Downloads & Upgrades
Gene Logic has released version 2.0 of its Ascenta system, a web-based software package for gene and biomarker discovery and validation. The new version includes Marker/X Tool, a suite of new algorithms and visual tools to identify genes with "distinctive expression behavior" in humans; Diff/X Summary Tables for viewing target gene regulation; PathwayPrioritizer, a tool for statistically ranking biological pathways regulated in altered biological states; and new human gene expression information, including inflammation content for multiple sclerosis and inflammatory bowel disease, and central nervous system content for Parkinson's disease.
Shimadzu and NEC have launched Solphi, a proteomics data-management software package. Solphi, which centrally manages test data and allows researchers to share information within a lab, is based on NEC's proprietary protein analysis support system BioPrism. A license for up to 10 users sells for 3,000,000 yen ($26,000). The companies said they expect to sell 20 packages annually in Japan.
BioPerl 1.5.1, a developers release, is available at http://bioperl.org/DIST/bioperl-1.5.1.tar.gz and http://bioperl.org/DIST/bioperl-1.5.1.tar.bz2. The release replaces BioPerl 1.5.0, "which had several bugs that made it incompatible with several bioperl-1.4.0 scripts," according to the BioPerl developers.
GenBank 150.0 is now available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/. The release contains 53,655,236,500 base pairs and 49,152,445 entries. Uncompressed, the 149.0 flat files require about 187 GB for the sequence files only. The ASN.1 version requires around 164 GB.
Bioconductor 1.7 is available at http://www.bioconductor.org. The release includes Rgraphviz as a binary package for Windows and the annotation data packages include protein information from IPI.
Affymetrix has released the Exon Array Computational Tool (ExACT), which enables probe-level analysis of the GeneChip Human Exon 1.0 ST Array, at http://www.affymetrix.com/support/developer/exact/index.affx. Affy has also released several commercial applications "for software development purposes and integration testing only" at http://www.affymetrix.com/support/developer/applications.affx.these packages include GCOS (GeneChip Operating Software) 1.4, GTYPE (GeneChip Genotyping Analysis Software), CNAT (Chromosome Copy Number Analysis Tool), and TAS (Tiling Analysis Software). The company has also released sample data for its exon and 500K arrays through its data resource center (http://www.affymetrix.com/support/developer/resource_center/index.affx), as well as updated specifications for the GeneChip Compatible program (http://www.affymetrix.com/products/software/compatible/compatible_specs.pdf).
Advanced Chemistry Development has released version 9.0 of its ACD/ChemSketch chemical structure drawing program and ACD/Name nomenclature tool. The new release offers full compatibility with the InChI chemical nomenclature protocol.
The Public Population Project in Genomics (P3G), a non-profit population genomics consortium, has released P3G Observatory, a central Internet repository for research tools developed and collected by the P3G consortium, at http://www.p3gobservatory.org. The repository includes research tools for population studies as well as tools for harmonizing population studies around the world.
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Accelrys has hired Richard Murphy as senior vice president of worldwide sales and services. Murphy was recently senior vice president, general manager, and chief sales officer of MSC Software, an IT firm focusing on mechanical computer-aided engineering software. Prior to MSC, Murphy held senior technical positions with PDA Engineering and Ford Aerospace. According to company SEC filings, Murphy will be paid an annual base salary of $250,000, and is eligible to participate in the company's sales management incentive plan with a targeted bonus of 60 percent of his base salary. For the company's 2006 fiscal year, which ends March 31, this bonus amount will be paid on a pro-rated basis and Accelrys said that it will guarantee payment of 75 percent of this amount.
John Hanlon, who most recently served as executive vice president and chief financial officer at Accelrys, has joined Synplicity, a supplier of software for semiconductor design, as senior vice president of finance and chief financial officer. Prior to Accelrys, Hanlon served as senior vice president and chief financial officer at MDL Information Systems for 10 years and also spent 10 years in public accounting at Coopers & Lybrand, LLP.
Richard Mural joined the Windber Research Institute as chief scientific officer, replacing Michael Liebman, who has become executive director of the institute. Mural was director of scientific content and analysis at Celera Genomics. Richard Somiari, formerly chief scientific officer and chief executive officer of the institute, has left to found Integrated Technologies & Services International — Biosciences.
Stephen Leicht has joined the board of advisors for iAdvantage Software, a provider of software for managing development and pre-clinical life science studies. Leicht is life science territory manager for IBM in North and South Carolina and the former chairman and CEO of International Telecommunications Distributors, a company he sold in 2001.