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KDE 3.0, Genedata Screener 4.0, Teranode XDA 2.8, UCSC Genome Browser, Mr Bump, BioCyc 9.6, ArrayAssist Exon, ArrayAssist Expression, SoftMax Pro 5, SMIDSuite, Eric Neumann, Robert Quinn, Todd Pierce


Downloads & Upgrades

InforSense has released KDE 3.0, which includes expanded support for personalized data manipulation and reporting. New features include additional file import/export options, improved performance for handling large datasets, interactive control of long-running jobs, more reporting and output options including e-mail notification, and expanded visualization options. In addition, the client graphical user interface has been redesigned to include workflow constructs that link multiple analytical workflows according to business rules. KDE 3.0 also includes support for Oracle Database 10g Release 2.

Genedata has released Genedata Screener 4.0, a scalable solution for high-throughout screening analysis. The software includes a public application programming interface to link Screener's database resources with the client's existing corporate information portals, as well as procedures for analyzing high-content screening data.

Teranode has launched Teranode XDA 2.8, which includes a new Batch Builder feature that allows samples and compounds from multiple projects to be processed as one batch, while providing tracking and reporting for each project individually. The new release also offers JAAS (Java Authentication and Authorization Service) support, which enables user authentication and sign-off via existing enterprise security systems; centralized lab configuration management; and new shortcuts that allow users to bookmark and access experiments stored in a Teranode Model Server. Teranode XDA 2.8 is available immediately, with pricing starting at $1,000 per user and $25,000 per server.

The Genome Bioinformatics Group at the University of California, Santa Cruz, has released a Genome Browser and Blat server for the D. persimilis genome, which was sequenced and assembled by the Broad Institute. The assembly joins nine other Drosophila species in the UCSC Genome Browser. Downloads of the droPer1 data and annotations are available via FTP at or through the Downloads page at

The UK's Daresbury Laboratory has released Mr Bump (formerly known as BMP), which takes as input a target sequence and experimental structure factors and searches for for homologous structures, creates a set of suitable search models from the template structures, performs molecular replacement, and tests the solutions with some rounds of restrained refinement. Mr Bump is available at

SRI International has released BioCyc 9.6 at New features in EcoCyc include the assignment of EcoCyc genes to Gene Ontology classes and curated information on RNA degradation and processing, DNA replication, and more than 70 membrane proteins, flagella, and transport proteins. The release also includes 81 new MetaCyc pathways.

Stratagene released its ArrayAssist Exon and ArrayAssist Expression software for Mac OS X version 10.4 at MacWorld this week. "Apple has always been a favorite platform for scientists, so it was a natural decision to offer the latest in Affymetrix data analysis to the Mac community," said David Weber, senior vice president of marketing at Stratagene, in a statement.

Molecular Devices Corporation has launched SoftMax Pro 5, data acquisition and analysis software for its line of microplate readers. The new software is available in two editions: SoftMax Pro 5 for use in research and academic laboratories; and SoftMax Pro 5 GxP, which includes FDA 21 CFR Part 11 compliance features and is targeted to the pharmaceutical and biotechnology industries. Both versions are compatible with Mac OS X and Microsoft Windows.

Unleashed Informatics has launched SMIDSuite, a small-molecule information suite that contains the Small Molecule Interaction Database (SMID), SMIDBlast, and SMID Genomes. SMID includes protein domain interactions derived from Protein Data Bank 3D structure records and currently contains more than 230,000 domain/small molecule interactions. SMIDBlast runs NCBI's Reverse-PSI BLAST program to match a protein sequence of interest against a library of more than 3,000 domain definitions with more than 5,000 biologically significant small molecules to predict binding sites on the query protein. SMIDGenomes contains more than 12 million predicted small molecule interactions spanning nearly 1,600 complete genomes. Unleashed has also launched UnleashedNEWS, a new feature for its DogBox data warehouse product that delivers news feeds from more than 450 science and technology news feeds


People in the News

Eric Neumann has joined Teranode as senior director of product strategy. Neumann will focus on semantic web collaborations with customers, partners, and standards bodies "to accelerate successful adoption of W3C standards by customers and within Teranode products," the company said in a statement. Prior to joining Teranode, Neumann held executive positions at Sanofi-Aventis Pharmaceuticals; Beyond Genomics; NetGenics; and Bolt, Beranek, and Newman.

Chemical Computing Group and the American Chemical Society's Division of Computers in Chemistry announced the winners of the CCG Excellence Awards at the 231st ACS National Meeting in Atlanta last week. The CCG Excellence Award honors graduate students in the field of computational chemistry. The 2006 winners include Xhua Chen of New York University, Xuhui Huang of Columbia University, Casey Kelly of the University of Minnesota, Valerie McCarthey of the University of Pittsburgh, and Devina Pillay of the University of Texas at Austin.

Genentech appointed six new vice presidents last week, including Robert Quinn as vice president of corporate information technology business and science applications, a newly created position. He will report to Todd Pierce, vice president of corporate information technology and will focus on a variety of IT solutions to support the company's corporate and commercial functions, as well as research and development. Quinn joins Genentech from KLA-Tencor, where he served as vice president and chief information officer. Prior, Quinn held executive and senior positions at Portera Systems, eBay, and Sun Microsystems.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.