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News Briefs from the O Reilly Bioinformatics Conference Floor


*Part I of the first-ever biohackathon, which preceded the conference, resulted in a new specification, Open Bio Database Access, for accessing biological sequence databases across multiple languages and platforms.

The biohackathon was organized and supported by Electric Genetics, O’Reilly & Associates, and other sponsors. The rest of the work on the spec, as well as a full performance test, will be completed at the second part of the biohackathon, scheduled to take place in Cape Town, South Africa, February 24-March 1.

Commercial entities or individuals interested in sponsoring the second half of the event should contact [email protected].

*Apple Computer announced that it has partnered with Genentech to develop an accelerated version of the Blast sequence alignment algorithm, called A/G Blast, on Apple’s G4 processor.

The enhancements, which must be patched into the OS X version that is now part of NCBI’s standard distribution, are freely available at hardware/ve/acgresearch.html.

Chris Hogue of the Samuel Lunenfeld Research Institute has released a distributed protein folding screensaver at

Hogue said the screensaver can run faster than other distributed protein folding projects, such as [email protected] and Folderol.

*The Open Bioinformatics Foundation released a statement on its position regarding publicly funded bioinformatics software.

Spurred by several months of debate within the bioinformatics open source community, the foundation determined it was time to release a statement to distinguish itself from organizations “with similar sounding names,” according to OBF board member Steve Brenner, of the University of California, Berkeley.

The OBF statement is based on the notion that “scientific software developed with public support should be distributed under terms analogous to those applied to biological materials.”

The full statement is available at

The Public Library of Science expects to begin publication of two journals by June, according to Michael Eisen.

The journals, PLoS Natural Sciences and PLoS Medicine, will feature only the “best science,” he said. The initiative is seeking funding to support its efforts to provide free online access to the scientific literature. It plans to support its publication activities with fees of $300-$500 per submitted paper. is in the process of incorporating as a non-profit entity, said Jeff Bizzarro, who heads the organization. The group plans to appoint a board of trustees and elect executive positions in the near future.

Eric Neumann of Beyond Genomics said that the I3C is in the process of formalizing a working draft of its technical architecture and expects to release it soon.

The first Mouse Genome Sequencing Consortium assembly has been released through Ensembl at

The site contains version 1 of the mouse genome draft sequence, based on whole genome shotgun data of ~4x coverage, frozen in October 2001.

*See for complete article.

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