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UCSC Genome Browser, UniProt Release 7.0, DecisionSite for Lead Discovery 8.2, ProteinLynx Global Server 2.2.5, Analyzer Suite 3.0, Michael Ashburner


Downloads & Upgrades

The Genome Bioinformatics Group at the University of California, Santa Cruz, has added the latest rhesus macaque (Macaca mulatta) draft assembly, v.1.0 (Mmul_051212), to the UCSC Genome Browser. This version was sequenced and assembled by the Macaque Genome Sequencing Consortium led by the Baylor College of Medicine Human Genome Sequencing Center, in collaboration with the Genome Sequencing Center at Washington University School of Medicine in St. Louis and the J. Craig Venter Institute Joint Technology Center. The assembly covers about 93 percent of the rhesus genome. Sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server at or the downloads page at

The UniProt Consortium at the European Bioinformatics Institute, the Swiss Institute of Bioinformatics, and the Protein Information Resource has made UniProt Release 7.0 available at The current release includes 2,812,716 entries (207,132 in the UniProtKB/Swiss-Prot section and 2,605,584 in the UniProtKB/TrEMBL section).

Ensembl 37 is available at The new release includes 11 million new mouse SNPs identified via on the Wellcome Trust Sanger Institute's alignment of the Celera mouse whole genome against the reference mouse genome. Ensembl 37 also includes new assemblies and gene predictions for Ciona intestanlis and Xenopus tropaclis, a new assembly of Anopheles gambiae, and new web display features.

Spotfire has released DecisionSite 8.2 and DecisionSite for Lead Discovery 8.2. DSLD 8.2 includes a new feature called Chemistry Services that supports the Isentris technology from Elsevier MDL and enables users to integrate any Oracle cartridge-based search engine or molecule-drawing program. DecisionSite 8.2 also supports Microsoft's .NET framework and includes a new set of APIs to enable developers to add context menus to guides.

Abrevity has launched BioData Manager, a software product for finding, extracting, classifying, and managing laboratory instrument files. The software can be used with flow cytometers, confocal microscopes, or other laboratory instruments, the company said.

Waters has released ProteinLynx Global Server 2.2.5, which includes new features for identifying and quantifying proteins and biomarkers. A new quantification module allows quantitative data to be generated at the protein or peptide level using any commercially available or user-defined labeling technologies such as SILAC, AQUA, ICAT, or iTRAQ. PLGS 2.2.5 also includes a new algorithm to identify proteins from MSE data acquired from a Q-TOF mass spectrometer. PLGS 2.2.5 supports a number of formats including peaklist, XML, and mzData.

Media Cybernetics has released InVivo Analyzer Suite 3.0, a software package for live-cell imaging. InVivo Analyzer Suite includes three scientific applications: the InVivo acquisition tool, the Image-Pro Analyzer analytical tool, and the 3D Constructor tool for 3D rendering. InVivo Analyzer Suite 3.0 also includes a FRET Experiment Wizard that guides users through the process of evaluating the relationship between two fluorescent molecules.


People in the News

The Bioinformatics Organization said this week that it will present the 2006 Benjamin Franklin Award in the Life Sciences to Michael Ashburner of Cambridge University. The annual award is presented to an individual who has "promoted free and open access to the materials and methods used in the life sciences." Members of Bioinformtics.Org, a non-profit open source bioinformatics advocacy, vote on the recipient each year. Ashburner was cited for his "fundamental contributions to many open access bioinformatics projects," including FlyBase, the GASP project, the Gene Ontology, and the Open Biological Ontologies project. The award will be presented at the 2006 Bioinformatics.Org Annual Meeting, held in conjunction with the Life Sciences Conference and Expo, held in Boston April 3-5.

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