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Discovery Studio GCG 11.0, SeqWeb 3.0, MetaCore 2.5, BioPax, PHENIX, BiNGO, PyMol 0.98


Accelrys has launched 15 new products across its entire software portfolio. New releases for bioinformatics include Discovery Studio GCG 11.0 and SeqWeb 3.0. DS GCG 11.0 includes ClustalW, updated algorithms, updated data, re-directable Blast searches that enable the implementation of a dedicated Blast server, and "script-friendly" algorithms that do not require initialization of the entire DS GCG package to run. SeqWeb 3.0 offers improved cross-platform compatibility, a revised and simplified interface navigation and design, and performance enhancements, the company said. Full details on all the new products are available at

GeneGo has released MetaCore 2.5. The new version of the company's pathway data-mining suite features fine mapping of human metabolism, transcription regulation, and signaling along with new network-building algorithms, filters, and statistical procedures for multi-variant interpretation of human networks in terms of canonical pathways and functional processes.

BioPax level 1, version 1.4, is available at The release is backward-compatible with prior releases of Level 1, which focuses on representing metabolic pathway data. Future levels of BioPax will expand the scope of the XML-based data exchange standard beyond metabolic pathways.

Version 1.1a of PHENIX (Python-based Hierarchical Environment for Integrated Xtallography) is available from Lawrence Berkeley Laboratory, Los Alamos National Laboratory, the University of Cambridge, and Texas A&M University at This version of PHENIX has three main user interfaces: command-line tools, strategies, and wizards.

The biocomputing research group at Ghent University has released BiNGO, a Cytoscape 2.1 plug-in to determine which Gene Ontology categories are statistically over-represented in a set of genes. BiNGO maps the predominant functional themes of a given gene set on the GO hierarchy, and outputs this mapping as a Cytoscape graph. It is available at

PyMol 0.98, a molecular visualization program, is available from DeLano Scientific at PyMOL source code is free and open source, but the company requests that users "sponsor the project" if they rely on it beyond a "finite honor-system evaluation period."

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