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Incogen, Joint Genome Institute, Proteomics Standards Initiative, Nonlinear Dynamics, BioCyc, Insightful, Ensembl 36, Waters, Martin Leach, Anne Lee, Albert Shieh, and Andrew Shapiro


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Incogen has released Version 3.3 of its Visual Integrated Bioinformatics Environment: VIBE. The new version is deployed on Java 5 and includes a number of new features, including automated discovery of VIBE servers, a software development kit wizard, a new vector masking algorithm, and a faster VIBE server installer. Further information is available at

The US Department of Energy's Joint Genome Institute has released the fourth version of its Integrated Microbial Genomes data-management system. The new version, IMG 1.3, contains 42 additional genomes sequenced by other institutions and 20 new genomes sequenced by JGI, bringing to 674 the total number of genomes in IMG. It contains 373 bacterial genomes, 26 archeal genomes, 15 eukaryotic genomes, and 260 viral genomes. JGI said 44 of these are finished and 90 are draft genomes sequenced by JGI. Organism phenotype, ecotype, disease, and relevance characterizations collected from literature have also been added to IMG 1.3. The new version also features enhanced comparative-analysis capabilities, including extended analysis carts and improved functional profiles across organisms, JGI said. IMG is available at The next update is scheduled for March 1.

The Proteomics Standards Initiative has released version 2.5 of the PSI Molecular Interaction XML (PSI MI XML) format and controlled vocabularies. Schema, CVs, and documentation are available at

Nonlinear Dynamics has launched its TT900 S2S 2D gel analysis software. This product includes tools for the pre-analysis alignment of 2D electrophoresis gel images, correcting the various gel inconsistencies that occur when running and imaging 2D gels, the company said. Once aligned to a very detailed level, images can be exported for traditional gel analysis. The new technology can be used with all staining or labeling methodologies, and has been enhanced to take advantage of in-gel groups when used within the DIGE workflow.

The BioCyc project at SRI International has released Version 9.5 of the BioCyc databases and Pathway Tools software. The BioCyc database includes 40 new databases, bringing the size of the collection to 205. the databases are available at

Insightful has released its Insightful Miner 7 data-analysis workbench. Insightful Miner 7 provides tools for data preparation, data cleaning, data modeling, and prediction. Insightful Miner 7 can be quickly adapted for users of Insightful's S-PLUS data analysis software to enable business users to create their own analyses and graphics without having to learn the S language, the company said.

Ensembl 36 is now available at The release includes a gene build for Rhesus macaque (Macaca mulatta) and new assemblies for cow (Bos taurus 6x assembly) and fugu (Fugu rubripes). In addition, the release includes a new gene build for the existing chicken assembly, WASHUC 1, using a modified version of the Ensembl pipeline. Updated information was also imported from Saccharomyces Genome Project.

Waters has begun shipping its MassLynx 4.1 software, which has been reconfigured to facilitate high-performance quantification and qualitative analysis so that users can process and review results, and generate reports more easily, the company said. The software also includes a new administrator toolkit that lets system administrators manage resources from a remote PC. The toolkit features software to monitor basic sample information and instrument status for all users.


People in the News

Martin Leach has left his position as director of bioinformatics at Curagen to join the life science practice of IT consulting firm Booz Allen Hamilton as principal. Leach told BioInform that he will be working with the firm's pharmaceutical customers. His primary role with be determining how to introduce new informatics tools under development Booz Allen Hamilton's technology development group into commercial practice in the biopharmaceutical industry.

Anne Lee and Albert Shieh, high-school students and interns at the Translational Genomics Research Institute, have been awarded the team prize in the 2005-06 Siemens Westinghouse Competition in Math, Science and Technology. The pair was awarded the $100,000 prize for developing a software packages called SNiPer, which improves SNP-genotype calling for Affymetrix 10K GeneChip microarray data. Their mentors at TGEN were their mentors were Dietrich Stephan, David Craig, and Matt Huentelman.

GEN ID Lab Services has appointed Andrew Shapiro as chief technology officer and as a member of the company's advisory board. GEN ID said Shapiro will take over the leadership of the software development department, which is currently developing a SNP-analysis software package. Shapiro has a BA in analytic philosophy from California State University Los Angeles.


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