The title “OpenHelix: bioinformatics education outside of a different box” (if you hit a paywall, or have trouble accessing, we will gladly send a reprint. Just email the corresponding author, Jennifer listed in the abstract or ask from our contact link- Trey) was a cool suggestion from one of the article’s reviewers – my original title was much tamer (ok, more boring). Regardless of the final title, what we wanted to do in the article is to discuss informal sources of bioinformatics education. By education we do mean acquiring applicable information that allows a researcher to operate within the field of bioinformatics. By informal we mean outside of traditional, credit based classes and degrees. Essentially we provide a bit of the knowledge and know-how that we’ve gathered over years of working with hundreds of resources, thousands of workshop attendees, and countless online contacts about where a researcher, or librarian, or whoever can turn for various informational needs in the field of bioinformatics.

Our contention is that not everyone needs to program in order to manage and manipulate their biological data these days. There are SO many fine publicly available databases, algorithms, tools and more, it is just a matter of awareness and training for anyone to be able to reformat and analyze their personal data sets. We maintain that :

…bioinformatics education needs to do a minimum of four things:

1. raise awareness of the available resources
2. enable researchers to find and evaluate resource functionality
3. lower the barrier between awareness and use of a resource
4. support the continuing educational needs of regular resource users

In the paper we walk through each of these – we first describe example needs associated with the point, and then cover possible informal resources that meet the needs. The article includes tables of resources and links to them and many many references. We really hope that is a very useful resource in the field of bioinformatics education.  I am already looking forward to contributing to the next special education issue, both to hone my writing skills and to extend the information we can provide readers. Please do comment, email, whatever and let us know about the resources that you use, what you learned from the article, etc. Oh, here’s the citation info:

Williams, J., Mangan, M., Perreault-Micale, C., Lathe, S., Sirohi, N., & Lathe, W. (2010). OpenHelix: bioinformatics education outside of a different box Briefings in Bioinformatics DOI: 10.1093/bib/bbq026

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?

NOTE: In the unending battle with spammers, we have to moderate comments. Your comment/question may not appear immediately after submission. We are notified when a comment comes in and we’ll get over and approve it as soon as we see it.

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Anyway, if you have interests or needs for data of the FGED type (that’s now the Functional Genomics Data Society…they used to be MGED–need a synonym list…) please have a look at the survey. And spread the word. It’s hard to get user input on stuff like this, I know, so I’m just trying to help.

email text:

Dear Colleague,

Please accept my apologies for the mass e-mail.  Several of the FGED (formerly MGED) community members are preparing a competitive renewal for the grant under the auspices of which we have developed tools for sharing and annotating microarray data.  We would very much appreciate it if you could take a few minutes to fill out a survey about data standards and their role in sharing data and supporting reproducible research.

The link to the survey is below:

http://www.surveymonkey.com/s/fged2010

Thank you for your time — your opinions are valued and will be useful in directing the future path for FGED.

Best wishes,

Catherine Ball

Department of Biochemistry

Stanford University School of Medicine

Off you go!  It’s no PZ Pharyngulation, but do contribute if you have thoughts on this.

New Drag and Reorder Functionality Released

....It is now possible to rearrange the order of tracks within the browser image.
To reorder tracks, click-and-hold the side label or gray mini-button of a single
track and drag the highlighted track to a new position within the image....

I’m going to do a quick movie of what that means–it has no audio just to keep it smaller and quick. But this will allow you to move the tracks you want closer together without going to the configuration page to do it now. It also means you may have to use the Default Tracks and Default Order buttons to go back to what the original views are. Keep that in mind if someone else shares a computer with you.

I want to mention a couple of glitches in this, though: some people have reported that in their stored sessions and custom tracks that the orders are being altered. And when you upload tracks now you don’t have the same configuration options, so you’ll notice that on your saved upload items.  Here’s a word from the team from the discussion mailing list:

We have noted your bug that some sessions that had tracks that were re-ordered using the old paradigm are now out of order. We are currently testing a fix and hope to have it out in a week or so.

New ENCODE Integrated Regulation track released

There are huge challenges in visualizing the wealth of ENCODE data that’s now coming out, and UCSC is actively developing new strategies and methods to manage the visualization needs. They have now added a new “super-track” to visualize some  of the data. I can’t link to this email as it is only for registered mailing list members, but here’s a piece of it. The whole thing is in the “News”  item on the UCSC home page right now http://genome.ucsc.edu/

The ENCODE Data Coordination Center at UCSC is pleased to announce the release
of the ENCODE Integrated Regulation super-track, a collection of regulatory
tracks containing state-of-the-art information about the mechanisms that turn
genes on and off at the transcription level.

Individual tracks within the set show enrichment of histone modifications
suggestive of enhancer and promoter activity, DNAse clusters indicating
open chromatin, regions of transcription factor binding, and transcription
levels. When viewed in combination, the complementary nature of the data
within these tracks has the potential to greatly facilitate our understanding
of regulatory DNA. (To view a browser session showing the ENCODE Integrated
Regulation super-track, see

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Example1&hgS_otherUserSessionName=hg18EncReg.

I know these came out last week, but I like to take a little while to explore the new features and get used to them before I speak to them–especially when they are significant alterations of the functionality. And it gives a bit of time to see if there are issues developing around the use of them.

We will update our training materials with these new features soon.  For the freely available materials sponsored by UCSC start here: http://www.openhelix.com/ucsc

According to GeneMANIA’s developers at the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto:

“GeneMANIA helps you predict the function of your favourite genes and gene sets.”

I’ve posted tips on how older versions of GeneMANIA worked, and recently I’ve had access to GeneMANIA’s development site. I watched the great changes and updates as they occurred, occasionally chimed in with ‘user feedback’, and MOST IMPORTANTLY got to develop our tutorial on the new version! So what you see at GeneMANIA is what we explain in our tutorial. They also recently published an article in the web server issue of Nucleic Acids Research that you might want to check out. Please check all these resources out for your gene relationship and functional research needs.

• 12 Must-have iPhone Apps for Biomedical Research (thanks for the pingback, Walter!)  [Mary]
• Is the internet forcing a change in peer-review? For Scholars, Web Changes Sacred Rite of Peer Review – NYTimes.com. (talks about Humanities, but could be asked of biology [Trey]
• Connotea, Mendeley and CiteULike could all be used for this, but there is also this site: JournalFire, an online journal club (private or public). (hattip: Nathan @ Biostar) [Trey]
• Updated cat genome assembly browser from UCSC announced this week. [Mary]
• Oh… and two species of ant genomes were completed with an interesting comparative analysis. E.O. Wilson should be happy . [Trey]
• Know a web developer interested in genetics? Genetic Alliance is looking for someone. Nice organization.  I checked with them–it is actually in play still, ignore the dates on that deadline. [Mary]
• Nice article on how whole-genome sequencing solved a family disease causation: A Family Mystery, Solved by a Genome [Mary] (Just came to add this same snppet , another example of the future possibilities of personal genomics, previous one here [Trey]) And another from Cyndy [Jennifer]
• IOM publishes workshop summary:  The Value of Genetic and Genomic Technologies: Workshop Summary (2010). H/T to Eric Topol. [Mary]
• ICGC has released another set of data–increasing the number of cancer types, individuals, and variations available. Also improved interface allows gene-centric searching, among other stuff.  [Mary]
• slide pdfs of the second biennial Building the Data Center for the Future workshop conference, just click on talk title. H/T Matt Dublin, GeneomeWeb [Jennifer]
• kinetic model database from EMBL-EBI named BioModels Database, as reported in this BMC Systems Biology article [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?

NOTE: In the unending battle with spammers, we have to moderate comments. Your comment/question may not appear immediately after submission. We are notified when a comment comes in and we’ll get over and approve it as soon as we see it.

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.