Monday, August 24, 2009

The Freedom to Cure Cancer: Open Source Software in Genomics: OSCON 2009 - O'Reilly Conferences, July 20 - 24, 2009, San Jose, CA

The Genome Center at Washington University in St. Louis has been at the forefront of genomics since its formation in 1990. Helping to lead the sequencing and analysis of the first multi-cellular organism, C. elegans, and the Human Genome Project, The Genome Center has long leveraged free/libre/open source software (FLOSS). One hallmark of these sequencing efforts has been the rapid dissemination of sequence data for all to download and use. Just as it supports freedom for data, The Genome Center supports freedom for software and its users as well. From it’s IT infrastructure to software development to bioinformatics tools, FLOSS has helped The Genome Center and others make possible the rapid advancements in genomics over the past two decades. The Genome Center has long used a common, customized Debian GNU/Linux build for both its computational cluster and its desktop workstations. It has long relied on an in-house laboratory information management system written in Perl, which includes a custom touchscreen and barcode scanner interface for lab technicians to input data. Other in-house software is written in Perl, PHP, C, C++, and Ruby, all developed on the GNU/Linux platform using free tools, e.g., Emacs, vim, subversion, git, and GCC.

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Presentation File: The Freedom to Cure Cancer_ Open Source Software in Genomics Presentation [PDF] (David Dooling - The Genome Center at Washington University in St. Louis - 10:45am Friday, 07/24/2009)

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