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BioLab Data Server Platform, BRENDA, ClearForest, Grid-Blast, Ensembl Release 18, UCSC Genome Browser, caCORE 2.0, caBIO, MINT, Build 118

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BioLab Software of Seattle, Wash., has launched the BioLab Data Server Platform, open source data management software that enables collaboration between researchers via local area networks or the web.


Biobase of Wolfenbuttel, Germany, has begun marketing BRENDA (the Braunschweiger Enzyme Database), developed and maintained by researchers at the University of Cologne. BRENDA contains information on 80,000 enzymes, which have been largely extracted by hand from scientific publications.


ClearForest has released version 5 of the ClearForest text extraction and analysis software suite. New features include plug-in modules for several vertical domain areas — including life sciences, which guide the automatic tagging and discovery of relevant textual elements for each specific domain or industry.


The National Center for Supercomputing Applications, along with the W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign, has released Grid-Blast, a web portal that enables Blast to be run on NCSA’s Platinum and Titan Linux clusters, at http://bioinf.ncsa.uiuc.edu:8181/gridblast/.


Ensembl Release 18 is available at http://www.ensembl.org. The release contains the Ensembl gene build on NCBI human assembly 34. It has 22,184 genes comprising 27,941 coding transcripts and 1,853 pseudogenes. The release also contains 22,159 rat genes.


The University of California Santa Cruz genome bioinformatics group has added the Drosophila melanogaster assembly to the UCSC Genome Browser at ftp://genome.cse.ucsc.edu/goldenPath/dm1.


caCORE 2.0 is now available from the National Cancer Institute Center for Bioinformatics at http://ncicb.nci.nih.gov/core. The release includes an expansion of caBIO (http://ncicb.nci.nih.gov/core/caBIO), as well as a full API to other caCORE components. CaBIO’s object model has been extended to cover model organism systems (caMOD). An implementation of the MAGE object model API provides access to the NCI’s gene expression data portal microarray database.


Version 2.0 of the MINT molecular interaction database is available at http://160.80.34.4/mint/. The relational structure of the database has been redesigned to meet Protein Standard Initiative (PSI) recommendations.


Build 118 of dbSNP is available from the National Center for Biomedical Information at ftp.ncbi.nih.gov/snp/.

 

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