Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.

So What’s Your Problem? And What’s Your Solution?

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

Is there a database of protocols?

That’s such a good question–and I can see why it would be so useful to bench scientists. Yeah, I can show you all the software we cover. But there are still other needs, and searchable protocols would be very handy.

Off the top of my head I pointed her to the Current Protocols publications. I relied on those in grad school–but at that time they were in the red binder on the second shelf, and Hiram would always pull out the old chapters and put in the new ones–on actual paper!!

I also mentioned JOVE–the Journal of Visualized Experiments.  Jennifer talked about this before as a tip of the week. Since then they had to move to subscription, but it’s possible this young scholar’s institution does subscribe to that.

Trey remembered Open Wetware.

UPDATES: Great stuff from readers–thanks:

APD offers: NAR Methods http://nar.oxfordjournals.org/collections/index.dtl

Natalie offers: Protocol-Online http://www.protocol-online.org/ and her collected list: http://www.bib.umontreal.ca/sa/laboratoire-indispensables.htm

Jennifer suggests BioTechniques http://biotechniques.com/ and for  protein structure notes this resource: http://kb.psi-structuralgenomics.org/

_____________________________________

Do you know of others? I’ll edit the post as people bring them along. Thanks!

(oh, and I point you to this tutorial on analyzing Desmond Tutu’s SNPs using Galaxy that I thought was interesting)

Al Akhawayn University, Ifrane Morocco

Last week I attended and taught a workshop for the Moroccan American Society for Life Sciences (Biomatec-US) at their 2nd International Workshop and 9th Annual Meeting, in Ifrane Morocco.

I was thoroughly impressed. Impressed with Morocco, Moroccan Scientists and Moroccan students. I had the opportunity to interact with all three. First this students. I taught three workshops, including a tour of genomic resources and two how-to’s for the UCSC Genome Browser and Table Browser. All were enthusiastically received. But more than that I was impressed by the enthusiasm these students showed for genomics and bioinformatic research. After each talk and later in the day, I was barraged with questions and requests (which I love). Their enthusiasm for science matches or surpasses any other group of science students I’ve met in my 20+ year career in biology. In addition to that, I met several students who I was able to discuss their research with a bit.

Also, I was able to discuss research in Morocco with several Moroccan scientists informally and attend a roundtable discussion about advancing Moroccan science, specifically biological and bioinformatics research. Moroccan scientists, both within and outside of Morocco, are doing worldclass research, including my host of course. The research done within Morocco and by the Moroccan ‘diaspora’ of scientists (there were Moroccan scientists from the US, Europe and the Middle East there), seems to be a ripe network that, together with the enthusiasm of the students, is a great resource for that nation.

If the level of research and enthusiasm of the researchers and students are any indication, Moroccan science will be making great strides in the years to come. Of course, this isn’t anything new I’m sure, just new to me .

I learned (relearned) two things on this trip. The world is very small, and very big. I met several people who with whom I had crossed paths with before or who we had mutual friends. There was the Moroccan scientist who I briefly met in Germany while doing a postdoc there and the Moroccan student who knew someone I knew from Qatar. I was asked to talk briefly and the roundtable discussion and I mentioned a virtual African conference I had given a workshop at, and that I thought there was a Moroccan hub at that conference. Sure enough, one of the scientists at the discussion had attended my workshop (and had good words for it ). Ok, you might say, that’s the ‘world’ of science. Well, it got down to even the woman I met in the hotel who was a Fulbright scholar doing research on Berber and Arabic music… and the man who gave me a ride from the conference the last evening, who just happened to be her Moroccan supervisor.

And it’s a huge world with a lot to discover and awe my sometimes jaded self (rarely, but I can be there). I never had heard of Argan oil before,

Street & shops in the medina of Fes, Morocco

produced from seeds collected from the feces of goats, or even considered touring the magical medina of Fes (to which I MUST return). I had no inkling of the existence of Al Akhawayn University in Ifrane, a small liberal arts school in the cool (it snows) mountains of Morocco in Ifrane (why do I want to keep writing that as iFrane ? ). Beautiful campus.

The other thing that came to mind while attending this conference and speaking with Moroccan scientists is the potential (and unnoticed reality) of the research possibilities outside of the US-European-Japanese triangle. Of course India and China are producing great research more and more over the years, but there are another 100 or so countries out there with another few billion people with huge potentials. Of course these smaller countries have always produced great scientists, but I was beginning to think that genomics and bioinformatics is beginning to assist smaller countries ‘leapfrog’ biological research much as cell phone technology allowed some developing countries to ‘leapfrog’ from traditional telephone lines (expensive, hard to do) to wireless (less expensive). Biological research has traditionally be resource intensive: labs, larger universities, equipment. Bioinformatics and genomics research, though still requiring infrastructure, has a lower barrier of entry I believe. I made a comment in my talk, “There is no lack of data,” and it’s true. The amount of data available for analysis is staggering. The number of publicly available tools and databases is overwhelming. One doesn’t have to do “big science” in genomics (though there sure is that) to do world-class research. Thar’s research gold in them thar data hills (sorry for the reference to the California gold rush, I _do_ live in what was the center of it all). Gold that can be mined by any individual, lab or nation with a bit of education and enthusiasm.

I hope to return next year to Morocco and next years conference. I have a lot more to learn . And maybe I can teach a bit too.

Get a workshop! Tell your bioinformatics support folks. Sometimes librarians are the  keepers of training rooms and schedules at other sites. Suggest it to them. It would be really great for your community of researchers.

• Accessing SEED genome databases via web services, hat tip to Jonathan Eisen. [Mary]
• Galaxy team wants to discuss location for the 2011 Developer’s Conference in Europe. @bffo suggests Vienna during ISMB. [Mary]
• Interesting comments w/ good article links on this CBC News article “MDs warn of online stem cell therapies” [Jennifer]
• Website mentioned in above article is found here, I believe. [Jennifer]
• Microsoft Biology Foundation v1.0 Ships – http://ow.ly/2dZz2 Via Paul Blaser. [Mary]
• Much buzz this week on the great newbie guide to GWAS interpretation at Genome Unzipped. [Mary]
• Pretty interesting results featured in The Scientist this week: Better housing fights cancer in mice, original research article here, if you subscribe to Cell. [Jennifer]

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.

We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.

So What’s Your Problem? And What’s Your Solution?

You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.

You may have been hearing about the 1000 Genomes project–it’s one of the ongoing “big data” projects that is going to yield a great deal of variation information about the human genome. The goal is to sequence well over1000 genomes to identify “most genetic variants that have frequencies of at least 1% in the populations studied”.  They are doing this by sequencing large numbers of samples  with 4x coverage. You can read more about their strategy in their About page on their web site. It also lists the anticipated sample populations.

In this week’s Tip of the Week I’m going to take a quick spin through their browser. (You can also download all the data, but I’ll be focusing on the browser.) They have begun to release data now, and there are 6 individual sequences available at this time.  These are part of their “pilot” studies.  You can get some details on the pilot from their about page, which links to this PDF about the samples.

They are using the Ensembl framework to display their data. So if you are familiar with using Ensembl you’ll have some facility moving around this browser.  One thing that isn’t apparent right away from the site is that you can click the Resembl link on the display to turn on a track that puts the read/coverage data on the viewer. I also liked the alignment display  of all 6 genomes–but I’m sure that’s going to get challenging to view later with more and more genomes.

In an exchange with their very helpful help desk yesterday, I got this quick summary of the samples you’ll see:

For the high coverage populations NA12891, NA12892 and NA12878 are the CEU trio, NA19238, NA19239 and NA19240 are the YRI trio both father, mother, child respectively and both children were daughters.

If you have questions about their data, be sure to go ask them for help–they were very speedy with answers for me .

Some of the project data has also been picked up by UCSC and you can access the same sequences in the UCSC Genome Browser in the Genome Variants track on the March 2006 human assembly. (You’ll also see Venter, Watson, and some other individual genomes there).

Quick links:

The Project: http://www.1000genomes.org/

The Browser: http://browser.1000genomes.org/

An article in Science with some background:  A Plan to Capture Human Diversity in 1000 Genomes

Ok, you couldn’t be there…but all of those trainings are available on our web site right now, except for ENCODE. The same material we do in the online materials is what we do in workshops. The only one of those that requires subscription is IMG. And you won’t find ENCODE as a stand-alone tutorial yet–but that’s coming. We now have sent the script to the studio and we’ll be assembling that soon.

I do want to mention one thing that we think is interesting, and we see in almost every training we do. Nearly every time, more than half of the attendees at our trainings are female. Based on what you read about women falling out of the pipeline in science, you’d think there would be no way we’d even get 50%. But generally it is more than half women in these trainings. (We have the data if anyone can think of a way we can use that to get a grant )

Our current theory is that women are more likely to admit they could use the training (something like asking for directions…you know…?).  Or do men prefer documentation? We don’t know. What’s your theory?