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The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
SeqWare has moved to GitHub, see https://github.com/SeqWare
SeqWare is a project to create a tool set to work with next generation genome sequencers (SOLiD & Illumina). It includes a LIMS, Pipeline, and Query Engine. Check out the wiki link below to see documentation. You can get the source from the Develop link.
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graphite: a portable graphics library, written in Java, JOGL and Postscript that allows rapid generation of high-quality graphs using an efficient, compact Javaengine.
The Internet Censor is a multi-platform, Internet clustering program, for which the resulting data will be used in the creation of a non-profit content-filtering Internet Search Engine for children.