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CellSpace Knowledge Miner, GenTerpret, Human-Mouse Synteny, RS3, CNX, HypoGen, HipHop, Confirm, BioGridRunner


Pittsburgh-based Cellomics has released version 2.0 of its CellSpace Knowledge Miner at The bioinformatics tool and content database allows users to query the relationships between molecules and diseases in the Medline literature.

According to Cellomics, version 2.0 offers several improvements over version 1.0, including more information, five times the number of journals, the ability to perform more types of searches, more filters to narrow the search, and an Explain Query tool that allows users to obtain an English language description of the questions they are asking.


British Columbia, Canada-based RabbitHutch Biotechnology has released version 2.0 of its GenTerpret genome interpretation and annotation tool for Solaris, Linux, and Windows. The program imports sequence files in multiple sequence formats and permits various third-party analyses to be run on the sequences. GenTerpret then presents a blended feature table containing both known features and features predicted by the analysis software.


A Human-Mouse Synteny server is now available from Softberry of Mount Kisco, NY, at The resource provides information about 18,915 human genes mapped to the mouse genome draft and 18,464 mouse genes mapped to the human genome draft, and includes 14,504 orthologous gene pairs. Softberry compiled the data using its proprietary programs for gene prediction, EST/RNA mapping, and genomic sequence comparison.


In line with its strategic alliance with IBM, Accelrys has ported five more software applications — RS3, CNX, HypoGen, HipHop, and Confirm — to IBM’s eServer pSeries systems running AIX. This group adds to the Wisconsin Package, CHARMm, Modeler, Delphi, and SeqFold, which were ported in February. Accelrys, headquartered in San Diego, said it expects to spend the next three quarters of 2002 migrating the majority of its life sciences applications to IBM systems.


A preliminary release of the BioGridRunner bioinformatics grid application is available from the Center for Genomics and Bioinformatics at Indiana University at The application offers resources discovery using computable directories of bioinformatics data and software; network transport for high-volume data distribution; security and authentication in use of resources; and peer-to-peer methods for data sharing. BioGridRunner is built in Java 1.3, using the Commodity Grid toolkit of the Globus project.

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