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WebSphere Portal for Life Science Syndicated Content, OpenMMS, AmberFFC, M-FISys, GeneSpring 6, GeNet 4


IBM has released the WebSphere Portal for Life Science Syndicated Content, a portal environment that will allow in-house life science R&D groups to integrate subscription-based external research, internal content, and collaborative applications together in a single environment that users can customize for their research needs. According to the company, any publicly available, in-house, or commercial database with a web interface can be integrated into the portal. Further information on the offering, which includes the WebSphere portal middleware along with Lotus Web Conferencing, is available at software/info1/websphere/index.jsp?tab=solutions/portallifesciences&S_TACT=103BEW01&S_CMP=campaign.


Version 1.5.1 of the OpenMMS software toolkit for parsing protein and nucleic acid macromolecular structure data stored in the Protein Data Bank’s mmCIF format is now available from the San Diego Supercomputing Center at This version contains all of the pdbx fields from the PDB Exchange Dictionary.


Version 1.3 of AmberFFC, which converts AMBER force fields for use with commercial molecular modeling packages is available from the Université de Picardie Jules Verne at


The Protein Data Bank has released several enhancements for its website and FTP archives: Biological unit coordinates are now accessible in a new directory on the PDB FTP site (, and new mmCIF files are now available from the primary PDB web site (, its mirrors, and on the PDB FTP site


Gene Codes has released M-FISys (Mass Fatality Identification System), the software it modified to identify more than 1,500 of the approximately 3,000 victims of the World Trade Center attack in New York on Sept. 11, 2001. Gene Codes founder Howard Cash said in a statement that he is in contact with “several other countries that are interested in the software” because of concerns about terrorist attacks or for other potential needs.


Silicon Genetics has released GeneSpring 6 and GeNet 4. New features in GeneSpring 6 include one- and two-way ANOVA and post-hoc tests; capabilities to minimize the memory required for large experiments; new filtering tools; annotations for Affymetrix gene chips; and a set of clustering methods including hierarchical clustering, k-means, self organizing maps, and quality threshold clustering. New features in the GeNet 4 enterprise analysis platform include a new viewer; Secure Sockets Layer Authentication to ensure data security; and remote execution so that GeneSpring users can offload tasks to remote servers.

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