The Broad Institute has released GSEA 2.0, an updated version of its freely available Gene Set Enrichment Analysis software, which classifies gene activity by using a public database of “gene sets,” or groups of genes that are connected based on their function, chromosomal location, or molecular control. GSEA 2.0 includes more than 1,000 new gene sets, which nearly doubles the number of gene sets in the previous version, as well as a gene set browser, which can pinpoint specific gene sets based on a particular gene or other parameter of interest.
Ariadne Genomics has launched ResNet Plant, a database that supports interaction and pathway analysis in plants. ResNet Plant contains more than 70,000 molecular interactions and relations extracted from plant-related PubMed abstracts and articles, and includes information on Arabidopsis, rice, barley, corn, tomato, potato, and tobacco.
Jivan Biologics has released SpliceFold, a software package for analyzing alternative splicing from microarray data. The company claims that the software is the “first dedicated solution” for splice variant microarray analysis, and that it’s scalable to whole-genome and whole-spliceome analysis for human, mouse, and other organisms. SpliceFold supports Jivan's human and mouse splice arrays, as well as third-party platforms. The current version of the software is available to all Jivan customers for free. The company said that it is considering charging for “premium versions” of the software in the future.
Cytoscape 2.4 is available here. The new version of the open-source pathway visualization and analysis package features improved image generation, node label position adjustment, an automatic visual legend generator, consolidated network import capabilities, a new ontology server, and support for SBML, BioPAX, PSI-MI, delimited text, and Excel.
SimBioSys has released ARChem Route Designer, an automatic retrosynthetic analysis tool for organic chemistry. SimBioSys worked with Pfizer to develop the software, which offers enterprise-level support to permit simultaneous use by hundreds of chemists.