Downloads & Upgrades
TimeLogic has released Tera-Probe, a probe-design application that runs on the company's CodeQuest workstation or DeCypher server. Researchers can use Tera-Probe to select highly specific probes with minimal cross-hybridization for microarray experiments. The program can identify oligo sequences 16,500 times faster than the Smith-Waterman application with comparable sensitivity, TimeLogic said. Further information is available at http://www.timelogic.com/teraprobe.html.
Applied Biosystems has released Sequence Scanner Software v1.0, a free software package, at http://www.appliedbiosystems.com/sequencescanner. The software allows users to view, edit, print, and export sequence data from the company's genetic analyzers. It also displays "thumbnail" traces to provide an overview of large amounts of raw sequence data and help identify anomalies. Files can be exported from Sequence Scanner Software in a number of files formats including jpeg and pdf files, either individually or in batch mode.
Affymetrix has launched Fusion SDK Release 1, which contains tools for parsing data files generated by the MAS/GCOS system and the upcoming Command Console software, at http://www.affymetrix.com/support/developer/fusion/index.affx. The company has also released version 4.0 of the IGB genome browser, which includes support for data loading from DAS/2 servers, at http://www.affymetrix.com/support/developer/tools/download_igb.affx.
Kinexus Bioinformatics has released KiNET, a cell-signaling proteomics database with embedded searching capabilities. The database includes 200,000 measurements of the expression levels and phosphorylation states of hundreds of signal transduction proteins from hundreds of different biological specimens, including over 200 tumor cell lines. The data has been collected from the company's Kinetworks immunoblotting services over the last six years, and the company said that more than 95 percent of the KiNET data is "unpublished and not available elsewhere."
Partek has released Partek Genomics Solution 6.2, which includes support for Affymetrix GeneChip expression arrays, exon arrays, and chromosomal copy number analysis of high-density SNP arrays. Additional features include improved import capabilities for two-color arrays, an enhanced genome browser, and capabilities for detection of alternative splicing. The software also includes the Partek Batch Remover, which can be used to estimate and remove biological and technical batch effects such as cell culture batches, reagent lots, and processing batches. Information about a free trial is available at http://www.partek.com.
GE Healthcare has launched the Micronucleus Formation Module, a new software application for the IN Cell Analyzer 1000 and 3000 that enables screening for genotoxicity. The micronuclei assay identifies DNA damage induced by genotoxic compounds. According to GE, the analysis software can image and analyze a 96-well plate of micronucleus assays in under 10 minutes.
CLC Bio has released two new bioinformatics software solutions for lab researchers: CLC Free Workbench 2.0 and CLC Protein Workbench 1.0. CLC Free Workbench 2.0 is freely available, runs on Windows, Mac OS X, and Linux, and includes new bioinformatics features, improved data management facilities, and improved sequence and alignment viewers. CLC Protein Workbench 1.0 is an extension to CLC Free Workbench for protein analysis. A demo version of CLC Protein Workbench 1.0 is available at http://www.clcbio.com.
Nervana has released Nervana IP Discovery version 1.0, a service that indexes information configured to six life sciences ontologies on a subset of US patent data to enable semantic patent searches. The company said it partnered with PatentCafe, a provider of intellectual property asset management software, to develop the service.
Terra Soft Solutions has debuted Y-Bio, a software package built upon the RPM Linux standard that includes NCBI Blast, EMBOSS, Glimmer, ClustalW, Hmmer, Wise, and Fasta with a web-based user interface built on the Pise package. Y-Bio is scheduled to ship in January and licenses begin at $9,500. A demo version of the software running on Terra Soft's 16-processor trial cluster will be available at http://www.terrasoftsolutions.com/products/y-hpc/y -bio/ in December.
New genome assembly annotations for Drosophila sechellia and D. persimilis are available at DroSpeGe, a comparative genome database of Drosophila species from the Genome Informatics Lab at Indiana University, at http://insects.eugenes.org/species/.
ChemAxon has added support for Chemicalinventory.org, an open source chemical inventory web application, to its Marvin editor and viewer and JChem Base chemical search and database management tools. ChemAxon is providing university users with free licenses to enable the application in their laboratories as part of its 'Powered by Academic Package' program, which provides academic labs with licenses and support for all ChemAxon products at no charge. Further information about the program is available at http://www.chemaxon.com/forum/ftopic193.html.
People in the News
George Rathbun, director of architecture in Pfizer's Global Research and Development Informatics organization, has been named chief technology officer of the SAFE-BioPharma Association, an industry organization that is developing a secure digital signature standard for use in the pharmaceutical and healthcare industries. Rathbun will oversee and administer all aspects of technology for SAFE-BioPharma and will serve as chairman of the SAFE (Secure Access for Everyone) technology and implementation working groups and as the chief systems architect for SAFE. Rathbun joined Pfizer in 1990 and has held a position as information and technology architect for the past five years.
ViaLogy, a provider of signal-processing software for analyzing data from microarrays, mass spectrometers, and other instrument platforms, has hired Michael Kelly as its CEO and president. Kelly is a general partner and manager at the Palo Alto office of First Ventury, a venture capital firm. Before joining First Ventury, Kelly was CEO of American Express Bank GmbH, Frankfurt, and senior banker with Commerzbank and Bank of America in the US and Deutsche Bank in Germany.
Orchid Cellmark has appointed William Lutz to the newly created position of vice president of information technology. Lutz most recently served as chief information officer at Genencor International. At Orchid Cellmark, he will oversee the company's global information technology infrastructure.