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Indian Institute of Technology, Pharmacopeia, UB Biomedical Ontology Project, H-Inv DB, National Institutes of Health, ArrayExpress, Bioconductor Training Course


India’s IIT to Connect Supercomputer with Biogrid

India’s Financial Express reported last week that the Indian Institute of Technology in Delhi (IIT-D) plans to connect its supercomputing facility with the Department of Biotechnology’s Biogrid network of 60 research centers.

The IIT-D supercomputer offers 150 Gflops of computing power through a 70-processor Sun cluster, two 16-processor Pentium clusters, and a four-processor SGI Origin 200. It will initially support 11 centers on the Biogrid, according to the Financial Express.

Pharmacopeia Settles on Dividend: One Share of PDD for Two Shares of Accelrys

Pharmacopeia last week said that its board of directors declared a dividend of all of the outstanding shares of common stock of Pharmacopeia Drug Discovery, the drug discovery business that it plans to spin off this month.

The dividend is at the ratio of one share of PDD common stock for every two shares of Pharmacopeia (to be renamed Accelrys after the spin-off).

The dividend is expected to be payable on April 30, 2004 to Pharmacopeia stockholders of record as of the close of business on April 16, 2004.

Volkswagen Foundation Donates $1.1M to UB Biomedical Ontology Project

The Volkswagen Foundation has awarded a $1.1 million grant to a project at the State University of New York at Buffalo to develop a formal ontology for biomedical information systems.

Barry Smith, a professor of philosophy at UB, leads the project under the auspices of the Buffalo-Leipzig Institute for Formal Ontology and Medical Information Science (INFOMIS). INFOMIS is a collaborative effort involving UB and the University of Leipzig, where the institute is located.

Smith said the project will involve collaboration between bioinformaticists, medical informaticists, biologists, and health-care providers who work in different linguistic and terminological systems.

International Consortium Releases Database of Validated Human Genes

An international consortium of 152 researchers has wrapped up a two-year “annotation marathon” in which it validated 21,037 human genes in public databases using cDNA clones.

The consortium, called H-Invitational and led by Takashi Gojobori of the Japan Biological Information Research Center in Tokyo, released the fruits of its efforts last week via a public database called H-Inv DB (

A paper describing the project appears in the April 16 issue of PLoS Biology.

NIH Seeks Commercial Developer for Protein Database Query Tool

The National Institutes of Health Office of Technology Transfer said last week that it is seeking a commercial developer for a query tool developed by NIH researchers for protein identification.

The software, developed by Rodney Levine at NHLBI, is a query generator that provides a script that identifies an isolated protein by using physical properties of the protein and submitting the query into a protein database. The method combines an accurate determination of the ratio of at least one amino acid per molecule and at least one physical parameter of the protein in order to make an accurate and unique match.

The licensing contact is Michael Shmilovich ([email protected]).

ArrayExpress Database Hits 5,000-Hybridization Milestone

The European Bioinformatics Institute’s ArrayExpress repository for microarray-based gene-expression data passed the 5,000-hybridization mark on April 2, 2004, the EBI said last week.

The resource was launched in December 2002, and has grown almost 100-fold in the past year, EBI said. In the past three months, the resource has grown at an average of 25 hybridizations per day. The resource now contains data from almost 200 separate studies of 15 different organisms, and contains over 150 gigabytes of data.

Bioconductor Project to Host Training Course

The open source Bioconductor microarray analysis project will host a training course for the package June 28-29 in Boston.

The instructor for the course will be Vincent Carey, a biostatistician at Harvard Medical School and a core member of the Bioconductor development team.

Further information and a registration form are available at

Filed under

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.