin from most of you, where I'm using your products. And I'd just like to thank you for everything you're doing. I'm going to try to not be negative here. Obviously there are some issues in online education and digital technologies that we all know about. And we've heard some themes already today.

What I would just like to say is to keep doing what you're doing, please. I know we're pretty early on in the game. We can see there's some opportunities here for improvement, but also, let's not lose sight of the fact that just having online education can bring someone like myself in who maybe wouldn't have thought to go back to school after eight or nine years out from undergrad, to take that leap back into graduate education.

Whether or not I would have, I don't know, but having online education as a possibility really helped me make that decision and brought my dreams of more education to fruition. So, I'd just like to thank you all.

We heard a couple of themes already. One was the design, which we'll get into, which we brought up as a question earlier. But also the discussion boards, where the graduate students really... That's kind of where I live right now. So, we're going to see a bit of that. Unfortunately, maybe they're getting a little worse for the wear over the past couple of years.

I'm here at Drexel. I'm in the Library School, just a few blocks away. I don't know if there's anybody here from the Library School. One person? OK, great, great.

So, we're the high-techie people, supposedly. I don't know how many over there actually knew about this conference today. So, there are some issues there, maybe, to look into, outside of technology but actually with the people behind the technology.

And it's really funny, how -- even in online education -- digital education mimics what you have in real life. I still have issues with financial aid. I still have to track down my advisor and all that good stuff, a lot of it online. Luckily, I can get down here in person, so I have that opportunity. But I'm just wondering if somebody was totally online, and if you need to get in touch with financial aid, there could be some real issues there.

Baby steps, definitely, right now, but we're getting there. You can see that I've been doing development for quite a while, and e-learning. So, I kind of know the behind-the-scenes world. So, it can be doubly frustrating for me, because I can see the potential there. But we're not quite to that point yet.

Here are some successes. I'm able to interact with people from around the globe. One of my favorite professors is from Pittsburgh. There's no chance -- if this was a traditional environment -- that I would have the opportunity to have an adjunct professor from Pittsburgh travel to Philadelphia every day to teach me.

So, things like that, that's a success story that we can see in online education. So, all the frustrations we're going to get to in a minute, I'll just couch them right now.

You know, geographic barriers: I was able to travel when I was in school. And, actually, I was interrupted by John Waters in a coffee shop up in Provincetown one summer, while I was trying to do my online discussion board postings. So, it's kind of neat that you can pull all of these thing in and kind of do what you want as a person, as a professional -- which I was -- and still get your education. So, there are some real kinds of neat things you can do. I can be in Seattle today if I wanted to and still do my work.

Am I hip? I'll leave that for you to decide. I'm glad I don't have a clicker for that question today.

Woman: Can I just ask, does that mean the on-line things don't get graded?

Mike: Oh, no, they get graded. I'm sorry. What this means -- this slide -- is the career professional. You know, I'm older than some of my professors, and I have more technical skills than maybe some of them, and there's a lot of web work being done in the library field right now. So, do I want to be graded by somebody who potentially I have a better skill set than they do right now? So, that's kind of where that was coming from.

Blackboard, I think, 64% of the people are Blackboard. I feel your pain. But, it's not all about Blackboard. I had expected to fire up Blackboard on a daily basis, or every other day or so. And that was it. That was going to replace the building. On Blackboard, I could go there and see everything. The reality is, I spend maybe 60-70% of my time in Blackboard. But I'm also branching out to other places.

So, we have Blackboard here, going to the Drexel site. This is where I got a little fancy with PowerPoint. Sorry.

We see here, even the computing services, with the thumbs up. That's important. I need to know if I can't email a professor, if the service is down, or if it's something that I'm doing. Am I going to be responsible if my paper isn't turned in on time.

I use the U Penn Library, Banner -- that's the IST Library School website -- our library and then Web Now. All of these things come in. And this is just what I thought of off the top of my head. We can add Word, we can add PowerPoint, any number of other applications as well.

I do have the opportunity to collaborate with my classmates and professors. Again, you can see people from around the world, especially the Delaware Valley and the East Coast, it seems to be skewed that way. And I haven't been able to figure out, is it Delawareans or Delawareans or people from Delaware? Any help there?

We particularly used WebX, which is not sponsored by Drexel in any way. There is a Blackboard collaboration tool which I have used with some success. Luckily, as most of the professionals in the online group, somebody has access to WebX through their profession, through their career. We can come and piggyback on that a little bit. Is that an unfair advantage for certain groups over others? I don't know. I think it probably is. But we're all out there trying to make it. So, we'll grab WebX if we can, Yahoo! Groups as well. Not as successful as maybe it could have been, partially because we're students and we don't have time to really investigate like some professors do, what actually works and doesn't. So, we just grabbed Yahoo! Groups and it didn't really work out. So, then we moved onto something else.

How much of our time is being wasted by this? I don't know. I feel like it's too much. I feel like there's a lot of frustration there because we're going outside of Blackboard. I don't know if there's any Blackboard...

Woman: Why don't any of the faculty members use it?

Mike: I've seen that turned on. I've seen that maybe not turned on. Maybe that's me not seeing it or my group not seeing it or the professor didn't enable that function. In the one case for the group where it wasn't turned on -- I'm relatively new to Blackboard as a student -- and I didn't' even know there would be that option.

Nobody knew this existed. It was the first class we took. Later I did see it and I wondered why it wasn't turned on in the first class. There was no opportunity to see what Blackboard fully had to offer. Maybe it's out there somewhere. I could have read the documentation.

Woman: But it sounds like the faculty weren't getting trained in it. The faculty...

Mike: Correct, yeah.

Woman: So that he or she could facilitate more as a teacher.

Mike: Yeah. And again, that mimics real life or classroom education, where maybe a professor is able to use all the tools in the classroom and maybe not. You know, it's really surprising how much it does mimic that.

I used my cell phone and got walloped with a $160 bill because I guess my plan isn't as good as some others. So there are some hidden costs there maybe. Sunday night, with the discussion boards, it's required most classes, if it's not required, nobody posted, it's a ghost town. Most classes it's required, at least one posting. Some professors don't have a required number.

So maybe you post once and the professor doesn't like that and maybe gives you a slightly lower grade than you thought you should get. Others say you have to post and also respond to somebody. So I try and post early on in the week and do some responses later.

Luckily, I'm not working right now, so I can do this all week and be one of those annoying kids in class, the teacher's pet. When I was working, Sunday and Sunday nights especially, that's almost like when the class meets. And that's when everybody posts on the blackboard, and you really start to see the thread develop at that time.

It's a little unfortunate that it happens that late in the class. But realistically, for a professional to do the reading and really digest the materials through the course of the week, Sunday night is when this is going to happen. Even now I reserve Sundays to be a classroom day, I would consider. Which is especially frustrating when email or the server goes down on Sunday, and who knows if their sysadmins, I'm sure they're working on it, there's probably not the same coverage we would get during the workweek. It's kind of interesting. Sunday night is the classroom sessions.

Here's my discussion experience. When I come in to blackboard, I've already chosen my class and I see this announcement, which there's never really anything there, so it's kind of fun. This is all framed space in 2007, so that's kind of fun too. Now I'm in the discussion board, we can see this search feature at the top, which I've never been able to get it to work, I don't know how this works.

I think everyone's probably upgraded their blackboard installations, as well. I think I'm a good computer user. I've been online for many years. I can't get the search to do what I wanted to do, and I've given up trying essentially. Which is really frustrating because there is an opportunity for me that is pasted, and it takes up a significant amount of real estate.

And now I scroll through and find week six or seven we're in now, and now we have our postings. Everything is great, and I want to see what I'm going to do next and I look here to posts websites to a discussion board. And that's the amount of this real estate of the screen and I want to use right now. I don't have the option to do anything else. What would you consider that? 20% of the screen, if that? And there's no text there, it's essentially useless at this point.

[inaudible question]

Below here, the highlighted part is where I would type in or read somebody's posting. The rest of the screen shows the thread or search for it.

[inaudible question]

There's a discussion going on, about how to address this because there are a lot of people in the same boat. And this word blackboard.com, we don't have a direct sysadmin here that I know of, who can fix this, or do anything with it, blackboard hosts it for us. Again I can still learn, obviously, I enjoy it enough to stop working to go full time. This is something where every day, I have to scroll again. The repetitive nature starts to wear you out.

You brought up a design point, this is an opportunity lost really. I'm taking a web design class right now and if I did this, the professor would give me F. That's just space lost. So again, an opportunity lost. It's particularly galling at Drexel in the Information Sciences to see this. But, blackboard enabled me to get in the online education to start, so I am kind of conflicted. I know behind the scenes, how impossible it is to make of this stuff work. It better work perfectly every time for me, as a student. But as the webmaster before me, I know how hard it is, so I can see both sides.

So outside of blackboard, were talking about multimedia resources, iTunes, podcasting and all this great stuff. So far in my classes, I haven't really had experience with that. I think I've used QuickTime once and one time, real time chat with a professor. And I think we use a phone conferencing thing. UC Berkeley does some things, youtube, wikiversity is out there. There are some other opportunities for professors to post. Within blackboard..a as part of a school or maybe on their own, people could have some opportunities to do multimedia that work.

Now whether or not that would actually prove my education, I don't know. It might be cool. I might love it. And I might think I'm the hottest thing going, because my professor is online in QuickTime window. But I'm learning really well right now, I'm getting the material. So maybe this would just be a distraction, I don't know. So when you're thinking about podcasting, that sort of thing. What we have now is pretty good.

[inaudible question]

One thing would be, if I posted something that was particularly interesting and I went away for a bit. I wouldn't have an opportunity to respond and nobody's ever going to go back to week five now. But again, if you're in a classroom and your three hours are up, maybe you continue it later and maybe you don't.

Here we are with some final thoughts. We can see the numbers, if this is correct, I'm surprised that I read this, there are more online students than actual on-campus students. We can see the growth here. Maybe some of the issues I've brought up, any school that is growing as quickly is going to have, some sort of issues serving their students. That's just the way the nature of the beast is here.

Generally, I feel when I was only online, I can take classes in person as well. I felt like a student, I felt part of the school. IST has done a great job with that. There are some opportunities you don't have as an online student. There are one or two classes I think, that offered where you really need to be in person. You need to have those books that are falling apart, raining dust and mold all over you, you need to have that experience in person. I think there are a couple fellowships or some sort of scholarship study, you wouldn't have an opportunity to get if you are online only.

And then of course the networking and kind of schmoozing with your classmates and professors. You don't have as great an opportunity but you still do get to know some people online.

[inaudible question]

We can see obviously, online education is extremely popular right now. And I expect this trend to continue going up. And hopefully more evangelists will be out there like us sharing are good stories, and not complain too much. So keep doing what you're doing and I thank you for it. Can I answer any questions?

Dan King

2007-03-09T14:49:00.000-05:00

Link to Screencast

Dan King: Kind of end up being a feed for this session.

This talk is not exactly what my abstract had.

Well normally when you submit an abstract that's relatively close to the talk you expect it to be pretty similar.

But as I was working through just that information from the environmental chemistry course, which is the focus of the abstract. It didn't seem like it was telling enough of the story and I started to look at some of the results from using the same two technologies in a different course and comparing the results from those two courses and that actually seems more interesting.

So, what I'm going to focus on here is looking at technological use inside the classroom and outside the classroom and the relative effectiveness of each.

So, I'm going to focus on two different courses, the first one is chemistry in the environment, an environmental chemistry course, that's the one that's actually mentioned in the abstract. So I'll be talking about data from two different years. This course is taught in the fall, enrolment this past fall was 40 students. The previous fall was 25 students.

The student population for that course are upper level under-graduates and first year graduate students, the primary population the course is designed for environmental science and environmental engineering students. It's required for those two majors. It also has a bunch of other majors and part of that accounts for the fifteen student jump come 2005 to 2006.

Suddenly we're starting to get a bunch of other students, chem majors, some bio majors, civil engineering, chemical engineering, some random students, [inaudible]

The other course I'm going to talk about, a very different course, physical chemistry, junior level class, enrolment about 34 students. I'm only going to give data from that class from one year because that's actually talking their winter term, so I'll do that data from last year, the next year is meeting right now, and in fact I'm missing class right now.

The student population in that class, all under-graduates, chemistry and chemical engineering students. One more comment about the environmental chemistry, the graduate and the under-graduate course actually meet together so they have slightly different requirements, it's a different course number but they do actually meet in the same class room for financial reasons.

Most of the graduate students are working full time so they're students, they're working at a company and they're coming back and getting their masters. So, their chemistry is somewhat suspect, at least they haven't had it for twenty years.

So, discussing two primary technological tools, the first one is in-class and that's the personal response devices or clickers. We'll come to those in just a second. The way I use them in class each student gets assigned a specific clicker, you'll notice on the back there is a number, and so when the students come in there is a list and they find their name on the list and they know what clicker to take.

My clicker questions are integrated throughout the lecture and as the students submit their response it is recorded on my computer and I have those data to work with at different times. I use the same way in both the physical chemistry and the environmental chemistry class.

Outside of class, the technological tool I'll address here is the use of a discussion board on the course management system. We use web-ct so the discussion board is accessible to web-ct which is where the course home page resides.

I encourage them to post anything of interest on the discussion board, it generally slips to just to a discussion of the weekly homework problems. Every once in a while a student will get brave and post some random comment and there will be a little bit of discussion about that. Realistically, the most part is "I'm having a problem, I don't understand how to do number four. Can someone help me out?"

So there are two primary clicker types, IR and RF, InfraRed versus Radio-Frequency. One big difference is the cost, IR are much cheaper, but the RF ones work much better for larger classes.

The IRs require a line of sight, so they work like your TV remote. So each receiver, which receives the signal, can only handle about thirty to eighty clickers per receiver depending on which brand that you purchase. The RF ones, radio-frequency, work more like your garage door opener, you don't need line of sight, and most of those on the market can handle up to a thousand per receiver. When you start submitting your results those all come to a little receiver that is plugged into a USB port on my computer. So, very portable.

Lots of different brands, some publishers have specific preferences that they bundle with textbooks. My choice is turning technologies, I chose that for several different reasons.

So, first question, "Have you ever used clickers in the classroom?"

What you need to do here is just press the number associated with the answer. Either one or two you don't have to click go or login. Just hit the number and it should record. What you see here is I can track how many students are responding, and if I wanted to look at who specifically has responded I can do it that way as well. I can pull up a little grid, so if anyone were to change their answer their box would change color.

So, if anyone wants to change their answer, you can change it back. If I use the grid in class, the first time I do this the colors just go back and forth as students love to play with the colors. Usually after the first few times they tire of that then they just go back to answering the questions.

So, once I'm convinced that everyone, or at least most people have submitted their answer, then I usually have a little ball drop that tells them they've go ten seconds left to submit their response. Then what shows up is a graph, totally anonymous to the other students, none of you now know what four or so of you have used clickers in the classroom, so it gives an anonymity to the students.

I know who has responded what, the devices are recorded, each clicker is assigned to a specific student, so if I want to go back and look at a specific student I can get that information.

So, clicker logistics, where do you get the clickers? Two primary ways, one, you can have the students to purchase them, a lot of textbook companies will bundle them with the textbook, or you can purchase a set for your self. That's what I did, I purchased my own set. The physics department here has purchased the same ones but they bundled it with their system.

So, I purchased it for my own for a couple of different reason, one, because I had the money to do it, and another reason was that I teach one lecture out of a multi-lecture course, all with common-grading. The other lecturers are not using the clickers. I do not feel comfortable asking my students to pay and extra fee to buy just because they happened to sign up for my lecture section.

It's a common course, it's not a separate course, common grading, common exams, everything else. The only thing that would have been different was that they happened to have a free spot in their schedule at eleven o'clock, so I didn't feel right asking them to spend extra money. So what I do is distribute and collect the clickers every day in each class, obviously if the students have their own they can just bring it.

Some of the other things you'll need are a computer and a projector. You need a computer to collect the responses and you need a projector if you want to display it immediately. If you don't want to display it immediately you could just have a computer that collects the data and just write the relevant responses on an overhead. If you wanted to combine that technology you'd have a computer that just collects the data, and then you wouldn't need a projector for that. Then you just look at the screen and then I could have just written on the transcribe screen 79 percent no, 21 percent yes.

In the physical chemistry course I usually have about two questions per 50-minute lecture. In the environmental chemistry course about four quicker questions per three hour lecture although it's really more of a three hour class, I don't actually lecture straight through, they have group activities in the middle, but that's a whole different topic.

So there are, I don't just do these for random purposes or specific learning objectives associated with using the clickers. One of the learning objectives is to test prior knowledge. So I will ask a question at the beginning of class. For example, I may put a question like this for my physical chemistry class. The correct answer here was actually number four. This is information the student should have had from their freshman chemistry class, so I'm really getting a feeling for what do they remember.

So, not only does it tell me that OK two-thirds of my students actually remember some of their general chemistry, but depending on what other options I give them, I can get some additional information. The fact that nobody chose number three means that I don't have to review the fact that to get this answer you don't just add up the numbers in front of each chemical. So that's important information for me, and I can use that as well.

Another learning objective is to test student learning, student understanding of the concept that I've just introduced, so for example, I may ask a question like this, this actually comes from the environmental chemistry class. So this is a question that I ask at the beginning, the correct answer is number two. Only about half of the students knew the answer, and a wide range of responses that I present the lesson, and in the theory at the end of the lesson, if I've done an effective job then everyone should know the answer. I feel lucky here actually most of the students actually got the correct answer at the end.

So, in addition to giving me some information, and often times you will find that this is a very humbling experience, you think you've explained something so eloquently and then you put it back up and you get that first distribution where you get only 50 percent got it right, even though you'll ask if there are any questions, and they say no, yes we understand you perfectly.

But also, this lets the ten percent of students who got it wrong know that they are not up to speed with the rest of their classmates. So the hope is that not only is it information for me, but it's information for the students. Sometimes when they all get it wrong hopefully that's a wakeup call for the students, oh I don't understand that as well as I thought it did.

Man 1: Do they know that you've been tracking individual things?

Dan: I don't mention it explicitly, but if they ask I tell them that I do collect that information although I've never used it and I never, you know it never gets displayed to anyone, but so I don't make a specific announcement, but if they ask, I do tell them.

OK, so we can one of the ways that I've used the clicker is as an assessment tool. Are the students retaining the information? So, here's some exam results from the environmental chemistry class. These are five questions from the mid-term exam. You can see the corresponding percent of how many students got that question right during class.

And then the corresponding question from the mid-term almost all the questions they did significantly better. Number three, they actually did a little bit worse although statistically I'm not sure if that's any different. Number five, I didn't ask a corresponding question in class and it turns out I didn't need to because they all pretty much knew that information. If we looked at the final we pretty much see similar results. So again, not always to 100 percent. So, number two, they didn't do well in class, they did better on the exam but still not perfect. But it does give me a measure of student learning. So it's not only a tool for getting students engaged in the classroom, but I can use it as an assessment tool.

Man 2: Is that the same exact question?

Dan: Sometimes it's the same exact question, and sometimes it's just similar content. In physical chemistry class, I think with this with one actually with physical chemistry, it was the exact same question.

And here you know they really remember those questions, but I'm still not sure what happened with number three [laughing]. So, they got in class, and they lost it for the exam. It's an outlier. So, but you know the clickers won't solve all your problems, but they give you a way to measure your effectiveness. The one thing that I wanted to look at was that could I come up with a correlation between students using the clickers in class, in the classroom, and how they did on the final grade. So what we see here is the y-axis shows the percent of clicker question students answered during the class. Not whether they got it right or wrong, just how many-what percent of students, or what fraction of questions did they answer over the course of the term. As you can see for the physical chemistry class, the reasonable correlation pretty much no correlation with the environmental chemistry since. So, whatever was affecting their final grade, it was not whether or not they used the clickers in the classroom.

Woman 1: I'm curious why just did response rather that success of answer.

Dan: Oh, it's just a matter of you know, time to work out work through the data, so that is an eventual goal to look through that. But some preliminary results I've done a little bit with the physical chemistry class, and I've seen, it's a similar correlation, but not necessarily a huge one.

Woman 1: You'd actually have a Cordeau correlation right? That they learn from the clickers, but cause otherwise it would be pre-knowledge. They already knew it so now they know.

Dan: Right, well I guess it depends on how you set up the correlation. Is it, you know how many students improved, so you can plot it in many different ways. So, it's not always just questions right, it's how many students got it wrong versus how many got it right on the exam. So you can set up little tables to look at that. At our end of term surveys I put some questions on our course evaluations asking students what they thought. So, these were all questions on the end of term evaluations. Clickers, you know maybe more likely in class, more likely to participate, maybe more focused on the lecture helped to improve my understanding, or made attending class more fun. Generally we saw that while physical chemistry students seemed to feel they got more out of using the clickers than the environmental chemistry students which sort of matches with the positive correlation we saw with students actually responding in physical chemistry versus environmental chemistry.

Man 3: Now that more likely to attend class I mean did you compare with the measured. Cause you know right?

Dan: I have not gone back and looked specifically at, well there's now way for me... I can only do percentages and that's a tough thing to measure because more likely to attend class, you know, how do you actually measure whether their likeliness to attend class. So the one thing that I have done is for both these classes, there's a small component of using the clickers in their grade. So, a small part of their participation grade comes from answering seventy-five percent of the questions. Whether they get it right or wrong, it just, if they answer 75 percent of the questions they get a small percentage of their grade.

Woman 2: Did you find out from students how they felt about these new [inaudible]

Dan: In general, those responses are actually a pretty good measure of older students versus younger students because the environmental chemistry class is two-thirds to three-quarters to graduate students. Ok, We're going to talk next about the discussion board, so please answer.

[silence]

Dan: Ok, so one of the nice things about using the clickers is, because I have this information, I see that 94 percent of you have used some type of course management system. I can now skip these slides.

[laughter]

Dan: Because those were slides to just show you my course website looks like, but since you all use those, you don't need to see that. So the only thing I'm going to show of those slides are the slides that just show you the listing of one week's discussion topics. What you can see, that there are several where there are only a single posting and several have multiple responses. What I'm going to do is look at the average number of postings, the average number of threads, and postings per thread in each class.

Dan: So, for the physical chemistry class, the students are required to post three times over the course of the term, a very minimal posting requirement. The first year that I did it, I did not require anything, and no one posted. It was a desert. So I figured, let me just do something to at least get them started and then hopefully it'll take off, and it turned out for the physical chemistry, it did not really take off at all, so you can see... Average postings per week 11. There are 34 students in the class. So average threads per week 5. Average postings per thread 2. So pretty much, one person posted a question, another person posted an answer, and that was it. So not really much of an extended thing. Average posting per student 3. Course requirement 3.

[laughter]

Dan: However, despite the fact that they spent very little time and did the minimum required to post, they read everybody's post. 104 readings. Now, this isn't broken down, so some of that 104 are people re-reading the same post over and over again. I haven't gone through that would be extremely time intensive for me to look at each student, how many time they read.

Man 1: What's the total number of postings?

Dan: That's not a number I have.

[silence]

For the environmental chemistry student, similar requirement: basically three postings for the undergraduate, which mirrors, the physical chemistry, five postings for the graduate student, part of the differentiation between the two courses. So, a lot more postings for the environmental chemistry students. The two numbers here are just 2005 versus 2006. You see similar results between the two years. And actually, keep in mind that the average number of postings per week - 34. There's actually 10 fewer students in 2005 than there were in the P. Chem. Class. A lot more different threads, where a thread is each different topic. The threads going for 5, questions in initial posting and four responses. If you look at the results on a student level, average postings per students, we're up to 10. If you break that down, all the undergraduates are still sticking with their required minimum, but the graduate students generally much higher than their minimum, so graduate students really seem to appreciate this technological tool.

Woman 1: Were your undergraduates [inaudible]

Dan: Oh yeah. It was a common discussion board, so they were all reading each others. So again, students reading a lot more than they're posting. So they're not just going in, posting and then getting... So even though the undergraduates are only posting their minimum required, they're also still generally reading and trying to get some information. They're just doing their little amount of initial intellectual thought required. The requirement for the postings was that it had to actually be a complete thought. They couldn't just post, "I agree with so-and-so."

I looked at the correlation between number of postings to the discussion board and the course grade. You see somewhat of a weaker correlation with the physical chemistry, which you would expect since they're not doing it as much, but its still somewhat of an indication of the students that are actively engaged in the material. A little bit better correlation for the environmental chemistry students than we saw for the clicker responses, but still not a great correlation.

I also looked at a correlation between students clicking in class and posting of those students engaged. There's absolutely no correlation in the environmental chemistry, and an in-between correlation between the two, as you might expect.

One way that I use to assess how the students felt about these two technological tools was an online survey known as the SALG Students Assessment Learning Games so it's a survey designed to ask the students to identify the effectiveness of various course aspects on their learning. It's online, its customizable, you can change the questions. It's very accessible, very easy to use. All the questions are set up on a Likert scale, five choices from 'strongly disagree' you know, 'no help' to 'a lot of help', number five.

So I had a list of six different course components for the environmental chemistry class these are the six. I really just want to focus on the two in red: the clickers and the discussion board. What you can see is that the environmental chemistry students thought that the discussion board was really effective. The percentages of the number of percent of students that either four or five they either thought it was helpful or very helpful. And clickers, not as helpful. Not a big surprise. We kind of saw that in the data.

The physical chemistry students same list of six topics. But they really liked the clickers, as we saw from the course evaluation, they did not think the discussion board helped them much at all. Despite the fact that they were reading a lot, they weren't posting and they thought, "Eh, helped a little but not very much."

Student comments: Some of them thought... I'll kind of let you scan through there. "Thought the clickers were beneficial." "Discussion board great." "Discussion board really helpful." This one I really like, "Clickers helped give confidence in class." That's one of the things we hoped to see. Surely that's not the case for all students, but it is one of the hopes of using the clickers, that students who ordinarily wouldn't raise their hand and participate in class, as they start to click and get questions right, then maybe they start to get a little bit more confident. And I do see that to some degree, anecdotally.

So in summary, both clickers and discussion board increased student engagement. Clickers primary used as an assessment tool for student learning, not necessarily a good predictor for student grades, although somewhat of a correlation in physical chemistry class.

Here the clickers were more helpful for student learning in physical chemistry class, as opposed to the discussion board. However, the discussion board seemed to be more effective for the environmental chemistry students. And I think that was in large part due to the fact that you had part-time students, and for the environmental chemistry students, since most of those students are off-campus, the only interaction they had with other students was through the discussion board.

The undergraduates can generally just meet up with each other at any time. They don't need that technological tool to interact.

And that's it.

[clapping]

Dan: Any questions? Yeah.

Woman 1: Just by the names, I would assume that the physical chemists might be more introverted than the environmental chemists. Do you think that might be true?

Dan: I would expect that maybe for the environmental science component of the environmental chemistry class, and some of the environmental policy students that are there. Not necessarily the case for the environmental engineering students in that class, the chemical engineering students in that class. Some of the chemistry students and the chemical engineering were actually in both classes.

So maybe, on an average, slightly more so. But because the environmental chemistry class is so mixed, I don't know that it's specifically...

Woman 1: So, not enough to account for the difference between the discussion boards, which I would think extroverts would like more, and the clickers, which I would think introverts would like more.

Dan: Yeah. I would say probably not a big enough population difference to have spawned that.

Man 2: Are you going to change the way you teach based on the data?

Dan: To some degree, yes. I would say one thing that I can take from this is, if I really want to use the clickers in the environmental chemistry class, then I need to do a better job of that. Because obviously they don't feel that they're getting much effectiveness out of it.

Certainly, on a day to day basis, I do a lot of real time adjusting, just as I did here. I was able to skip those slides. So one of the things that I do is, if I ask a question at the beginning and I'm trying to assess their prior knowledge, then I will sometimes put some slides that I might need. So sometimes I'll ask a question where I'm hoping that they have some prior knowledge before I discuss the next topic. And if they don't have that, then I know I need to review this topic before I go on to the next topic. Otherwise they're going to be lost and I'm just talking to myself for an hour.

Woman 2: Where I work, some people use these for attendance in large classes. And it actually made me start wondering. Your physical chemistry students were all undergrads, right?

Dan: Mm-hm.

Woman 2: Where there was a higher correlation between using the clickers and getting a good grade. Could it possibly have represented students who were actually in class more?

Dan: Oh, absolutely.

Woman 2: OK. I was wondering if attendance was required, or not necessarily.

Dan: Well, the requirement is implicit, not explicit. So they get a small participation grade for answering 75 percent of the questions.

Woman 2: OK. So in fact, it might represent students who are better prepared there.

Dan: Right. Although let me give you one caveat to that.

Woman 2: OK.

Dan: I also used these in my general chemistry class. We have a regular general chemistry sequence, and then we have a trailer sequence for the students that have failed one, or had to take a prep temp course, or transferred in. They're in there for a variety of different reasons. So in the general chemistry, we have multiple sections, so I can't require attendance, because the other lecturers have no way of recording that. So there's no attendance requirement at all for the lectures. Students attend if they want to.

In the trailer course, there's just one lecture. So last year we put, five percent of their course grade is attendance, and you get those points if you answer 75 percent of the questions. You don't have to get them right. You just have to be there and buzz in. So the thought was, oh, I'm going to get all these students in class, and they're going to be engaged, and they're going to do much better. It didn't quite work out that way.

One of the problems that I had was, I had students that were in the class to get their five points. And those were students that actually became somewhat of a disruptive influence, because they didn't want to be there. And ordinarily they wouldn't have been there, and I would have just had the students in class who were paying attention and wanted to be there. So I ended up bringing in some students who shouldn't really have been in the class, and it created a more difficult lecture environment.

And there's also a concern that the information that I get, which is really valuable about do the students understand the information. To some degree that's skewed if you have a bunch of students who are just randomly buzzing in every time they see a question come up, and then going back to their conversation. Because I could think that most of the class doesn't understand what I've just explained, when actually the students that are paying attention do understand. And it was just students that were randomly pressing buttons that skewed, that just pressed number five.

Woman 2: That sounds like a horrible story.

Dan: Well, it's one of the realities of it. So I guess one of the take out messages is that clickers will not solve your problems. They are a tool, as anything else is, and they can solve some aspects and help you do some things better. But just having the clickers is not going to turn your classroom into a wonderful, happy place.

Woman 2: Right. But it just sounds like the students who don't want to come to class and might just come to class for the points, won't really bother to understand the questions and might not even bother to read the exercises. These don't sound like very successful students.

Dan: No, they're not. And you can't make them successful just because you've put a piece of technology in their hands.

Man 3: Have you thought of using the data you collect for mid-semester? Just to see if there are specific students that are always getting questions wrong?

Dan: In my dream world, yes. I have enough time that I can go through the data and I can identify the students that are struggling and call them into my office and say, listen, I noticed that you're struggling, and you're getting all the clicker questions... Right, I wish there was some way I could do that. But this term, I'm teaching two of the general chemistry lecture sections. I have close to 400 students in my class. For me to wade through all of those numbers. Unfortunately, I just don't have the time.

But also, with the 10 week term, it gets very difficult to get that done. But that is my dream to eventually get to the point where I can do that.

Man 3: Do you think that's a shortcoming of the client software? Because I've noticed that the Turning Point software generates really impressive statistics for a single class. It doesn't really seem to have any way to aggregate [inaudible].

Dan: There actually is a way to generate report summaries, where I think you can actually combine them. I have not. Because when I go to generate my reports, I see those options, and I just haven't had a chance to play with it. But I think that that actually is built in, where you can get kind of get some of that aggregate information.

Man 3: The newest generation of their software creates much better reports. [inaudible] I guess you can just go onto Turning and download it.

Dan: Yeah, you can always get the software for free. One of the reasons I went with Turning technology is that their software, in addition to being able to integrate right into PowerPoint, we saw that those data and graphs showed right up. And when I save this file, it's in that file. And in addition to this, this software can use other companies' clickers. So I thought it was a very powerful software tool.

[applause]

Man 4: Do you want these back?

Dan: Yes, I do want those back. [laughs]

Man 4: I thought that you might.

Pritchard and Gall on iTunesU

2007-03-06T16:23:00.000-05:00

Link to presentation and podcast

Russ Pritchard: As I've already said, my name is Russ Pritchard, and I'm an Assistant Professor of Instructional Technology at Philadelphia University. Brian and I today are going to talk a little bit about our implementation of iTunes University, but we have more of a two-pronged attack. I will talk more about the pedagogical aspects, or the aspects we've tried to approach from the cognitive sciences, and why we believe iTunes University fulfills the mission at Philadelphia University.

Brian Gall: And my name is Brian Gall, Instructional Technology Specialist with Philadelphia University. This is one of my charges as the instructional technology specialist, along with Blackboard and faculty development. I'll present the technical aspects of anything from doing your first podcast, all the way to the trials and tribulations of implementing iTunes University.

Russ: As we began a few years ago to decide what technologies we wanted to implement, we decided that we did not want to implement technology for the sake of technology. That is, we want to have a well-thought-out strategy of what we picked and what we implemented, and why we thought it would help us toward performance with respect to the cognitive sciences.

I teach an introductory course called Introduction to Instructional Technology. I've been teaching it now for about six years, and each semester, I ask the group, after the first class, go home, back to your institution, high school or whatever, and take a very quick survey of the uses of instructional technology that you see, and report back on it next week. And every year, I tabulate the data, and I'm not surprised, but they are, at the uses of technology.

Most people are still performing very much the way they once did, say, 25 years ago. Literally, sometimes, dittos. Some people don't know what dittos are, but they are still using those in some cases. But in all the cases, what we found out, is that when they are using technology, it is really at a lower level. And when I ask, "why are you using technology in this fashion?" they really don't know. They're not quite sure why we're implementing a technology that we are.

Brian: In the past, as Russ said, over the past 25 years, technology has definitely blossomed to the point where we can't keep up, in many ways. Schools are still trying to play catch-up, so we have a phrase called "learning from technology." Which basically means we have a lot of tools available to us, our administrators at the K-12 level, and even somewhat our administrators at the university level, is that we've given you all these tools--use them.

So, in the past, we have traditional use of static PowerPoint, just like you're seeing today, so we've really embraced 21st century technology with this. But, the fact is, a lot of the lessons that I see, and I've seen about eight or nine lessons since I started at Philadelphia University, every single professor uses static PowerPoint as his or her only method of technology in the classroom. This is interesting to me.

We use Blackboard to store documents. Most of use know that Blackboard, or any content management system, is more than just a document repository. But our use of Blackboard, and at many other schools, is just to store documents so you don't have to make copies.

Administrative uses. Word to type up business letters, syllabi, and so on. Excel, possibly to keep grades, possibly to keep a department project. But are they teaching with Excel? Are they using it in the classroom? And then, Outlook. Sure, emailing colleagues, and emailing students as well. But using it purely as a flat communications tool.

And then, teaching uses. Electronic grading. Most of our teachers have at least gone on to Excel, or something like Blackboard or GradeQuick or something like that, to keep grades electronically. And hopefully, possibly, grades on the web, as well, in the K-12 area. And, audio and video, we're still showing those videos from the 1980s and 90s, but now, the question is, can we put it on iTunes University so we don't have to show it in class anymore? That's a question I get, and we'll explain that a little bit further.

But basically, what this means is, we're teaching the way we've always taught, but we're just doing it more efficiently. We're not doing it more effectively. We have a lot of money invested in technology, but is it changing the way we're teaching?

Russ: So, when we spoke about this a few years ago, we said we were going to make a conscious decision to move away from teaching from technology to teaching with technology. So, we had to step back and say, what does it mean to teach with instead of from. So we came up with about five guiding principles.

The first one said that when you use technology, does it give you authentic and varied evaluation? Now, evaluation is of course a big topic unto itself, but it says, the professor looks at what they do and evaluates. We're saying, is it authentic, because you're only evaluation from one person. Can we have the peers do it? Can we have other schools do it? Or can we even have people from other countries do it?

We then said, in addition to that, can we have varied practice and assessment? And I think the only study I've ever read that said, absolutely, positively, we know it works, is TOT or time on task. And time on task is a fancy way of saying the amount of practice you give them. But it's not just the amount of practice, it's how varied the practice is. So, we said that, if you're going to implement technology, can you have more practice, more timely practice, and can it be more effective?

Making learning active is a big buzz phrase. But we said, what does active mean? What do you want the student to do to make it active? So we said it must be: investigate, discover, apply, or solve. So when you implement the technology, does it make it active by doing one of those four things?

This idea about making learning active--once again, I tell my teaching classes every year, at the end of the night, if you're more tired than the students, you're doing something wrong. And that begat student-centered responsibility. It says, can we take what I call the locus of responsibility--who's responsible for learning?--and can we push it back on the student? That's what we say about active learning.

This is the one where I'm getting, really, the most resistance. So, when I give them the monkey, they give me the monkey back. They want--I paid my money, therefore, I want you to teach me. But we're constantly pushing for them, saying, you learn yourself, help yourself, guide yourself, collaborate, ultimately, since you were a part of this.

And, our last strategy then said, we form collaboration. We think that the social constructivist model is the way to go, especially at the graduate level. So they learn by collaboration. Certainly, there are lectures. Certainly there are discussions, but they're going to learn by collaboration. So, does the technology we implement help us to collaborate?

Brian: And I'll pay you back on that. Especially at the graduate level, but, coming from a high school environment for the past eight years, this is really K-12 now that they're working together. I taught in a block situation, we had 82-minute classes. Our principal said, day one, every year, if you don't have more than five activities in that class, you're doing something wrong. You're not teaching.

Russ: Yeah.

Brian: So, it even goes all the way up from K-12 to undergraduate, to graduate, with collaboration, and getting people to work together.

Russ: This idea about collaboration, we're talking about, for example, the discussion board. We have a lot of discussions, but a lot of times, it becomes what I call a barfly conversation. Ain't it awful? I've done this. I want to have a discussion, but I want to be informed. I want the technology to say, where do I get information from? Then we'll have discussion, but only after that happens.

The question then becomes, if we decide upon it how then do we teach it of course to the faculty? How do we get them on board?

How do we get the knowledge inside their brains? The issue became what I would call, working on the work of Everett Rogers, how do you get them to adopt the new technology? And so those of you familiar with the management of change know about the work of Everett Rogers, and he said, you got to get the adoption rate up. Because we don't have forever to get them to use the technology or whatever, we'll run out of time.

So, we then decide to use six things that are kind of expounded upon by Rogers, when we go through the training session, one of the first issues we come up with is relative advantage.

So were explaining a technology, we say, here's what you're doing now, here's what you want to move on to possibly. And then decide, why is it better than what we did before?

If the technology advantage is this big, they're not going to do it. It's not worth their time. There's got to be and you've got to teach them the relative advantage to the way we were doing it before. And we'll talk about iTunes in just a few minutes, and we'll say why is it better than Blackboard? And we'll talk about that.

It's got to be compatible with what they currently use, if it's too radically different, it's not that it won't work, they may not adopt it as quickly. It's got to be simple. Everybody here is obviously somewhat technological savvy, and so when we see a new technology we like it, we use it even if we think it doesn't work because we like it. What I like to say is that sometimes we work with, if you'll forgive the phrase, Luddites, which is what I was at one time. They've got to see that it's not that hard to learn. The other day we showed some teachers Movie, they said, this is easy, even I can do it.

They have to be able to try it before they buy it. So in the training sessions we set up, or even within their classroom, is there a way we can say lets give it a trial run, maybe not in training, but in your classroom can someone be there to help you?

Can they see it work? They've got to be able to see the relative advantage, or how they're going to be able to teach better.

And finally, one of my favorites once again is, what we call the channel of communication, who's telling them about it? When they make the decision to adopt or not adopt, we call the persuasion stage, they don't like mass media information, they like information from people they are working with. So we have these small sessions, kind of like what we're doing now, we have a group called TLTR, and it's in that group we discuss it together and say, does it work or doesn't it? If we decide it does, and we get that information from their local channels, they're more likely to adopt.

Brian: And even a big thing like that, faculty involvement from day one, as we all know probably from our positions, is definitely a key. One of the things that I was told when I first started, if you don't get the faculty behind you, don't bother suggesting something new. So it's interesting how you can pull a group of people together, try and get them turned on, but those six things are exactly what, the faculty are not going to listen unless those six things are met with the technology that you are implementing. So one of our solutions with learning web technology, of course, is our installation of iTunes University.

ITunes University is a product that came out from Apple a little over a year ago, in principle. And basically it provides us a place where we can store 500 GB of audio, video and enhanced files. During our session yesterday we were talking about, what if we lower 500 GB? There's nothing from Apple they said they're going to charge, but nobody knows how much. So it's interesting from a big school environment, if you have a lot, like Temple has, like we talked about yesterday, well over a terabyte of information already. So that could be an interesting dynamic.

But the reason they are giving this to Universities free is, and the sales person told me, they hope we buy more products. But yet they also understand the needs of our millennial learners, and seeing how we can present more information to them in an easier way.

So how does it meet our goal?

Russ: So we decide then to try the iTunes University, we look back at its able to do and say how would it fit into either one, or a combination of those five cognitive principles. And we said it gives us authentic demonstration. Meaning that the students can do a pod-cast, an enhanced pod-cast, PDF files, they take it from their place of work and their the ones that build the site, and therefore becomes more authentic.

Now again I'm saying authentic because it comes from real life, true situations were they have to be working.

They also get varied evaluation. And there's a lot of discussion about this role beginning in just a couple of minutes. When it goes into iTunes University, it's open for everyone to see it. So other classes will look at it, of the same section, other schools will look at it within Philadelphia University, and indeed the whole University will look at it. They have an idea then of what other people are doing and they can kind of benchmark themselves against it.

You can do that in Blackboard, but it's not easy, so the relative advantage here that iTunes provides is much greater. It can be active, and so when the information becomes authentic, I can then say to my graduate students, I want you to go into iTunes University and discover this. It's authentic, I know it's up there, it makes it more accurate.

I like the idea of becoming student centered, where students in the classes are then asked to build the content, build and manage the content. Those of us who are working with blackboard know, it is really course centered, and it's really built around what the teacher wants to put up there. This once again shifts the burden back to the student to organize the content, which I like.

And finally, because it's up there for all to see, it's informed collaboration. It forces them to work together, even if it wasn't something that they might have tried before.

Brian: Going back to the student-centered responsibility.

[clears throat]

Excuse me. Faculty can create content and put it up there. They way we've approached this from almost day one, is to come up with activities that teachers can use in their classroom to get students to produce the content. So again, it's one of those things, pod-casting out one more thing from the professor during the day. We put a spin on that by saying let students populate the content, let students share the information, and actually show the professor what they learned in their class.

Of course the faculty perspective is there as well, they can put up things as they see fit. So just a quick demonstration of our installation of iTunes University, I'll show four different examples. One audio, one enhanced, and two vi-casting examples. And I apologize, I didn't bring my speakers with me, but you'll get the idea.

So this is our site, and even before this, what Apple does, we'll get into this a little bit later, but they present us a white store-front, and that's what it is, its an iTunes store. They give us all the code, all the examples and those kind of things. And then depending on who you have on your staff, you need somebody to design the back-end of it. Luckily for us we had an expert programmer that took their code that didn't work and implemented it in for our system. So we were able to do that. I know from looking at the message boards, a lot of universities signed on to the system over six months ago, but are not live as of today. So it's an interesting dynamic that we'll talk about.

And then our PR department designed the actual interface to take advantage of the branding mechanism that you see.

One example that I wanted to show you, our foreign language department up until about three months ago, all of their practice material that went along with their text books, was on a website, that website was only accessible in the learning lab, learning language lab which had six computers. And it was also accessible in the library. But in the library you needed to checkout headphones, and we had four sets of headphones, depending on whether the students brought them or not.

At most ten students at a time could listen to material. They logged onto the website, they found their lesson let's say a Spanish one, lesson five they received 25 links. They would click on a link for the first one, it would download, it would play, they would listen to it. Then they would have to go back to the website, click on another link, download it, listen to it. A lot of steps for them to do.

So the advantage of learning the foreign language material on iTunes, is the fact that a Spanish one student can come in and log on to their course, and they can see all of their lessons, there's five lessons in their text book. And let's say that on lesson one, they can get individual songs, or they can subscribe. And that's really the difference between podcasting and MP3. It's not the fact that you have to have an iPod, because we all know that you don't. I mean, you need some kind of music source, you need iTunes or Windows Media player, Real Player, or WinAmp or something that plays music on your computer.

If they subscribe they're going to get this first song. And once that's downloaded they'll have a link to Spanish one. Then they can check off each song, download them all automatically, and have them on their computer at one time.

A disadvantage of course is that if you click subscribe, you don't get all of them at once, you only get the most recent what they call episode.

But if I put new content under lesson one tomorrow, let's say I'm a teacher and I have a project where my students have to give a one minute presentation on cultures in Spain. They can record that, they can upload it. If I log on as a professor, I'll get all of those presentations automatically. So that's the advantage of anything subscription based, not just iTunes university, but just anything that's a subscription.

And you'll see that you have all the songs here. But if you click on one, you can play it. And we actually made these enhanced by integrating some of the images from the textbook. I had two graduate students working on putting images from the textbook, we have right to do, through the usage from the textbook of different lessons and what they're talking about.

So an audio podcast that was on a website turn into an enhanced podcast instantly. An example of an enhanced podcast and this is actually a project one of our business faculty did, it was a project where students had to collect five images from the Internet, and had to give a two to three minute discussion about either, artificial intelligence, robotics, gaming theory, e-commerce, or something "the future of technology" related.

I'll quickly get this one. You can preview all of these, but unfortunately, with enhanced NVIDIA you won't see images as you preview, you'll only hear the audio. So you ought to download something.

And they use "Garage Band" to produce this, "Garage Band" is the only software that we know of currently that produces enhanced podcasts. And enhanced means audio, video, PowerPoint, JPG, GIF and even PDF documents can be distributed through enhanced podcasts.

And finally, our occupational therapy department has a capstone program where the seniors had to sit down one on one with the patients, a clinician type interview. And they basically asked wrap-up questions in their time with the patient. Previously in the project, they recorded the interviews on their own, they brought in a VHS tape, or a DVD, depending on whether the put it on DVD or not. They took a class to look at all the video tapes, then the next class they peer-reviewed and critiqued and analyzed what the interview style was and what the answering style was. So they could do better interviews in the future. So it's a three process, and additional time outside.

Because of podcasting and iTunes university, we reduced this to no outside time, and only two classes. The professor brought all the students in for a class and videotaped their interviews. The between that day and the next class, they had to log-on to iTunes university, and view five different videos. They had their own presentation style, and then the presentation style for other interviewers. That second class they got together and had a really high-level discussion about how to improve their interviewing techniques.

So where before the third class was just basic technique, they didn't go into anything high-level about how to interview. This enabled them to do higher level type skills.

You'll notice how I am switching around in my library. If you subscribe to a course, it will go in your podcast area. If you get a song or get a movie, it will go into either music or movies. So that's just the way iTunes looks at it.

Man 1: Once you've downloaded the content, will it organize it by the course?

Brian: If you subscribe you have. Here's "Alta 342 lesson one". The thing that's frustrating me right now is the use of tabs. If you use another tab, you have to subscribe to each tab. But if you put everything in one tab, it's too much. Do you know what I mean?

Let me go back to Spanish. By the way, that video was about 400 megabytes for about five minutes, and with iMovie we reduced it to, I believe it was, 24 meg. It looks crystal clear in the iPod.

The different tabs.

Man 1: Oh, I see.

Brian: Yeah, right. We decided to do the tabs because of the amount of content; the Spanish three and four course has 600 files. So just because of the level of content we had to do it in tabs. But it's frustrating too; it takes a little bit away from the user views, being able to do that.

Woman 1: I don't know if I will need 600 files for my course.

Brian: Sure, right. Oh absolutely. But I think that like for early occupational therapy, this is all they're doing in there currently; they can subscribe and get everything.

The thing we talked about also with this is that this is an automatic scaffold in your reading material. The professor is going to pick the five best interviews, no actually, the students pick the best five, and they are going to leave them up there for the next year.

The forty students doing interviews next year are going to be able to see these, and they are going to be able to see what the good techniques are. So year after year after year the skills of your students are just going to increase, hopefully automatically, that may not happen.

Woman 1: Now you said this is student centered, and students can load stuff, this looks to me kind of traditional, you know lesson one, this is what you're supposed to listen to for class...

Brian: Right.

Woman 1: How would students create it? Can they create tabs, you know, are they encouraged to record themselves doing the Spanish lessons? What's the student centered part of that?

Brian: Right, when the faculty representative, when somebody on the faculty asks for a class I ask them a couple questions. Number one, what their course number is, all that administrative stuff. But I'll ask them if they want drop-box access or full editing access. Drop-box access means students can upload their own material, they can upload MP3s, m4as for enhanced, or m4vs for a garage band, for video, for iMovie, and that content will be given to the professor so they can evaluate it. In the interface, they'll be able to listen to the content, approve, or deny. If they give them full editing access, they can just upload content.

So I'm encouraging people to pick one of those two. They say, so why would I want that? And I say, I want your students to be able to contribute to this course And that's how we're approaching our training, by doing that. You don't have to do that, you can keep it completely closed off, for faculty centered. We didn't believe in that when we set this up, but it's a great question.

Man 2: [inaudible question]

Brian: Our particular installation is not publicly accessible. Much to my chagrin. You have to have a Philadelphia University user name and password. I'm hoping within six months I'm able to convince our IT and our administration to. UC Berkley was one of the first schools on iTunes University, they want a public collaboration of iTunes University sites. And they're trying to organize something, I like that, which we'd love to be a part of we're doing a project, hopefully, Russ's department's doing a project with India, be great to share information with them. Currently we don't have that ability.

Man 2: The thing about sharing information is you're putting your knowledge, you're testing your knowledge, and you're vetting what you've done with a wider population. You're going to get feedback that's probably sometimes wrong, and maybe unprofessional, I don't know, but the point is they're going to look at it; they're going to give you ideas. This is good, this is not so good. And that's what we're looking for.

Russ: It is my impression that in terms of the iTunes you service and the contract they are offering these institutions, it is possible to implement your particular iTunes U so that you have both a public area and a private course based areas as well.

Brian: Correct.

Russ: So it's just how your units have implemented, other schools have implemented a more open space versus closed private space.

Brian: Right, there's four levels, one completely open, UC Berkley was completely open, they now have a private side, they actually have a separate installation. You can have public and private within the same. You can have all private, and you can have it to a point were if I'm registered in L342, Spanish 1, only those students see that content, you have to have a full LDAP authentication model, which we don't have.

If you have Blackboard Enterprise, it works seamlessly. Because it just dumps the data from our version of data to Enterprise into the system. We don't have that ability. So we would like that public and private side, if a professor wants to make it private, OK, fine I'll let you do it, but we want the public side too on the same.

Man 1: This had never occurred to me, is there a way to get your data back? Like, say somebody uploaded something and then they loose it, which...

Brian: That's a good question.

Woman 1: Maybe Apple looses it? or...

Brian: Is that what you're saying? Because this is hosted at Apple.

Man 1: No, that's what I mean, since you have no physical control, I guess my question is, if a student, or even a faculty member, uploads something important and then they inadvertently wipe the disk...

Man 3: Where's the backup?

Man 1:...yeah...

Brian: In Cupertino, California. I guess we could travel out there to hound them to do it.

Woman 1: No, in fact I talked to the IT people and said, we're totally responsible for backing it up.

Brian: It's in the contract.

Woman 1: Yeah, they would help us, but obviously since the server is in California, they provide those so you can connect to it so that you could make a backup.

Brian: Right. And you can take it one step further, if you decide to move away from this after two years, eventually, they said by the end of the year, they're going to have a way that you can download all of your course material, directly. It will be a function within the administration section. They promised by the end of the year.

Woman 2: I think I remember this coming out about a year ago, that they were giving this away free to everybody, but that they would encourage you to strongly suggest the student use iPod Nano MP3 players. Can you get around that? Can you use any MP3 player? Because all of those...

Brian: The video, they can use Zune if they have it, I know SanDisk has a video MP3 player. You do need at least a video player to see the enhanced or the video. But we've kept the word iPod out of all, unless we've done raffles as part of PR, we've kept iPod completely out of the terminology. They encourage it of course.

Man 3: But iTunes, you can't, because everybody has to use it then.

Peer Review in the Google Age Morrison

2006-04-10T06:23:00.000-04:00

Screencast

Peer Review, Heather Morrison

Heather Morrison: This is Heather Morrison, author of the blog "The Imaginary Journal of Poetic Economics," talking about open peer review and collaboration. Peer review is a tradition that has been around for a very long time. As Peggy and Jay have told us, there has been a very great deal of research on peer review, hundreds of thousands of articles. We learn by building on traditions like peer review, but we also learn by challenging some of our basic assumptions.

So let's look at some of the basic assumptions behind peer review. Is it necessary at all? Is the answer to this question the same in every research area? If it is necessary, do we need to continue to do it in the traditional way, or are there new approaches which would allow us to do a lot more?

The expert might not need peer review at all. After all, they can review the article and decide for themselves. For most of us, however, everyone from the general public to the researcher reading outside their own area of specialty, peer review does provide some assurance of quality control.

Ah, but how much assurance of quality control? From my experience, and here I'm not talking about the rare exceptions, but the regular everyday work of peer review, the range of quality is all the way from extremely poor to extremely thorough. For example, I once found an article in which the researcher concluded that the reason human subjects could not memorize nonsense syllables because they could not extract the meaning. How did this pass peer review? On the other hand, I have interviewed a researcher in the area of pharmacology who was extremely thorough, checking all of the article, checking all of the references.

Does peer review have the same meaning and significance in every research area? In my opinion, no. In the area of pharmacology and toxicology the difference between a drive in poison can be the dose, a matter of life and death. Here we would want to be very, very careful about messing around with peer review. We'd want to be very sure that we have another method of quality control that was just as good, if not better. But this is not true in every research area. Consider, for example, literary opinion. If something has passed that probably should not have passed peer review, this is not good, but it's certainly not a matter of life and death. What I'm trying to say here is that in some areas of research there's probably a lot more scope to experiment with new methods of peer review than there is with others.

There are many ways to experiment with peer review. In my blog, "The Imaginary Journal of Poetic Economics," I talk about one theoretical model for a new way of doing peer review. The idea is to have a process that is completely open and transparent. Peer reviewers sign their work and the peer reviews, along with the articles, are openly accessible to anyone.

As much as the processes as possible are automated. For example, there could be a profile of the reviewer up on the web, which ties to a calendaring system, which would know when the reviewer is available. This model could potentially accomplish a number of goals. The openness and transparency would facilitate research to improve peer review. Science literacy could be enhanced. This is because high school students, undergrads and people in developing countries could all see the peer review process in action. The automation aspects would introduce some cost efficiencies into the scholarly publishing system.

But what is most exciting to me is the potential of this model to facilitate new means of collaboration that would work well across the global. Imagine, for example, that I put my profile up on the web. A researcher in a country on another continent could potentially find my peer reviewer profile and realize that I am available. Both of us could learn from this process. I, from learning about research in another country, and the other person from having a reviewer from a completely different background.

So far, we've talked about one new approach to peer review, after the article is written. But why wait? Why not talk to your peers about the research that you're thinking about doing. If there's a better research method, why not find out about it before you do the research, not after it's all done and you feel it's ready for publication. Research funders review projects before they even fund them. Why not share your data as soon as it is ready? Perhaps one of your colleagues could use it for a different research question.

As a final thought, we advance our knowledge by working together, by sharing ideas and critique. Peer review has been a good method for doing this, and in some areas we need to be very careful to ensure that quality control is followed. But other areas, a research is not life and death, and here we can inform to experiment to less.

Peer Review in the Google Age Dominy

2006-03-15T12:47:00.000-05:00

Screencast/Podcast

Peer Review in the Google Age Dominy


Peggy Dominy:	Hi I'm Peggy Dominy, and we are going to be going through my PowerPoint that Jay and I kind of collaborated on. So, forgive me if I am a little anal here, I have to go back to the beginnings. Where did peer review begin? Some believe that it goes back as far as the seventeenth century and was known as the inquisition of the Holy Roman and Catholic Church. Scholars' works were examined for hints of heresy and we see the first victim of peer review as Galileo has to recant what he wrote. But in modern times what is it used in? Well, peer review it is used in a variety of places. We've been talking more or less about the publication process, but it is also used in the awarding of funding research and in patents and in standards. Although all of these use slightly different practices, ultimately it's colleagues evaluating each other. Maybe this is old hat for some of us, but what is the process of peer review? A paper is submitted, the editor will select one or two or three scholars from a pool of volunteers, and I want to emphasize that these are volunteers, to read and evaluate the paper. Typically it's a double blind process, the author doesn't know who the reviewers are, the reviewer doesn't know who the authors are. Although, in reality, if you have a very small universe of scientists you recognize the writing of people so you tend to know your reviewers are, you tend to know who the authors are anyway. But, supposedly it's a double blind process, that way only the merits of the paper are evaluated. Supposedly, within a reasonable amount of time the reviewers respond, it's up to the author to reply or comply with the reviewers comments. This can go back and forth adding months to a publishing process, and this is what we historically know. In the modern age, with electronic sending of text back and forth this process has certainly sped up, but the imposition on the overburdened scientist has not changed. Why do peer review? Well, it is a filter. More papers are submitted than could be printed. And I put that in quotes now. You use it to eliminate bad science, you use it to eliminate pseudo science or harmful science. It's also an aura of quality, only the best gets in. It's also a collegial stamp of approval, your colleagues have said "This is good, publish it.". Also, within a particular discipline, it's your obligation to the principles of your discipline, how you keep the high levels of integrity of your discipline. So, what's the problem? This is a very busy slide, I won't go through all of it. Essentially there are three problems to peer review. Not all papers get peer reviewed, even if they are in a journal that normally does peer review. Sometimes it's a good thing like Watson and Crick's paper on DNA structure, the editor realized right away this does not need peer review and put it right in. But then you also have a situation of Allan Sokal's paper did not get peer review it and it actually turned out to be a hoax, so not every paper gets peer reviewed. Some papers were published, passed peer review and turned out to be fraudulent. We have some examples there. Then we have famous papers that actually got rejected and then turned out to the seminal works. We have the famous example of Krebs and Johnson's paper on the role of citric acid on metabolism which turned out to be how cells convert food into energy, it's now known as the Krebs cycle if he got a Nobel prize for it. So, we do have these examples where peer review breaks down. So who's worried about peer review now? A simple search on Google, and I know this is not scientific, I went into Google Scholar, I put in peer review as a phrase. You can limit by different disciplines, naturally these are very broad disciplines, but you can get an idea about who's writing about peer review in these various broad disciplines. Again, I don't claim that this is scientific, but I think the numbers of pretty impressive. Two recent articles, why we are even here today, "Is Peer Review Broken" by Alison McCook from the Scientist and new journals are starting to take away the blind process of the reviewers, making them public. Is this a good thing or bad thing? Papers are published on the web without the constraint of peer review, you can put anything you want, it's out there. Also, papers can be published on the web with the constraints of peer review. So, what's the difference? Without constraints, it's a wild and open area, there's no gate keepers, no censors. So, if you have this wide open area and there is good stuff amongst all the bad stuff, will the good stuff percolate out? Who's got the discernment, where is the discernment, how do you know if it's good and where is the authority? These are the questions. With the constraints, the good stuff is vetted, scholarship is monitored and maintained, exposure beyond that the internet. I mean this because if you are in a peer reviewed established journal your stuff gets indexed and extracted into a lot of different databases, so when people are searching these databases your stuff is exposed, which might not happen if it's just out there on the internet. There are lots of publishers out there sharing their content with the internet, in other words, these publishers are allowing you to put up a preprint or a PDF form of your paper on your own website as long as it's not the "final version" but it will be allowed to put up as open access and accessible and this is just a short list of publishers that are allowing this. It's not perfect, there's grist for lots of mills, the web has made it less of an obstacle to access. When you are published in a peer review journal you had to be able to subscribe to it, that meant money. A lot of people weren't able to subscribe to these expensive journals that were highly peer reviewed, so there was always an obstacle to your information if it was in a peer review journal. The web has made that less of an obstacle. Defend disciplines have different perspectives, they have different issues. In some disciplines they are more concerned with funding, is peer review fair in funding. Is there sexism or prejudices that come out in peer review? Other people not getting fair treatment? But also I think at least from Jay's and my own point of view as librarians there is also a pedagogical reason for peer review. It's a yardstick for students. There's got to be something that tells a student that this is good stuff. They have not develop their skills or discerning yet to determine whether something is good or not. So we see it as a pedagogical yardstick. There is all sorts of collegial peer review on the internet and we just go through a few these, there's email, wikis, blogs that's essentially peer review right there, that's opened up. Yes Jay?
Jay Bhatt:	Can you just click on the link "Blogging as Tool"? This is an example of a post publication comment, this is a paper that I got published in the Library HiTech News and some of my colleagues were looking at this paper. When you scroll down you will see the comments posted about the paper and you can see at the top one of the comments was posted by my colleague, a library information professional, which we would value their comments very much. Not only has that person critiqued my paper, but also provided some valuable positions. This kind of dialogue is only possible because of the internet and that really enhances the quality of the paper.
Peggy Dominy:	So, the internet has changed peer review in that it's more common, it's more informal peer review then what we've always had before which was more formal peer review.
Man:	This post publication blogging is a no brainer.
Man 2:	Absolutely.
Peggy Dominy:	I mentioned this before, also with authors putting their papers on the web, even though the papers themselves have gone through the peer review process it's making their papers more accessible, so you are removing a lot of the barrier of a subscription database or a subscription journal. We're seeing more access to scientific literature as we see more and more institutions preserving their own publications. Again, we're talking about the global benefit here as scientists from less developed countries are able to put their own papers up on the web. You are seeing material and resources that you might not have otherwise had access to. Journals that come from other countries, that are in other languages in some cases, would not necessarily find their way into your library. Finally, I won't go any further here but this is just a brief bibliography. When I started looking at peer review I was overwhelmed by the amount of literature on the topic. People have been worried about this for a long time. Again, it's quite interesting to see from the different perspectives of different disciplines what about peer review they're worried. It's fascinating. This is a very short list, you can look at your leisure. Are there any questions, comments?
Man:	I have a question. You were saying that normally the peer review is double blind. I know in chemistry we have never experienced that. The reviewers always know who the paper is from. Are there some fields where that is not true?
Peggy Dominy:	Yes. In other fields that is -.
Man:	Like what?
Peggy Dominy:	Physics, anthropology I know for sure. My son, who not only is an author, but is also a reviewer, he often doesn't know who the author is. He doesn't know who the reviewers are, but by their comments he is able to...

Peer Review in the Google Age Bradley

2006-03-04T04:12:00.000-05:00

Screencast/Podcast

Peer Review in the Google Age - JC Bradley


JC Bradley:	Ok, so this is our 22nd RSS club meeting, it's a special meeting that's going to be on peer review in the Google age. This follows up on a blog post that I put in, having to do with how being able to search on Google and these kinds of search engines actually changes or might change in the future the way that scientists use peer review. I've invited a couple of librarians, we've got Jay Bhatt and Peggy Dominy from our Drexel Haggerty Library. I have Heather Morrison from Simon Fraser University that is connected to us via NetMeeting. Can you still hear us Heather?
Heather:	Yes I can.
JC Bradley:	Ok, so she'll be giving a talk after we do here, and hopefully all the technology will work and this will be recorded and everybody who was not able to attend will be able to benefit from it. So I want to keep this fairly short. I'm basically going to give you the perspective of the scientists, because I think the librarians will give you their viewpoint of what's happening here, but for me the important thing with peer review is, before the Internet and after the Internet, how that's actually changed it. I remember as a Grad student, using the books, there was no way to electronically search, or if there were we couldn't afford it. You know, to search if other people had been working on your area, and it was a very, very time consuming process, because you'd have to go into these big books, and once you found a reference you had to look in another book, and then you had to find out if the library actually carried that, and if it didn't, what are you going to do? So, peer review, actually, the way I used it as a scientist was to make a decision as to how much time I should spend trying to hunt down a particular reference. So if I was looking for a synthetic strategy, and I found a Journal of Organic Chemistry article, I knew that would be worth getting. Well, first of all, I knew the library had it, and secondly I knew that you could follow their experimental section pretty well, and same thing with the Journal of the American Chemical Society and all of these things. If there was something you didn't recognize, now unless I was really desperate, I would just skip it, because it was so time consuming. But what's happened now is we're no longer in that situation, at least we shouldn't be, and there's no reason to be anymore. Now search is actually extremely fast and extremely easy and there are open tools that Jay's actually talked about, Google Scholar and these different free services, there's also SciFinder that is a pay service and will get you, usually, better information. But there's actually quite a bit on the Google Scholar, on the research we've been doing lately. What's interesting here is I'm not really that interested in whether the article is peer reviewed or not. I'm more interested in, do they have the experimental conditions for the compound that I'm trying to make, and I can judge whether their description of the experimental is actually valid, or how likely is it to be good, just based on the way in which they describe it. So it's kind of an interesting situation, because, I'm not using peer review in the way that I used to use it, to protect my time. So now it's something completely different that determines the value of an article. It's whether or not I can get it online immediately, and if I can't I usually don't bother. Again, unless I'm very desperate, and then I'll try to hunt it down. But honestly there's so much repetition now in the scientific literature that you can usually find what you're looking for online directly, or at least know that it hasn't been done, that's the other way to look at it. So, here peer review is actually changing, for one more reason, because in the past there were far fewer publications and those publications had a pretty long life before you got to them. So you could really understand and get to know these various publications. Today, really anyone can set up a journal online and can call it peer reviewed and you don't even who the peers are, because almost by definition they're anonymous. So, I could decide that you guys are all peers in something, and you would validate or not, and so I think that simply stamping something being peer reviewed or not, today, doesn't make much sense. I think if we say that something is in the Journal of Organic Chemistry and it was peer reviewed, that still has meaning, because the editors are going to use the same set of reviewers, and they have a whole system in place to maintain their quality and their trend, or what they're trying to focus on. So I think this has definitely changed. Again, this whole idea of what does peer review mean today, from the scientist's perspective, it has to do with when you come up for tenure or promotion, justifying the value of your scholarship. When you report the papers that you have, you have the peer reviewed and the non-peer reviewed. Then again, if you have a paper that you don't even know who the reviewers are, it's a new journal that just came up, what does it really mean? Or if you do a conference proceedings, that's supposedly peer reviewed, but we all know how closely the reviewers usually look at that. I think it's a term that we might have to refine a little bit more, just exactly what we mean. I think that, in terms of peer review we have to remember there are two separate problems here. One of them is communicating science; how do I communicate my science to another scientist, which is completely different from justifying myself once a year, as to what I've done. I'll show you some alternate ways of communicating science that don't include peer review and that might actually be useful. In the journal article, The Best Way of Communicating Science, here's an example of where we've recently been using a public blog, a simple Blogger account, and just using it as a research notebook. It's been really interesting to see how people around the world have been responding to that. Here's an example of an experiment, which is a fairly complex experiment. It's called a UG reaction, and it involves mixing four components together, and making this compound. As we report this, this experiment is not actually completed yet. It's still going on and we're still waiting to collect the data. But what's interesting is that people have been coming in and putting comments. So here we've got, Matt Todd, who's actually an Australian chemist, and he made a comment that, "You know, a quick comment on this reaction. You're trying to do a condensation, so a high concentration of reagents would be favorable. I think your current level of milligram per milliliter is quite dilute, try it again in five mils of methanol". So this actually has no analogue in the normal print. This is an experiment that not only hasn't been published formally, but hasn't even been finished. We're in the process of doing it, and already people are responding to us. That's why I see the power of these new technologies in doing science. It's that you can actually do something at a different level of immediacy. So there's a lot of these examples, I just wanted to highlight a couple of things. The other way in which we can have connections is through looking at how people are finding your blog. There's a little tool called Sitemeter, that is free, that you can put at the bottom of your blog and find out how people are finding it. Here's an interesting thing, when I looked at, recently, the Sitemeter listings, one of them was for adrenaline decomposed, and here is the actual entry inside of our lab notebook, where we actually used adrenaline, and the contents of the reaction lies decomposed, and we aborted this experiment. So this is an experiment that would never make it in a normal publication, because it was aborted, something went wrong. But the person who was looking for adrenaline decomposed, which is interesting because they're searching for English and Japanese and they're actually in Jersey, so who knows who these people are that are looking for this. But the point is, if they were looking for a way that adrenaline can decompose, they found it, and this would never make it a normal journal. So those are some of the elements that are coming together. I don't want to talk long here, because a lot of this I've actually written in the blog and I can give you links to go to that. But just to put it out on the table, there are lots of these little information aggregators, or people trying to do this kind of thing that are kicking around, and it's a completely decentralized operation. You know, I started this, using Blogger to report our lab results. There are other people, the Synaptic Leap, these are people who do Open Source biomedical research. They, so far, have not actually put experimental results but they've actually been talking about, you know, "What do we need to do to solve things like Malaria and other tropical diseases?" So these are connected, all these arrows show that there's some kind of link, some kind of Internet link between each of these. The one that we were looking at is the Useful Chem Experiments blog, where that's actually the hardcore experimental details, every last detail of how to do stuff in the lab. This is connected to the Useful Chem Wiki that has a high level of organization, so if you wanted to see the big picture, you go to the Wiki. The Useful Chem blog is where we discuss synthesis, synthetic strategies, what's important, what's not important. The Useful Chem Molecules actually is a blog that has each of the molecules we're working with in a separate post. So all of these are completely interconnected and you can follow from one to the other. The point I wanted to make on this slide, is we're doing all this, and we're doing this in the open, and then the Synaptic Leap basically said that they were looking for an alternate synthesis for a drug that's currently effective in one of the tropical diseases. And at the same time, well, very shortly after, that was put in the Useful Chem blog, this company, Chemrefer, these are people that search the literature for free for you, and answer chemical questions, and their plan is to make money by advertising. But they have an RSS feed to our Useful Chem blog, so when they saw that people were looking for that, they came in and found a thesis that was not already in the database that everybody was looking at. So I thought that was kind of cool, because that's actually a commercial sector that is connecting, doing Open Source science for free, and trying to find a way to make money at it. This is a very, very small snapshot of everything that's happening in Open Source right now, but I think that it gives you a good perspective on how things can go very quickly in the future. So that's pretty much all I wanted to do on my side. On the last slide here, there is a link to the Useful Chem Wiki, Usefulchem.wikispaces.com, and we've got a summary of everything that I just told you here, and I also have some links to some other people who are doing Open Source science. So Open Wetware, Bioroot archive, NABOJ, Physics Comment, all of these are sites that actually have experimental details, and then you have Open Source coordinating sites, Synaptic Leap we were just looking at, Chemists without Borders, World Community Grid, Bioforge, CODATA, and the ACS actually just started a chemical biology Wiki, which I'm not sure if you're aware of that, but it's kind of interesting. So these are actually, there's no experimental details here yet, and there may not be, but that's fine, because these people are coordinating one group with another and that's just as useful as putting primary data. At the very bottom here I gave you some links to some general information on Open Source science. So there's a presentation there and a couple of things. So that's pretty much all I wanted to talk about. We've got a couple of minutes, do you have any comments?
Woman1:	You mentioned the chemist from Australia suggested a higher concentration for your experiment. So you're going to get comments and statements from all over the place, when you put your experiment out there for the world to see. In the traditional sense of, you've got the interaction with the colleague next door, in the office down the hallway or something like that, and this has opened up your connections, but then how do you in your paper, how do you acknowledge contribution like that?
JC Bradley:	The contributions, you mean in the final paper?
Woman1:	Yes.
JC Bradley:	Well, most of this stuff will never be published in a formal paper, because I can't publish a failed experiment. If you try, you'll see it's very, very difficult. A paper has a small fraction of all the experiments that you ever did, and it has to tell a story. It can't just be random experiments put together. Of course, if I do end up using them, I'll put them in the acknowledgments, but it's pretty unlikely that I would use those experiments ultimately.
Woman2:	How do you work that in to the typical paper?
JC Bradley:	Well, you know it's also possible that someone would really get involved, and we'd have a true collaboration. That could happen also. I hope that happens at some point. Heather Morrison: This is Heather, I'm wondering if one possibility there, to have that acknowledgment, rather than it be in the formal paper, would be to have the paper have a link to the blog with the comment on it.
JC Bradley:	Yes, Heather, absolutely, when we publish this stuff, there would definitely be a link as a reference, because this is the first official publication. Much in the same way that if you go to a conference and you give a talk and you disclose things, that's a publication, it's a disclosure in terms of patent rights and all that stuff. So it's nothing new in that sense, it's just a different modality of doing it.
Jay Bhatt:	What I would like to add is, these new means of communication like Wiki and blogs have resulted in an enormous amount of opportunities in terms of communicating with other fields which I believe that these other peers are going to give you feedback on your own research ideas and topics, and that will really help to go forth the research, and I think the new Internet has created this enormous potential, and people and scientists all over the world have started to take advantage of these opportunities. [xx] [xx] [xx] [xx] Bloglines, if people subscribe to these, they can get RSS feeds, can monitor thousands of feeds in a very short amount of time, and also be able to give positive feedback in the process.
JC Bradley:	Yeah, Jay makes a good point. One of the things that maybe I didn't make very explicit, is the reason that I'm using Blogger or one big reason, is that I can easily put RSS feeds. So this Praziquantel, that was the drug that I was talking about earlier, and you see here that I have the standard RSS feed, so Chemrefer was probably subscribed through RSS. The idea is that if you have a bunch of scientists working together, nothing is faster than RSS. As soon as it's put in the blog, everybody in the group knows that we've done another experiment.

Workshop 1 How to create a podcast

2005-12-25T07:05:00.000-05:00

Transcript of podcast Workshop 1 How to create a podcast

provided by:

Workshop 1: How to create a podcast


Professor Bradley:	We have just enough time, why don't we do this. I want to set up a blog for you. Okay so we're going to go to Blogger. And I don't want to log in as myself. So, I'll...
Male Student:	Yes that's fine.
Professor Bradley:	And, I will tell you the password after we're done here. You can change it later. All right put your full name. You can even delete this thing after. You know if you don't like it. And?
Male Student:	Smp42h.
Professor Bradley:	Okay, so we accept the terms of service. Oh it's already taken.
Male Student:	I think that was me actually.
Professor Bradley:	All right. 6 characters. That should all be good. Okay so this is the one that we're going to do for the conference.
Male Student:	Yeah, yeah. So it'll be hbes@hbes2006.
Professor Bradley:	Hbes?
Male Student:	Yes.
Professor Bradley:	Okay Now we're going to do the same thing over here. Under the blog address. See we're typing in the word verification. And then you choose a template, which again you can change at any time.
Male Student:	Okay.
Professor Bradley:	I kind of like the Rounders 3.
Male Student:	Okay.
Professor Bradley:	I like it for the colors.
Male Student:	[laughs]
Professor Bradley:	Well some of them are on black, which is hard to read. So that's it. Now you've got your blog. Okay, so this will be for example your first session.
Male Student:	Oh okay.
Professor Bradley:	Okay, so you would say 'this guy talked too much. He just explained what you did.' Right. So we're going to publish that. Okay so now you've created your first blog. You've created your first post. We can view the blog. So this is the first post. Now we need an MP3 file. But before we do that, lets go back and put your settings up. There's a couple of things you would have to worry about. Let's start at the right. So members. Lets say you wanted me to contribute. You can just invite me. You would just 'Add team member'. Put my email in it. And then I would become a member. By default I'm not allowed to modify the settings. But I can write my own posts. But you can promote someone to be an administrator also.
Male Student:	Oh okay.
Professor Bradley:	There's actually a way you can email to Blogger, instead of logging in. I've never done it, and I don't really see the point of it right now. The site feed. This is if someone wanted to subscribe to your blog. If you didn't do anything else you'd have to give him his Atom feed.
Male Student:	Okay.
Professor Bradley:	But we're not going to be doing that, for some reasons that'll become obvious. Archiving. So I would just leave all this as default.
Male Student:	Okay
Professor Bradley:	Comments. We want to show the comments. We want to let anyone comment.
Male Student:	Okay. That means it's open. It's not just to the members that I ask to join.
Professor Bradley:	Yeah, anyone can comment. Fill the backlinks.
Male Student:	What are backlinks?
Professor Bradley:	This is actually a new thing that they have. I think it's when people are pointing to your blog. It's kind of like a trackback. I haven't used it yet. And the time format. You can change that later. Word Verification. Always put yes to this. Because if you don't people are going to spam you.
Male Student:	Oh okay.
Professor Bradley:	And it's funny how they do it. 'I really like your blog. Come and buy my Viagra.'
Male Student:	[laughs]
Professor Bradley:	It's always got that format. I can't possibly believe that it actually works.
Male Student:	It's an automated thing, so they can't do the word verification.
Professor Bradley:	Exactly, because they got bots going all around and filling it out. This is also new. Comment moderation. You can have it so that before the comment appears on the blog. You get an email that you have to agree to. That's just a couple of weeks...
Male Student:	That is a nice feature.
Professor Bradley:	And definitely do this, so whats your email address again?
Male Student:	Smp43.
Professor Bradley:	So this will email you whenever somebody puts a comment.
Male Student:	Oh nice.
Professor Bradley:	Otherwise you wouldn't know.
Male Student:	Right.
Professor Bradley:	Usually you have to republish the blog. Okay, lets go back to settings. So we did comments. Okay so for the formatting, it defaults to 7 days.
Male Student:	Okay.
Professor Bradley:	And I don't like that. I put 999 posts. Reason for that is if you only use 7 days, it will keep fragmenting your blog. And it will make it harder for people to find it. For example if somebody uses a keyword combination, and you talked about psychology here, and you talked about chemistry. If you wanted somebody to find that in a Blogger search as an AND query, you would have had to have posted within the seven days.
Male Student:	Oh, I see. Okay.
Professor Bradley:	Now this way makes it a lot longer. And if it's too long you can always come here and change it. But I always leave it like this until it turns into a problem. You can play around with all this stuff. Time stamp. Time zone is defaulted to California. So you want to change that. I have no idea why they have all these lists, but they do. Encoding, that's all fine. All this just leave like that. Save Settings. And then you've got to republish it.
Male Student:	So any changes you make you have to republish it?
Professor Bradley:	It'll tell you when you have to republish the whole thing. And we are almost done. We also have to go to the publishing. Notify weblogs. This will make sure your blog gets archived. I don't know why defaults the 'no' but it does. Once again we republish. Okay, so the last thing we have to do here is, you can put a description. This is about a psychology conference. You can go back and change that. And I don't think you need to change email post links. I haven't used it, but if it's a little mail I found.
Male Student:	Okay
Professor Bradley:	Lets say you found a post that you liked. You want to send it to Mike, you just click on the mail icon. Oh okay. But you know it's not a big deal either way. So we are going to save the settings. So this is how I set up all my blogs. It would be nice if I could just apply a button.
Male Student:	Right.
Professor Bradley:	But I don't know anyway to do it. Okay so we're actually going to have to come back to this, but we're going to have to set up your RSS feed.
Male Student:	Okay.
Professor Bradley:	Before we can come back to this. But as far as Blogger is concerned, you're done.
Male Student:	Now I can go in and edit, and other people can too.
Professor Bradley:	Other people can comment.
Male Student:	Comment. Right. Ok. Right.
Professor Bradley:	But they can't ask them unless you invite them.
Male Student:	Okay.
Professor Bradley:	Which is the big difference between a wiki and a blog. In a wiki usually anyone can modify it.
Male Student:	Right
Professor Bradley:	So the only other thing that we wanted to do is go to Feedburner. And I have to... Okay I'm not signed in. Actually lets go back. This is the URL to your blog.
Male Student:	Okay.
Professor Bradley:	We're going to copy that URL and we are going to go to Feedburner. We are going to paste that here. We are going to say you are a podcaster. Actually I hope it doesn't think it's me here. Lets see. Create an account password? Sm43?
Male Student:	Smp43.
Professor Bradley:	And we are just going to activate the feed. Okay great. So now you actually have an RSS feed.
Male Student:	Okay.
Professor Bradley:	So that means that people can subscribe to that feed and you can count them. That's the first thing that it does. In the Blogger people could subscribe to your feed, but you would have no idea of how many people were subscribed or how they were subscribed.
Male Student:	Okay.
Professor Bradley:	So now you have a feed.
Male Student:	And you can subscribe to it. Does that mean they get updates? Is that how it works? They can check updates or that sort of thing?
Professor Bradley:	Yeah, like they'll be using something like Bloglines.
Male Student:	Okay
Professor Bradley:	So you can see here I've got all these feeds.
Male Student:	Yeah.
Professor Bradley:	Just to go to some recent ones, like here's a feed for Drexel University. So it shows up bold if there are any new feeds, and we are just going to activate this. So basically, Drexel is searching for [xx] library or something, but you can see.. Actually here's a good one. You can see actually a course from Michelle Francl from Bryn Mawr.
Male Student:	Okay.
Professor Bradley:	And here is her class today. It's on quantum chemistry.
Male Student:	Okay
Professor Bradley:	So basically that's how it's going to show up for your students. But in order to do that we have to finish the feedburner. So while we're in the feedburner, we are going to see if the smartcast is selected. We are going to look a little bit closer at the smartcast and this is where you talk about iTunes. So you can actually podcast anything you want theoretically. I podcast my PDFs as well as my MP3s.
Male Student:	Okay.
Professor Bradley:	So that students can listen to it, rather than watch it. You can podcast powerpoints, but iTunes doesn't support that, or rather didn't the last time I checked.
Male Student:	Okay.
Professor Bradley:	But if you use another podcatcher, like iPodder, it will in fact read the PowerPoints. Just a little something to keep in mind if you want to do more than audio. But you can only do one per file. So if you've got your PDF, your MP3, and whatever else. It's going to default to the MP3 first. But if you don't have an MP3, it'll do the PDF.
Male Student:	Oh okay.
Professor Bradley:	So, but you can't do more than one. So I do an extra post. That's why you see an extra post and it's just the PDF, so that it'll podcast. You can play around with this. Any media rich file. You can put a picture of yourself here. You can describe it. You can put your keywords. I'll let you do that later. You can say that it's porn, which I haven't had to use so far. And you can also put your copyright message here. You can say 'Use with attribution. Only non-commercial.' So we can discuss that in another point, the whole copyright thing. So I'm going to save this file. Lets see, you're actually set up to do a podcast now and the last thing we want to do is publicize it. So how are people actually going to find that they should subscribe to you. Well, see I'm under publicize in feedburner. There's a friendly thing called chiclet. I'm going to put the XML chiclet on your blogger. So the way I do that is very simple.
Male Student:	It's called a chiclet?
Professor Bradley:	It's called a chiclet, yeah. Then I highlight than code. Control-C that. Now we are going to go back. Choose your Blogger account, and we're going to the template. Now the template in Blogger is actually all of the HTML and we are going to have to modify that. You don't need to delete anything here because you need all of this stuff. But there's a little place a little bit past the middle that says blog header. We want to go right into the middle of that right under your blog title. And we want to dump that code.
Male Student:	Is it necessary that it goes there.
Professor Bradley:	I put it there, but it can go anywhere you want. I just like it there on the top.
Male Student:	Okay.
Professor Bradley:	Yeah you can go back and change this. The other thing we want to do is put a subscribe using bloglines button.
Male Student:	Okay.
Professor Bradley:	Because if people have never heard of RSS, it's going to be hard to explain to them how to actually do it, but by having this button. It'll automatically take them to bloglines. Okay so then I go back. Over here and I want to put it in the next line like that. And you can keep putting whatever you want here. Let's look at a preview, and make sure we are doing the right thing. So you can see it shows up here. Okay so we want the preview. And let's save the template changes. And this is one of them you have to republish. Okay. Now look how sweet this is. Now you've got your blog. Anyone can now click on this bloglines button. And it will take them to bloglines. And if they don't have an account it'll ask them to create a bloglines account.
Male Student:	Okay.
Professor Bradley:	And I'm going to put your blog in my highest priority for now. All right. So now I am subscribed, and it'll show up probably as the last one of this folder. Shold show up right at the end of this. Here it is. You see that. One unread post. Click on it. 'this guy talks too much.' So ten minutes you got your blog. You got your RSS feed. Now this is what you can do with Feedburner even more. Just going to go back to the publicize. Lets look at the analyze. It recorder that I had that one subscription. Okay. You can see the circulation. You can see the readership, so you can tell what kind of people are reading it. You can look at Atom stats. Looks like they upgraded this one, which is not a big deal. Click on standard stats. This is the first time you do it, it's asking you to. Actually because it's only one, it's not showing the graphic, but what you will see here is a pie chart. It will show you, you know so many Blogliner subscribers, so many Newsgater subscribers, and it'll show you how many iTunes subscribers you have. So you can tell how many people are reading your podcast and how many are looking at your text. And the only thing we haven't done here, because we've just run out of time is you're going to have to upload an MP3 file, anyways I've got to create an account for you. I have an account created. And maybe do a quick recording and you can upload that file. And all you have to do is make a link to it. Inside of your Blogger account, and a link is as easy as doing this. I'm going to edit this guy. All right. Is I would do this. Here is the MP3. And you can highlight that. You can click on the link...Now actually Feedburner is smart. It'll detect that you've got a file there.
Male Student:	Okay.
Professor Bradley:	And it'll convert it to a podcast.
Male Student:	Really.
Professor Bradley:	You're done. So that's it. So there's a couple of things you didn't see here either, right.
Female Student:	Yeah, it was a great review too.
Professor Bradley:	Right, I'm going to terminate this...