Downloads & Upgrades
Rosetta Biosoftware has released Rosetta Resolver 6.0, which includes capabilities to support toxicogenomics research. The software enables users to observe expression signatures of toxicity, determine dose effects across multiple treatments, and compare toxicity from one animal model to another, the company said. Resolver is also interoperable with third-party databases, including GeneGo's MetaCore, Iconix's DrugMatrix, and Ingenuity Pathways Analysis.
Affymetrix has released several updates through the Affymetrix Developer Network: Fusion SDK 1.04, which includes improvements to CHP file writing, is no longer available; sample data for the upcoming Human Promoter 1.0R Array is available at http://www.affymetrix.com/support/technical/sample_data/demo_data.affx; and ExACT (Exon Array Computational Tool) 1.21, for the primary analysis of exon expression array data (no longer available).
BioRuby 1.0.0 and ChemRuby 1.0.0 are available at (no longer available), respectively.
The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest zebrafish assembly, Zv5, through the UCSC Genome Browser and Blat server. The Zv5 assembly was produced by the Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology and the Netherlands Institute for Developmental Biology. The assembly includes 1,630,306,866 base pairs in 16,214 scaffolds with a sequence coverage of approximately 6.5-7x. The sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server at ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer3/ or downloads page at http://hgdownload.cse.ucsc.edu/downloads.html#zebrafish.
Molecular Connections has released a new version of its NetPro curated database of protein and small-molecule interactions. The current version offers kinetic information, which includes data on time, concentration, association/dissociation constants, and inhibitory constants, and is available for free for all existing and new NetPro customers. The new version also includes Mutation and Knockout database modules, which are optional.
Accelrys has released the Catalyst Jubilant Small Molecules Databases Suite 2006, which provides a collection of known inhibitors of kinases, proteases, GPCR, nuclear receptors, and ion channels. The databases, curated by Jubilant Biosys, contain more than a million compounds and are available in Catalyst 3D format.
The National Center for Biotechnology Information has released RefSeq 15 at ftp://ftp.ncbi.nih.gov/refseq/release/. The release incorporates genomic, transcript, and protein data and includes 2,273,764 proteins and sequences from 3,244 different organisms.
Protein Lounge has released Pathway Builder 2.0, a program for drawing signal transduction pathways. A demo is available at (no longer available).
The official release of CCP4 6.0 is available at http://www.ccp4.ac.uk/download.php. The latest version of the CCP4 suite of programs for macromolecular crystallography includes several new programs and packages, such as ccp4mg, coot, phaser, cctbx, bp3, crank, pirate, chainsaw, superpose, and chooch. It also includes many changes to existing programs, according to the CCP4 development team.
The National Institute on Aging has released the NIA Primate Aging Database, which was developed to collect data on normal aging in a wide range of non-human primate species. The database includes approximately 400,000 data points from 16 different species, although the predominant amount of data is from rhesus macaques. The database is available at http://ipad.primate.wisc.edu. Access is restricted to investigators and veterinarians in academic and commercial laboratories with interests in aging research.
Proxeon has launched ProteinCenter, a "protein-centric" data warehouse that integrates public protein sequence databases with in-house experimental data and bioinformatics tools.
People in the News
Lion Bioscience has appointed Werner Hacke as a new member of its supervisory board. Hacke, director of the Neurological Hospital of the University of Heidelberg, will succeed Christoph Mutter, who has resigned from the board.
Nikolaus Rajewsky, professor of biology and mathematics at the Center for Comparative Functional Genomics at New York University, will move to the Max Delbr ck Center for Molecular Medicine in Berlin, Germany, this summer, where he will replace Jens Reich as research group leader in bioinformatics.
Teranode has appointed Paul Bleicher to its board of directors. Bleicher is the founder and chairman of clinical trial software firm Phase Forward and has held management positions at Paraxel International and Alpha-Beta Technology.
Carnegie Mellon University said this week that it will present its Dickson Prize in Science to David Haussler, professor of biomolecular engineering at the University of California, Santa Cruz, on March 9. Carnegie Mellon announced Haussler as the recipient of the prize in October [BioInform 10-3-05].