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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.

Filed under

The Scan

Back as Director

A court has reinstated Nicole Boivin as director of the Max Planck Institute for the Science of Human History, Science reports.

Research, But Implementation?

Francis Collins reflects on his years as the director of the US National Institutes of Health with NPR.

For the False Negatives

The Guardian writes that the UK Health Security Agency is considering legal action against the lab that reported thousands of false negative COVID-19 test results.

Genome Biology Papers Present Epigenetics Benchmarking Resource, Genomic Architecture Maps of Peanuts, More

In Genome Biology this week: DNA methylation data for seven reference cell lines, three-dimensional genome architecture maps of peanut lines, and more.