If you’re a proper nerd, you probably use The Omni Groups excellent charting tool OmniGraffle.

And if you’re a serious nerd, you’ll definitely want to check out Graffletopia. They have over a million stencils for Omnigraffle. Hours of fun.

“Targeted gene deletions in C. elegans using transposon excision” is now available in advance online publication form at Nature Methods.

Even after 40 years of intense genetics in the model system C. elegans, a large majority of genes have not yet been disabled by deletion. Although targeted deletions have been possible in flies and mice for years, the technology has been elusive in worms.

At WormBase, we’ve been busy re-writing the website from the ground up to build a modern information discovery space that will generically handle genomic data.

As the project manager, I made the executive decision to switch from CVS/SVN to a distributed version control system (DVCS). I’d used both git and mercurial personally for over a year and enjoyed their flexibility.

And given the already distributed nature of our project, DVCS was a natural fit. (In fact, I believe that DVCS should be roundly adopted across the genomics/bioinformatics research sector precisely for this reason).

Nonetheless, for small teams accustomed to the quirks of SVN, the transition to DVCS can be a rocky road. Recently I came across Joel Spolsky’s excellent HG Init: Mercurial Tutorial.

If you’re considering or in the process of switching to Mercurial, I highly recommend checking out Joel’s tutorial and circulating it to your team.

The utility of genome sequencing projects would be greatly reduced without the efforts of finishers and curators.

A few days ago, Elie Dolgin wrote in Nature News about the role that finishers are playing to complete and make sense of the human genome (see “Human Genomics: The Genome Finishers”, 16 December 2009 | Nature 462, 843-845 (2009) | doi:10.1038/462843a).

Having worked on model organisms for two decades on both the bench and sequencing sides — including working with a team of curators annotating one specific model organism — it’s clear that the field of genomics wouldn’t be where it is today without the toil of genome finishers and curators.

Sure, the raw and basic assemblies have been deposited in public repositories. And they’ve been useful to a degree for basic researchers. Still, sequence gaps remain. Assembly errors are rampant. Without annotation, bench scientists spend their time piecing together sequence and doing piecemeal analyses instead of the next Big Experiment. Often, results from those experiments then remain buried in publications, not associated with the sequence it is intended to clarify.

Finishing and annotating the sequence serves to make sense of the jumble that remains after the sequencers have been powered down and moved to their new digs in the basement of the industrial park across town.

Let’s face it: the primary sequence is the easiest information to acquire but it isn’t the most information rich. It’s the layers of annotations that rest upon that sequence that make it useful. Generating and curating those annotations are a difficult, tedious, and usually thankless job, but a required one if we are ever to talk about “completing the genome.”

So at the risk of sounding like a Budweiser commercial, “Here’s to you, finishers and curators!”

Thanks to @bmahersciwriter for drawing my attention to Elie’s article.

23andMe is now tapping their user base to look for links between H1N1 susceptibility/severity via another user survey. I can’t keep up with all the surveys they’ve been launching recently!

The Worm Breeder’s Gazette was an early model of open access publishing. Today, it returns.

The C. elegans research community has a long tradition of open access.

This spirit led the community to adopt early a standard nomenclature for genes, alleles, proteins, strains, and mutant phenotypes. Standardization made it vastly easier to discuss biological concepts and to share reagents. As the community grew, a stock center was established which thrives to this day. As the genome was cloned as proof-of-concept for sequencing a large genome, cosmids were available with just a quick email.

But it wasn’t just shared nomenclature that bound the community together. The annual C. elegans meeting was a single session. It was believed that in order to understand the corner you were trying to tease apart that you needed to understand the entire organism. To this day, presentations often include raw and unpublished data. Posters are rarely limited to just what’s in the publishing pipeline.

The C. elegans community also pioneered electronic collection, curation, and dissemination of data, through the standalone genomic database AceDB, gopher, BBSs, early websites, and in 2000, with the launch of the comprehensive curated online repository WormBase.

In general, people in the worm field are psyched to share what they know regardless of its publication status.

This is particularly evident from The Worm Breeder’s Gazette. The WBG began as a printed newsletter in December 1975 as an ad-hoc collection of preliminary results, methods, and sometimes pure speculation. Each abstract was limited to one page in length, mimeographed and assembled into a printed booklet complete with a cover depicting worms in various absurd endeavors. No editors. No peer review. Freely available (well, nearly so).

The Gazette continued in printed form until May of 2003. It provided many young researchers a chance to hone their writing skills and to report preliminary data. And it was a model for the Open Access revolution now taking place.

Some of these things have changed as the community has grown larger. But today I’m happy to announce the return of The Worm Breeder’s Gazette. We’re following the casual format of before, with short abstracts limited to a printed page in length. Abstracts are cross-linked to WormBase for genes, variations, and proteins, as well as to external resources when appropriate. To retain the feel of a newsletter, we’ll be publishing the Gazette twice a year.

DTC personal genomics company 23andMe has just launched a new Longevity Survey that aims to tease out the genetic basis of a long life.

Early studies in longevity were pioneered in the model organism C. elegans, a roundworm. C. elegans is a perfect model system for studying aging. It’s small (1mM in length), it develops from an egg to an adult quickly (2.5 days), and has a short lifespan (2-3 weeks). Coupled with the ability to conduct chemical mutagenesis, it’s relatively easy to look through 1000s of animals with an extended lifespan, and in turn to identify the genes responsible. One of these genes, daf-2, is a receptor tyrosine kinase and the C. elegans insulin/IGF receptor ortholog.

Typical lifespan is about 2-3 weeks. And since you can do chemical mutagenesis, it’s possible to easily look for

You can read more about the survey on 23andme’s blog, The Spittoon.