This blog focuses on the role that good design plays in the succcesful online presentation of biological data. Topics include data visualization, user interfaces, general bioinformatics, open access publishing, and inspirational notes from the design world and may include mundane system level development tricks and project management rants.

The Worm Breeder’s Gazette: now accepting online submissions!

October 26, 2010

Last year I wrote about the return of an open access scientific newsletter (see: “An early model for open access returns: say hello to the new Worm Breeder’s Gazette“.) Today I’m happy to announce that we’ve enhanced the Gazette with online submission of articles! You must first register as a contributor before submitting an article [...]

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OmniGraffle Stencils galore at Graffletopia

May 17, 2010

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. url=’http://toddharris.net/blog/2010/05/17/omnigraffle-stencils-galore-at-graffeltopia/’;size=’small’;username=’tharris’;

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Targeted gene deletions in C. elegans using transposon excision

April 28, 2010

“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 [...]

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A Worthy Mercurial (hg) Tutorial from Joel Spolsky

April 4, 2010

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 [...]

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Weekly Digest for December 26th

December 26, 2009

New Post: Weekly Digest for December 19th http://bit.ly/4SElTB [tharris] Weekly Digest for December 19th http://ff.im/d6I2H [tharris] Uploading my #23andme data to @decodegenetics; done #personalgenomics #fb [tharris] 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] Ratings @nikonfestival nonintuitive: tooltips should be clearer ("click here to rate this [...]

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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 to see it go-live! [tharris] Writing #php makes me physically ill. [tharris] Great short film: RT @audreyhallphoto: Very proud to be a [...]

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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 [...]

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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 SSD #bioperl [tharris] Exploring Moose-based BioPerl: http://github.com/cjfields/biome/ Yay! @bioperl [tharris] Published 23andMe launches Longevity Survey. New Post: 23andMe launches Longevity Survey [...]

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