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MedScan Reader 1.0, Reactome 16, DogRun, CERF 2.5, AlleleID 2.00, NetworkAnalyzer, Sren Brunak, Michael Ashburner, Helen Berman, Phil Bourne, Sean Eddy, Don Gilbert


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Ariadne Genomics has released MedScan Reader 1.0, a new desktop software product for automated extraction of information from scientific text. MedScan Reader is derived from MedScan, Ariadne's natural-language-processing technology. A 20-day free trial is available at

Reactome 16 is available at The release includes the annotation of host-pathogen pathways in the form of Influenza A infections, as well as new modules on the human electron transport chain and its integration with mitochondrial ATP synthesis and thermogenesis, the Drosophila melanogaster signaling pathway mediated by insulin-like proteins, and a "substantially revised" module covering the G2/M transition of the human mitotic cell cycle. Reactome now includes 1,451 curated human reactions and 1,179 annotated human proteins.

Unleashed Informatics has launched DogRun, an application environment designed to run ad hoc Blast searches against the data in the company's DogBox data warehouse. DogRun includes NCBI's blastall (blastn, blastp, blastx, tblastx, and tblastn), blastpgp (psiblast, phiblast), and megablast. DogRun operates on a "robust but inexpensive" Sun V20z server, the company said.

Rescentris has released CERF (Collaborative Electronic Research Framework) 2.5 and the CERF Development Kit (CERF-DK). CERF is an electronic laboratory notebook "built on semantic web technologies," including XML, RDF, and OWL, Rescentris said.

Premier Biosoft has released AlleleID version 2.00. The software aligns sequences and analyzes species-specific regions to design probes for microarrays and primers and probes for TaqMan qPCR assays. According to the company, the assays are designed to detect only the strain or species of interest from the mix.

The Max Planck Institute for Informatics has released NetworkAnalyzer, a new Cytoscape plug-in, at NetworkAnalyzer computes network topology parameters such as diameter, average number of neighbors, and number of connected pairs of nodes, and works with Cytoscape 2.1 and 2.2.

People in the News

The Villum Kann Rasmussen Fonden, a foundation that supports scientific, artistic, cultural, and social projects in Denmark, has awarded Søren Brunak, director of the Integrative Systems Biology research group at the Technical University of Denmark, a research prize worth €350,000 ($424,000). Brunak received the prize for "his work as a pioneer at the implementation of bioinformatics as a research discipline in Denmark," according to the university.

The Bioinformatics Organization has named its nominees for the 2006 Benjamin Franklin award, which is presented annually to members of the bioinformatics community who have promoted open access in the field. This year's nominees include Michael Ashburner of the University of Cambridge, Helen Berman of the Protein Data Bank, Phil Bourne of the University of California at San Diego, Sean Eddy of the Howard Hughes Medical Institute and Washington University, and Don Gilbert of Indiana University. Further information about the award is available at

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