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PathwayAssist 2.5, Phylomat, Genome Knowledgebase, Osprey, VEGA-WE, EcoCyc, MetaCyc, BioCyc, Pathway Tools, BioMart

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Ariadne Genomics and Stratagene have released PathwayAssist 2.5, desktop software for visualization and analysis of biological pathways. A demo is available at http://www.stratagene.com/SoftwareSolutions/. The software features the ResNet database of interactions extracted from the literature using the MedScan text-mining tool. MedScan is included with the software so that researchers can update pathways with new data.


The University of Illinois at Urbana-Champaign and the National Center for Supercomputing Applications have released Phylomat, an online data-mining tool for phylogenomic analysis, at http://alg.ncsa.uiuc.edu/pmat/do/index.


Version 9 of the Genome Knowledgebase of annotated pathways is now at http://www.genomeknowledge.org/. The release includes new modules and cross-references to LocusLink and Ensembl genes.


Version 1.2.0 of Osprey, a software platform for visualizing interaction network data, is available from the Samuel Lunenfeld Research Institute at http://biodata.mshri.on.ca/osprey. The university has also released a commercial version of Osprey (licensing details at http://biodata.mshri.on.ca/osprey/servlet/CommercialRegistration). Commercial firms may evaluate the software for free for 30 days.


Milan’s Istituto di Chimica Farmaceutica e Tossicologica has released VEGA-WE, a web-based version of the VEGA 3D visualization software, at http://galaxy.farma.unimi.it/vegawe.


SRI International has released version 8.0 of the EcoCyc, MetaCyc, BioCyc pathway/genome databases, and an upgrade of the Pathway Tools software to query and visualize those databases at http://biocyc.org/metacyc/. Enhancements to Pathway Tools include redesigned main menus, a pathway hole-filling algorithm, a P2P database sharing mechanism, and support for protein features.


The European Bioinformatics Institute has launched BioMart, a data integration system for large-scale querying, at http://www.ebi.ac.uk/biomart/. BioMart builds upon the query system originally developed for Ensembl, which has been extended to other databases including UniProt, the Macromolecular Structure Database, Vega, and dbSNP.

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The Scan

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