bbgm - the discussion - Latest Comments

Re: The hypocrisy of academia

Tom Roud — Wed, 10 Mar 2010 15:42:26 -0000

Well, well, I do not think this is so true. In many places, PIs have to pay most of the things from their grants, from their students to the software licenses, and also even have to pay a fixed share of their grants to the university just to have lab space. So they are very aware that labor (AKA grad students) is not free (most of the time). The other thing is that I think you underestimate considerably what really is expensive : when you need to get money to buy a 200 000 $ microscope, I do not think you really care about paying a subscription to Nature or an annual 200 $ license to use a software.

Re: The hypocrisy of academia

Gregg TeHennepe — Wed, 10 Mar 2010 08:16:57 -0000

Check out the five presentations at #10 on this list around funding IT infrastructure for research: http://www.airi.org/about/detail.aspx?id=86.

Re: BioStar – A bioinformatics stackexchange

Melanie — Mon, 08 Mar 2010 17:12:37 -0000

And there went my lunch hour...

Thanks for this, though- I was aware of StackOverflow, but hadn't seen StackExchange or BioStar

Re: The hypocrisy of academia

martijnvaniersel — Mon, 08 Mar 2010 06:45:52 -0000

I totally agree that academia hides costs. You often see that when there is a choice between something that saves money and something that saves time (e.g new equipment or software), the choice is nearly always for the cheap option - because peoples time is practically a sunk cost. Think of all the labs that are still purifying their own Taq polymerase.

On the other hand, there is a plus side. Academia is there to focus on the long term, something that companies can't or are unwilling to do. Worrying about costs encourages short-term thinking. These are two sides of the same medal. A certain amount of inefficiency is the price that you have to pay for safeguarding some long-term thinking in our society.

I think open science and open access are long-term strategies that do not always make (financial) short-term sense.

Re: The hypocrisy of academia

Jerm — Sun, 07 Mar 2010 21:05:40 -0000

Strong words - fight the power!! Let's expose those hypocrites one by one!

Re: BioStar – A bioinformatics stackexchange

facebook-24405444 — Fri, 05 Mar 2010 23:58:59 -0000

A fascinating look. I've got some thoughts on the practice of establishing Knowledge Trading Zones (what a horrible term, do you have a better one?) like these here (please properly linkify that, I'm not sure if HTML is supported here.): http://www.urgentevoke.com/profiles/blogs/the-i...

More to the point, I'd love to get your feedback on applying a stack overflow model to something like EVOKE.

Re: The distributed web of data – messaging included

Jack Vaughan — Mon, 22 Feb 2010 12:12:26 -0000

Wondering if this paradigm shift in computing architeture wont take quite awhile to occur..when one gets into it they may next decide that XML is not the way to go...and then a generation of re-writes is required...

Re: Science Online 2010 – Where are the geeks?

varunimast — Sat, 06 Feb 2010 23:20:43 -0000

Science Online 2010 – Where are the geeks?

Re: Science Online 2010 – Where are the geeks?

mndoci — Tue, 26 Jan 2010 10:55:53 -0000

I am not sure I quite understand what you're getting at, but I've been in more than enough situations where just the mix of 20 smart people from very different backgrounds have come up with some killer discussion topics and had a ton of discussion.

Re: Science Online 2010 – Where are the geeks?

Radoslav Bozov — Tue, 26 Jan 2010 01:22:02 -0000

To have full success in science we need to integrate 3 biological theory, network, mutation and free radical. Don't be an illusionist that simply a gig, person who is highly intelligent will make sense of all that chaos. The problem is that science today is way to segregated, chemists care about selling drugs, biologist often ignore chemistry as expanding in space trows us in uncertainty. How do we deal with it? We need to bridge physics concepts with biological phenomena through comprehensive chemistry as we made teh first step of sequence technology, but that is no sufficient. Gentlemen and Ladies, this is just the beginning..Biotechnology must evolve, and integral part would play teh advancement of physical methods in spacial dynamic analysis although lagging, they come slow but secure. Then we can have parallel world interfering at some moment, when someone will say. Hey we can determine it. Why live in a chaos? It may be just that simple, but what eyes see is what mind chooses. The gigs are coming, and they are going to hit the world with a power you have never imagined. Just give them a chance, provide the environment and the output will be there.

Re: BridgeDB: Middleware for ID mapping

martijnvaniersel — Tue, 12 Jan 2010 15:55:56 -0000

@Neil That will never happen, for several reasons: First it would require a huge collaboration effort which is unpractical. Second, you need identifier mapping anyway for between e.g. microarray reporters and genes. Finally, the way identifiers are used depends on your point of view. For example, are lactate and lactic acid a single entity or two separate entities? The answer depends on whether you are a biologist or a chemist. See also http://www.helixsoft.nl/blog/?p=133

Re: BridgeDB: Middleware for ID mapping

martijnvaniersel — Tue, 12 Jan 2010 15:50:14 -0000

Thanks for the encouraging words.

Please let me know when you see those exceptions again. I really want to make sure that everything works "as advertised". You can email us at bridgedb-discuss {AT} googlegroups.com.

Re: Loosely coupled tools

neilfws — Tue, 22 Dec 2009 02:54:07 -0000

I also think we will, soon. Everywhere I look in web apps and APIs, I see the phrase "small pieces, loosely coupled", or some variant of it. It must be filtering down to even scientific software developers.

Re: Intelligence in Chaos

mndoci — Sat, 19 Dec 2009 01:37:04 -0000

Yes it was premature enthusiasm, but it's also true that to date we have not been successful, precisely because it is more complex that we thought it would be.

Re: Intelligence in Chaos

Shastri Philip — Sat, 19 Dec 2009 00:12:04 -0000

"we have spent a lot of time trying to develop an Artificial Intelligence, a task at which we have not been successful."

This statement or observation is not entirely correct. While it is true that we have not been able to attain our goal so far, we now understand that it was premature enthusiasm. We also understand that the task is more complex than what we once thought it is.

Shastri Philip
www.ShastriPhilip.Com

Re: Bioinformatics and mythology. You still need to manage the data

Anirban — Thu, 10 Dec 2009 17:04:51 -0000

Good blog-post. Biologists and computer scientists need to work together and two realize that there are two parallel approaches that can be done separately or in tandem.

1) Defining the biological problem and using technology to approach it.
2) Using technology to define biological problems that can be answered.

Re: Scaling out for analytics

chrisbaglieri — Sat, 05 Dec 2009 01:13:21 -0000

I concur and think you really hit the nail on the head when you mentioned the need for domain specific tooling. Non-engineers (and I'd even argue most engineers) will not speak raw map reduce natively. Pig, Hive, and Cascading get the job done in an elegant fashion, but in my opinion, the greatest potential for broad adoption in informatics hinges on the need for further abstraction. Rethinking algorithms that take advantage of such infrastructures out of box (think CrossBow and Bowtie) is a step in the right direction. Bundling and sharing AMIs another step in the right direction. Baby steps, but steps nonetheless.

Re: Academic software and infrastructure – AKA more ranting

mndoci — Mon, 30 Nov 2009 11:31:17 -0000

Sort of adding on to this discussion

1. Open Source does not preclude commercialization. You need to choose the appropriate license. The reason companies buy software is to get support, custom patches, more input into the dev cycle etc. There is an entire, well established model on how you can make this work.

2. The one problem with niche software is that it requires you to have licensing fees, the kind no one is willing to pay which is why scientific software companies do not usually make money for most algorithmic software (you can make money on platforms, data management solutions, etc). This makes open source even more attractive really as it broadens out development and results in better code. Think of CHARMM. I think one reason the software has not evolved in quality (it has had oodles of algorithms thrown in) is because it's not open source. IMO the benevolent dictator model works really well in these cases

Re: Academic software and infrastructure – AKA more ranting

harijay — Mon, 30 Nov 2009 10:00:35 -0000

I agree with you Cameron, a researcher needs to do research, not worry about funding mechanisms and such. It will be great when every researcher realizes that opening things up builds community in away that almost guarantees continuity and maybe eventually profitability.

It is also an unfortunate by-product of closed to non academics cases that "hobbyists" and non-profit users get caught in the crossfire , there is nothing worse than alienating the motivated.

But my point still is that , to demand or even expect academics to adopt open source because of funds coming from the public is unrealistic and impractical.

From my own experience , the best crystallography software I use happens to be split down the middle, 50% of them are closed source and non-free for non academics and the rest of them are free and open source. The going is equally good for both of them and I cannot live without either. I would never expect the non-free software to adopt the model of the free, because what they have going just works! If I have to stop using the non-free version because I move to a non-academic setting , then so be it! , I still have the free version to fall back on.

I think the best way to persuade academics to adopt open source is to adopt a "Gandhian" attitude to persuasion. Contribute selflessly and hope they see the point. If you are a hobbyist, I would email the author and request him to allow you to use it. If the email works great, if not just sit back and hope the software gets liberated sometime soon, or better yet fund an open source alternative.

Re: Academic software and infrastructure – AKA more ranting

CameronNeylon — Mon, 30 Nov 2009 05:08:36 -0000

Disagree pretty violently with this. It is not the responsibility of researchers to determine funding mechanisms to ensure the effective continuity of research outputs, it is the responsibility of funders to ensure that their (public) money is effectively spent. And if that includes funding continuity for important software projects (or data projects, or specialist materials) then we have to have that discussion.

Okay realistically this is not going to happen but given that the interest of the researchers is in having the software used, and in finding a way of keeping it supported surely it would be preferable to allow it to be available for any non-profit use? The more people using it the more likely it is for them to come up with something that might turn a profit - limiting use to people who have neither the time nor the inclination to actually make it useful seems farcical.

And of course, open sourcing it would be be even better in this regard :-)

Re: Academic software and infrastructure – AKA more ranting

mrflip — Sun, 29 Nov 2009 18:50:51 -0000

I recently tried to talk a friend out of going to grad school in bioinformatics (computer side), arguing that

* since he had no interest in further academic work -- only in the knowledge gained and the signaling mechanism thereto -- grad school is vastly expensive for that purpose
* interesting parts of the field are so immature that huge chunks are accessible to the motivated amateur: eg hadoop, command of the baseline machine learning toolkit
* armed with those tools, he can get a job to fill out his toolbox at a bioinformaticist's salary rather than at a grad student's salary
* much of the interesting research done on the computer-engineering end of bioinformatics is done in a commercial and not academic setting

It's frustrating to be reminded of the many petty obstacles to amateur science -- not only academic-only software with no carve-out for the amateur scientist, but lack of access to journals and all the rest.

Imagine if we had to prove our bonafides to contribute to Linux or view its mailing lists?

Re: Academic software and infrastructure – AKA more ranting

Hari — Sun, 29 Nov 2009 12:47:37 -0000

I was just saying that for Robetta or whatever to restrict useage to academia is perfectly acceptable. You get your grants rejected ! , your funding dries up..what do you do . Reign in the give it all away ideals, and start getting pragmatic!. Allow academics to use your software free , and charge everyone else to use it!

That said open source works and works very well, there is no denying it. Numpy/Python, R , Ruby on Rails etc succeed because they are open source and quite universally applicable. Its a different matter to open source a niche application that which is used by a small group of people. I dont think its fair to expect the same model to translate to other platforms or software.

Although I can see your point that setting things free guarantees their long term survival , helps keep quality up etc etc , it rarely pays the bills! Accordingly, I think the biggest way to encourage open source is to start contributing to projects , and hit those paypal buttons everytime an open source projects makes your work easier. I would rather do that than expect academics or government funded projects to give things away everytime.

Re: Academic software and infrastructure – AKA more ranting

mndoci — Sun, 29 Nov 2009 12:42:43 -0000

I'd like to add that where there is value, companies will and do fund software development, either directly, or through consortia and that is fine.

This half-way model is the one I have always had problems with and more now than ever. It also results in academics not appreciating open source.

Re: Academic software and infrastructure – AKA more ranting

mndoci — Sun, 29 Nov 2009 12:28:15 -0000

Open source does not close avenues for commercialization. Most of the current models (and I've worked in those for a long time) do not really work. Well perhaps for a few individuals, but not for the quality of the code and the improvement of science.

The reason is that almost none of the software by itself is worth that much in the first place, i.e. unique enough to be absolute must. Bioinformatics has done fine with very little closed source software (in fact, closed source has lost) and the places where money is paid is in areas such as data management, not algorithms. Pharma etc will pay for custom development and would rather be contributors to the open source world. Can you imagine if R were not open source? Would all of you be even talking that much about it? Would it be half as successful and it's actually broadly usable and has a lot of value.

Re: Academic software and infrastructure – AKA more ranting

harijay — Sun, 29 Nov 2009 11:23:00 -0000

One way out is for companies and individuals to fund science that they get value from. If an academic site that had some value to the general community goes down, then the community should rally to write to the authors/maintainers and port it to a suitable platform like google app-engine or an AWS account backed by a loosely constructed paypal donation backed foundation. In these cash strapped times, I would not blame any government entity that shuts down a service that costs money to keep running.

Also along these lines , I dont think it is practical or right given the funding situation that academics be expected to close all avenues for commercialization by giving away their developed algorithms . The markets involved are too small for academics to sit and wait for value to accrue from the application of any open-source model. The cash rich entities in the equation a.k.a most big Pharma companies should be expected to pay for software /algorithms developed with public funds. That helps academics stay afloat as government funding gets more and more scarce.