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GenomeQuest 3.0, CLC Free Workbench 2.5, BioTech VPC, BioCyc, DogRun Online, RefSeq 16, Proteus, ClassPharmer 4.0, Murthy Srinivas, John Ohrn, Yoram Lapid, Dexter Pratt, Thomas Casavant


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Gene-IT has launched GenomeQuest 3.0, an updated version of its biological search tool for sequence patent queries. The new release includes sequence patent content that previously could not be searched, according to the company, including more than 25 million sequences found in more than 148,000 patent documents. An additional 278,000 patent documents are referenced and organized into 85,000 patent families. The new release also includes search methods to find SNPs, motifs, RNAi probes, diagnostic primers, microarray targets, and whole genes.

CLC Bio has released four new software products: CLC Free Workbench 2.5, a freeware program with a number of basic bioinformatics analysis packages; CLC Gene Workbench 1.0, which includes "advanced" DNA sequence analyses such as sequence assembly, primer design, and molecular cloning tools; CLC Protein Workbench 1.5, which includes protein sequence analysis tools such as 3D molecular viewing, protein structure prediction, transmembrane helix prediction, motif search, and pattern discovery; and CLC Combined Workbench 1.0, which aggregates all the bioinformatics tools in the other three packages.

Massively Parallel Technologies has added two new features to its BioTech Virtual Power Center: user selection of search speed and secure support for Blast searches against proprietary databases. Users can now set up a private account and securely upload proprietary databases to BioTech VPC. The company is making this service available free of charge at during an introductory period.

Version 10.0 of the BioCyc databases and Pathway Tools software is available from SRI International at Improvements include an updated version of the EcoCyc database "to reflect many aspects of the revised E. coli genome annotation," support for Gene Ontology terms, additional regulatory information for EcoCyc and RegulonDB, and 47 new metabolic pathways for MetaCyc.

Unleashed Informatics has released DogRun Online, a free and open access version of the company's DogRun application server, at The system allows users to run ad hoc Blast queries against the DogBox Online data warehouse.

The National Center for Biotechnology Information has released RefSeq 16 at The release incorporates genomic, transcript, and protein data and includes 2,520,485 proteins and sequences from 3,397 different organisms.

GenoLogics Life Sciences Software said that it has integrated its Proteus data-management software with the Institute for Systems Biology's open-source Trans Proteomic Pipeline so that users can launch TPP applications directly from Proteus.

Simulations Plus has released ClassPharmer 4.0, which includes revised algorithms and a faster programming language, and offers a "ten- to thousand-fold speed increase" in critical tasks such as substructure matching, predictive model generation, and chemical class identification, the company said.


People in the News

Teranode has appointed Murthy Srinivas as vice president of product and platform development, John Ohrn as vice president of sales, and Yoram Lapid as vice president of services and support. Srinivas was founder and chief technology officer of Consera Software, an enterprise data center management software company that was acquired by Hewlett-Packard in 2004. Ohrn most recently served as director of sales and support at Accelrys. Lapid has held a variety of positions with Cadence Design Systems, most recently as group director of design and consulting services and as client partner.

Genstruct has promoted Dexter Pratt to vice president of knowledge modeling. Pratt began consulting for Genstruct in 2002 and joined the firm in 2003 as director of biological systems modeling. Pratt previously served as director of the user interface group at LISP Machine, and as chief technology officer at Webkick and CineMetrix.

Thomas Casavant has been named the Roy J. Carver, Jr., chair in bioinformatics and computational biology at the University of Iowa — one of three endowed chairs recently established at UI with total gift commitments of $13.7 million, including $10 million from the family of the late Roy J. Carver Sr. Casavant is a professor of electrical and computer engineering and biomedical engineering in the College of Engineering and he directs the UI Center for Bioinformatics and Computational Biology.

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