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Rosetta Syllego, dbSNP 126, SOAP E-Utilities, BioCyc 10.1, Phenyx 2.1, TeraGrid Bioportal, Metabolic Vision, Pfam 20.0, Galileo LIMS 3.2, Modware 0.1, Krishna Kodukula, Anthony Day, John Green, Peter Rock

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Rosetta Biosoftware has released the Rosetta Syllego Genetic Data Management and Analysis System, a platform for managing genetic data from disparate sources and for combining genotypic and phenotypic study data. Syllego also includes basic data analysis tools and the ability to integrate study data with common statistical packages, such as R.


The National Center for Biotechnology Information has released dbSNP 126, which includes a new dbSNP human build mapped to genome 36.1, at ftp.ncbi.nih.gov/snp/. The previous dbSNP mouse build 126 based on genome build 35.1 has been updated to 36.1. NCBI also announced that it will release a new version of its SOAP E-Utilities next week to include recent changes to the NCBI sequence databases schema. The new version is available for testing at http://web.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl.


SRI International has released BioCyc 10.1 at http://biocyc.org/. Improvements include updated links from EcoCyc proteins to UniProt to reflect changes in UniProt IDs, new links from EcoCyc proteins to the ModBase and Swiss-Model databases of predicted protein structures, and 47 new pathways in MetaCyc. The BioCyc database collection includes 205 databases.


Geneva Bioinformatics has released Phenyx 2.1. New features include an expandable submission window, an improved resubmission functionality, a management module for profile submission that includes several pre-defined profiles and allows users to define their own profiles, and enhanced interaction with the MSight LC-MS imaging software from the Swiss Institute of Bioinformatics.


The Renaissance Computing Institute has launched the TeraGrid Bioportal at http://www.tgbioportal.org, which provides users of the National Science Foundation's TeraGrid access to a range of bioinformatics and biomedical applications and databases. The Bioportal includes more than 100 applications and biological data sets and provides access to a dedicated cluster and TeraGrid systems across the US.


Ariadne Genomics has included Integrated Genomics' Metabolic Vision microbial pathway collection as an "ancillary pathway database" for its PathwayStudio and PathwayExpert software, the company said. The Metabolic Vision collection expands the company's pathway software to include microbial pathway analysis for basic, medical and industrial microbiology, and food and environmental research in addition to mammalian pathway analysis.


The Wellcome Trust Sanger Institute has released Pfam 20.0, which includes 8,296 protein domain families, at http://www.sanger.ac.uk/Software/Pfam/. The release includes 123 new families and 10 families have been deleted since the last release.


SequenceBase and FIZ Karlsruhe are previewing the USPTO Genetic Sequence Database, or USGENE, and plan to release the product this summer. USGENE covers all peptide and nucleic acid sequences from the published applications and issued patents of the United States Patent and Trademark Office from 1982 to the present. It supports freedom-to-operate, prior-art, validity and infringement patent sequence searches, as well as competitive analysis of biosequence patents.


Thermo Electron has released Galileo LIMS 3.2, which includes user-definable study types and customizable calculations for ADMET assays. Galileo 3.2 also includes user-configurable decision trees that allow researchers to define scenarios under which flagged results require further review.


The first release of the Stickleback (Gasterosteus aculeatus) genome is available via the Pre Ensembl database at http://pre.ensembl.org/Gasterosteus_aculeatus/. The assembly, provided by the Broad Institute, has a base coverage of approximately 5.93X.


Modware 0.1, an API that creates BioPerl object representations of biological features stored in a Chado database, is available at http://sourceforge.net/projects/gmod-ware.

People in the News

Krishna Kodukula has joined SRI International's biosciences division as senior director of systems biology. Kodukula comes from Sarnoff, an SRI subsidiary where he was a member of its technical staff. In his position at SRI, Kodukula will establish new programs and will work closely with SRI's Center of Excellence in Infectious Disease and Biodefense and Center of Excellence in Computational Biology. Prior to working at Sarnoff, Kodukula helped launch Small Molecule Therapeutics, a drug discovery firm, and co-found Pyxis Technology Solutions, an IT tools developer. Before that, he was a senior research investigator at Bristol-Myers Squibb Pharmaceutical Research Institute and a fellow at the Roche Institute of Molecular Biology.


Solazyme, an algal biotechnology company, has tapped Anthony Day as vice president of R&D. Day was most recently a research director in the R&D division of Genencor, where he spent twelve years and played a number of roles, including head of structural biology and head of bioinformatics.


ComScore Networks, a market research firm that specializes in Internet usage patterns, has appointed John Green as CFO. Green joins the firm from Invitrogen, where he served as the CFO and US services business leader for the company's BioReliance subsidiary. Green joined Invitrogen as the COO and CFO of InforMax after it was acquired by Invitrogen in 2002.


Gene Network Sciences has hired Peter Rock as CFO. Rock is chairman of the business solutions advisory board for the Biotechnology Industry Organization and was previously co-chairman of the Massachusetts Biotechnology Council's finance committee. For the past four years, Rock has served as the principal of Rock Consulting and provided financial guidance to a number of start-up biotech and technology companies. He was previously vice president and corporate controller of Dyax. Prior to that, he held various financial management positions at Avery-Dennison, AEG Schneider Automation, and United Technologies.

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