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BioInformatics Briefs: Dec 1, 2003


CytRx Subsidiary Araios Taps 3rd Mill for Informatics Platform

Araios, a subsidiary of CytRx based in Worcester, Mass., has hired bioinformatics consulting firm 3rd Millennium to build its drug discovery informatics platform, 3rd Millennium said last week

Araios uses CytRx’s RNAi-based technology in combination with structure-based medicinal chemistry. The informatics platform will support the company’s RNAi-based development programs focused on type 2 diabetes and obesity therapeutics. CytRx said its scientists would use the system to generate focused libraries of compounds for major targets for these diseases.

3rd Millennium is advising CytRx on the selection of software and hardware for virtual library construction, homology modeling, and virtual screening workflow.

Eric Meyers, chief operating officer at 3rd Millennium, said that Araios does not have an in-house bioinformatics team, and 3rd Millennium was brought in to advise the firm on what software and hardware systems to purchase. “We’ve helped them negotiate their contracts with the various vendors, and are in the process of implementing the system now,” Meyers told BioInform.

IBM to Build Prototype Platform for German Genome Research Network

IBM said last week that it has signed an agreement with the German National Data Center for Genomic Research (Deutsches Ressourcenzentrum f r Genomforschung, or RZPD) to build a prototype data platform for genomic researchers across Germany.

IT architects from IBM’s laboratory in La Gaude, France, will work with researchers from the RZPD to create the prototype system, which will be based on IBM’s DiscoveryLink integration software.

If adopted, the system would provide a consolidated “virtual database” of genomic, proteomics, and other biological data for both public and private researchers in Germany. IBM said that the system is being designed so that users can consolidate their data with that of RZPD and other public bodies without giving up complete control of their data.

ORNL Wins $4.5M Grant to Build High-Speed Science Network

The Department of Energy’s Office of Science has awarded Oak Ridge National Laboratory $4.5 million to design a high-speed network dedicated to scientific computing.

The so-called Science UltraNet project will support high-performance computing at DOE facilities and universities.

According to the DOE, genomics research and other collaborative large-scale projects will be the primary beneficiaries of the project because current networks do not have adequate capacity, are shared by many users, and are based on software and protocols that were not designed for petascale data.

The UltraNet will operate at 10-40 gigabits per second. A testbed network will link ORNL to Atlanta, Chicago, and Sunnyville, Calif.

GNF Licenses Ingenuity Pathways Software

Ingenuity Systems said that the Genomics Institute of the Novartis Research Foundation (GNF) has licensed its Ingenuity Pathways Analysis application for use in its research programs.

“The Ingenuity Pathways Analysis application allowed us to immediately identify interesting biological insights in our gene expression data that we did not identify in many months of previous analysis,” said John Hogenesch, senior research scientist at GNF.

Financial terms of the agreement were not disclosed.

Merck Installs SGI-based Hardware Platform

SGI said last week that the Department of Bioinformatics at Merck Research Laboratories has installed an informatics system based on SGI hardware.

New SGI equipment, installed in October, includes one 256-processor Origin system and one 32-processor Origin server. In addition, Merck has purchased SGI InfiniteStorage with 10 TB of disk, a mix of 10 Silicon Graphics Octane and Fuel workstations, four SGI Origin 300 servers, one SGI Altix 3000 server with 12 Intel Itanium processors and 300 seats of Platform LSF from SGI software partner Platform Computing.

GSK Expands Agreement with BioWisdom

Biological ontology provider BioWisdom said last week that it has extended an existing 18-month agreement with GlaxoSmithKline.

The renegotiated non-exclusive agreement is for three years.

Under the terms of the agreement, GSK will import components of BioWisdom’s ontologies into its internal thesaurus, and BioWisdom said it will consult the pharmaceutical firm “in areas related to the development of ontology-based applications that improve productivity in drug discovery and development, and support knowledge reuse.”

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