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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.
A taxonomically intelligent biodiversity searchengine
This is a pure Python CGI-based implementation of a taxonomically intelligent species searchengine. It searches biological databases for a taxonomic name. The search is done "on the fly" using web services (SOAP/XML) or URL API's.
Platform for parallel computation in the Amazon cloud, including machine learning ensembles written in R for computational biology and other areas of scientific research. Home to MR-Tandem, a hadoop-enabled fork of X!Tandem peptide searchengine.
TSE is a test bed for a web service approach to federating taxonomic name databases. Put in English, it takes your query and talks to a number of different databases, asking each one whether they contain that name.
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This projects intends to develop a complete distributed peer-to-peer environment
for running heuristic optimization, modelling, artificial life, etc applications. This involves a network engine, libraries and different user interfaces. All this in java.