The OpenHelix Blog

There’s a new carnival in town.  It was all the buzz on the #bioinformatics twitter feed the last couple of days.  Byte Size Biology delivers the first edition of:

Bioinformatics Blog Carnival #1

For those of you who aren’t as immersed in science blogginess as others, a carnival is a collection of blog posts usually around a given theme or goal.  They are nice–they generate networks in the community, and you might find blogs and bloggers that you wouldn’t have been aware of otherwise.  In this case there is quite a range of topics, maybe there will be something you’ll connect with.  Go check it out!

Bioinformatics Blog Carnival #1

I would have submitted something if I had heard about it in time, but I was away. Alas. There’s always next time. But I can’t fingure out when next time is yet…

HapMap has had a few minor updates to their browser, and importantly, new phase 3 data was released early last year (drafts of that data were released in 2008). Haploview, the downloaded software that allows the user to perform in depth LD and haplotype analysis, has been recently updated from version 4.1 to version 4.2. Haploview can be used with user data or data downloaded from the HapMap project. Though, version 4.1 did not work for phase III HapMap project data, so the user had to use phase I and II data if they wanted to use version 4.1. Haploview has now been updated to version 4.2, allowing the user to use HapMap phase III data.

That’s a lot of versions and phases . The short of it is, if you use Haploview 4.2, you can view and analyze data from any phase of the HapMap project.

Today’s tip briefly shows you how to download data from the HapMap project and view it in Haploview.

So last week I treated myself to my first vacation in a long time.  It was my birthday, and I wanted to disconnect a bit and recharge.  Mostly it worked, although the hundreds of emails I’m facing this morning are a bit daunting.  But just before I left I got an email from a colleague who asked me a really great question:

….I would love to know where you would start when you get back a personal genome sequence….

And I couldn’t shake this out of my head.  I was sitting on a bridge outside Windsor Castle thinking about it as the sun set on my first day.  (On subsequent days I found that the far superior ciders in the UK were able to push this question out of my head for some periods of time. And also pie.)

I’ve spent some significant time thinking about the onslaught of personal genomics, of course.  It’s all been very theoretical, because I would have refused to even begin the process of obtaining my personal genome sequence until the GINA legislation fully kicked in.  But now that barrier is down.  I’m still not ready to get mine done for a variety of reasons (cost, quality, informative value).  But it’s still worth thinking about what I would do with it if it was handed to me–in specific terms, with concrete actions.  So here’s what I decided I would do.  Your mileage may vary.  And I’d love to hear what others might do with theirs.  Follow the link for the specific actions I’d take.

If you use MyNCBI (which I like) and eRA Commons (got an NIH grant? Then you probably do), MyNCBI now has a handy new feature I just discovered (of course if I looked at the NCBI news last month, I’d have discovered it earlier ) and thought I’d point out.
The new feature allows you to link your bibliography in MyNCBI (which is absurdly easy to build with your eRA commons account. Then, when you view your bibliography, you’ll find a new $ icon. Click that icon and it will give you the following information about all your citations: Whether the citation complies with NIH’s (sort of) new public access policy and if there is NIH funding associated with the citation (which you can link if you have an open grant in your eRA Commons account). Nice feature you might want to check out, and it might be a nice subject for a Tip of the Week in a couple weeks .

Just wanted to point out that our fellow blogger Mary had an excellent post the other day entitled “What if Bt saved human lives?” over at Biofortified, which she mentioned here earlier.

Well, it was chosen at “Research Blogging” as an editor’s selection this week. Check it out when you’ve got a moment.

This next post in our continuing semi-regular Guest Post series is from Xiaowu Gai, the Bioinformatics Core Director at CHOP . If you are a provider of a free, publicly available genomics tool, database or resource and would like to convey something to users on our guest post feature, please feel free to contact us at wlathe AT openhelix DOT com.

Thanks to Mary for running a Tip of the Week – “CHOP CNV database” a couple of months back. CHOP CNV database is a high-resolution genome-wide survey of copy number variations of a large number (2,026) of apparently healthy individuals. It is publicly accessible and has been widely used by a large number of research groups world-wide. I am now pleased to announce the public release of our software system behind it: CNV Workshop. CNV Workshop is a suite of software tools that we have developed over the last a few years. It provides a comprehensive workflow for analyzing, managing, and visualizing genome copy number variation (CNV) data.

It can be used for almost any CNV research or clinical project by offering the following capabilities for both individual samples and cohort studies:

CNV identification
Implements a modified circular binary segmentation algorithm that reduces false positives
Fully configurable parameters for sensitivity/specificity management
Annotation
Individual locus-specific annotations such as position, type of variation, call metrics, and overlap with CNVs of other data sets, including the Database of Genomic Variants.
Functional gene annotations such as genes affected and known disease associations
Accepts user-provided annotations
Presentation
GBrowse-enabled visuals for querying, browsing, interpreting, and reporting CNVs
Export of results into Excel, XML, CSV, and BED files
Direct links to public resources such as the UCSC Genome Browser, NCBI Entrez, Entrez Gene, and FABLE
Project and Account Management
Authentication and permission scheme that is especially useful for clinical diagnostic settings
Analysis result sharing within and between projects
Simple Web-based administrative interface
Remote access and administration enabled

CNV Workshop currently accepts genotyping array data from Illumina’s 550k, 610- and 660-Quad, and Omni arrays, along with Affymetrix’s 5.0 and 6.0 arrays, and can be easily configured to accept data from other platforms. The package comes preloaded with publicly available reference data from more than 2,000 healthy control subjects (the CHOP CNV Database). CNV Workshop also allows the user to upload already processed CNV calls for annotation and presentation.

The software package is freely available at http://sourceforge.net/projects/cnv/. It is also described in more detailed in our recent paper on BMC Bioinformatics.

-Xiaowu Gai

I’ve always had a thing for infectious diseases.  I mean: not me personally getting them.  But the fascinating arms race from the smallest biological elements to larger parasites — man, the tricks and strategies are really just amazing to me.  In fact, as an undergrad I was really attracted to the study of infectious disease as a career.  But an advisor talked me out of it.  Eh, who knows — I might have ended up in the same place ultimately.

Anyway, since this isn’t an infectious disease blog and the paper I wanted to talk about touches on a whole other area that interests me (genetically engineered plants), I was granted the opportunity to guest post on a cool paper I found and you check that out over at Biofortified. 

What if Bt saved human lives? if you are so inclined.  It’s about this article:

Hu Y, Georghiou SB, Kelleher AJ, Aroian RV, 2010 Bacillus thuringiensis Cry5B Protein Is Highly Efficacious as a Single-Dose Therapy against an Intestinal Roundworm Infection in Mice. PLoS Negl Trop Dis 4(3): e614. doi:10.1371/journal.pntd.0000614