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Proteome Systems GlycoSuite, The Broad Institute s GenePattern, and GMOD s LuceGene

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Proteome Systems last week released GlycoSuite, a set of bioinformatics analysis tools and data for glycomics — the study of the role of carbohydrates in biological systems. The suite includes an annotated database and search engine of glycoprotein-derived glycan structures. Further information is available at https://tmat.proteomesystems.com/glycosuite/.


The Broad Institute has released GenePattern, a software package for gene expression analysis that allows researchers to record and replay analyses, and use tools from many different software sources within a single interface. The package is available at http://www.broad.mit.edu/cancer/software/genepattern/. GenePattern can be used as a standalone application on a laptop, or in a client-server installation. It is packaged with a core library of analytic and visualization modules that can be connected as a pipeline or method. New modules are “frequently” released for download from the GenePattern web site, according to the Broad Institute developers. Future plans for the software include integrating additional modules into the package for sequence analysis, proteomics, and metabolomics methods.


The GMOD (Generic Model Organism Database) project has released LuceGene, an open source search and retrieval software tool for genome databases. It is available at http://www.gmod.org/lucegene/ and http://eugenes.org:8081/gmod/lucegene/. LuceGene is built on top of the open-source Lucene text search engine, with additional input adaptors for HTML, XML, FlyBase flatfiles, and biosequences. According to the LuceGene developers, the package is “similar in concept” to Lion’s SRS.

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