Welcome! This is the research blog of Todd Harris. I design and build information systems for large-scale biological data. This blog discusses genomics, bioinformatics, and science policy in general, with a particular focus on the development of biological databases, user interfaces, and data visualization.

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.

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“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.

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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.

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New Post: Weekly Digest for December 19th http://bit.ly/4SElTB [tharris]
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Weekly Digest for December 19th http://ff.im/d6I2H [tharris]
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50 finalists for #nikonfestival tonight! Support Hi-Lonesome and See You Then-be sure to comment! http://bit.ly/6mEDqI http://bit.ly/7rSdOQ [tharris]
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Ratings @nikonfestival nonintuitive: tooltips should be clearer ("click here to rate this 3 stars"), diff color when voting, confirmtn msg [tharris]
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See You Then a finalist in #nikonfestival! Go vote for this beautiful short film shot with a #D5000 http://bit.ly/6mEDqI #seeyouthen [tharris]
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Thanks for the RT, @23andme! “Here’s to you, genome finishers and curators!” http://bit.ly/7ZGIM0 (via @tharris) [tharris]
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All I want for Christmas is to have an inbox that doesn’t have any email in it. I’m easy. [tharris]
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Weekly Digest for December 19th

December 19, 2009

Published Weekly Digest for December 12th.

New Post: Weekly Digest for December 12th [tharris]

Weekly Digest for December 12th http://ff.im/cPics [tharris]

Hanging out with @audreyhallphoto, she’s uploading first submission to the @nikonfestival! Super-psyched [...]

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Finishers and curators are the unsung heroes of the Genome Era.

December 18, 2009

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, [...]

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New 23andMe and H1N1 survey

December 17, 2009

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!
url=’http://toddharris.net/blog/2009/12/17/new-23andme-and-h1n1-survey/’;size=’small’;username=’tharris’;

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An early model for open access reopens (say hello to the new Worm Breeder’s Gazette!)

December 16, 2009

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 [...]

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Weekly Digest for December 12th

December 12, 2009

Published Weekly Digest for December 5th.

New Post: Weekly Digest for December 5th [tharris]

Weekly Digest for December 5th http://ff.im/cuuPI [tharris]

Bio::DB::SeqFeature store loading scripts are surprisingly fast on a MacBook air equipped with [...]

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23andMe launches Longevity Survey

December 11, 2009

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 [...]

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