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Tube Formation BioApplication, GeneDirector 3.0, EMBL Nucleotide Sequence Database, caGrid 0.5, BASE, X! Hunter, Pfam 18.0, ActivityBase, MIRA 2.4.0, Burkhard Rost, Michael Gribskov, Christopher Yoo


Downloads & Upgrades

Cellomics, a Fisher subsidiary, said it will release the Tube Formation BioApplication, an image-analysis algorithm that allows scientists to quantitatively analyze angiogenic tube formation in vitro, in the fourth quarter for all versions of Cellomics' ArrayScan HCS Reader and KineticScan HCS Reader.

BioDiscovery has released GeneDirector 3.0. New features of the microarray data-management platform include integration with the Affymetrix GCOS server, enhanced project management features, HTML-based project summaries, text-based search queries across projects, integration with Tecan hybridization stations, and an ImaGene results reviewer.

Release 84 of the EMBL Nucleotide Sequence Database is available from (UK) and mirror sites. The file size is about 53.2 GB (compressed), and 293 GB (uncompressed).

The National Cancer Institute's Cancer Biomedical Grid project has released caGrid 0.5, a testbed grid infrastructure for caBIG. The infrastructure defines two types of grid services that can be registered as nodes on the grid: data services and analytical services. Data services provide data query and retrieval services to clients, while analytical services provide data transformation, processing, and statistical analysis services to clients. The caGrid software and documentation are available for download at

The alpha 5 release of BASE (BioArray Software Environment) 2 is available at The release includes the first version of a web-based GUI for the open source microarray database.

The Global Proteome Machine Organization has released X! Hunter, a peptide identification search engine that directly compares an input spectrum to a library of spectra that have been assigned to a particular peptide sequence, rather than predicting spectra directly from the peptide sequence. X! Hunter is available at

Pfam 18.0 is available at It contains 7,973 proteins domain families matching three quarters of UniProt 5.0.

IDBS has launched ActivityBase Xtended Edition (ActivityBase XE), a module for data capture, visualization, verification, quality control, and storage of high-throughput screening data.

The Max Delbr ck Center for Molecular Medicine has released a human protein-protein interaction network database at The database includes 3,186 interactions between 1,705 human proteins, including 531 previously unknown interactions involving 195 disease proteins. A paper describing the database has been published in the Sept. issue of Cell.

MIRA 2.4.0, a sequence assembly system for genome and EST sequences, is available at The MIRA genome fragment assembler is designed for sequencing projects with a high number of similar repeats.

People in the News

Burkhard Rost has been elected as the next president of the International Society for Computational Biology. Rost currently serves as ISCB vice president. He will begin his one-year term as president-elect on Jan. 21, 2006, followed immediately by a two-year term as president. Rost, an associate professor at Columbia University's Bioinformatics Center, will succeed Michael Gribskov, professor of biological sciences and computer science at Purdue University, as president of the society.

Christopher Yoo has joined the InnovationXchange Network, an Australia-based non-profit business development organization, to lead business operations in the Americas and internationally. Yoo was formerly director of marketing, commercial operations, at Applied Biosystems and previously worked at IBM as global strategy executive for the company's Information Based Medicine business unit.

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