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IBM and Ecole Polytechnique Fdrale de Lausanne, NIGMS, RZPD and Insilico, and Geneva Bioinformatics and Hitachi


IBM, EPFL to Use Blue Gene in Brain-Modeling Project

IBM and France's Ecole Polytechnique Fédérale de Lausanne are collaborating on a two-year research project nicknamed "Blue Brain" that will put IBM's Blue Gene supercomputer to work on building a detailed model of the circuitry in the human neocortex at the cellular level.

The collaborators plan to expand the project to model other areas of the brain in the future, eventually building an accurate, digital model of the entire brain.

"Modeling the brain at the cellular level is a massive undertaking because of the hundreds of thousands of parameters that need to be taken into account," said Henry Markram, the EPFL professor heading up the project, in a statement. His lab has compiled a comprehensive set of empirical data on the micro-architecture of the neocortex that will be used to build the three-dimensional computational model.

"With an accurate computer-based model of the brain much of the pre-testing and planning normally required for a major experiment could be done 'in silico' rather than in the laboratory," Markram said. "With certain simulations we anticipate that a full day's worth of wet lab research could be done in a matter of seconds on Blue Gene."

The Blue Gene system that will be installed at EPFL will have a peak processing speed of 22.8 teraflops.

NIGMS Commits $800K in FY '06 for E. coli Model Org Database

The National Institutes of Health has issued a request for applications for the development of a model organism database for Escherichia coli strain K-12, related strains, and their phages and mobile genetic elements.

The proposed resource will include "information specific to E. coli K-12, as well as relevant data from strains C and B, and information and data on the principal phages and plasmids that contribute to our basic knowledge of gene transactions, self-assembly processes, and bacterial functioning through the host-parasite relationship," the NIH said. "The content must be current, documented, and reflect uncertainties."

The NIH said that about $800,000 will be provided in 2006 to a single grant in response to the RFA. An applicant may request a project period of up to three years and a budget for direct costs up to $500,000 per year, exclusive of subproject indirect costs.

The RFA, which is being overseen by the National Institute of General Medical Sciences, is open to both profit and non-profit organizations.

Additional details about the RFA can be found at

RZPD to Use Insilico Data Warehouse

RZPD, the German Resource Center for Genome Research, said last week that it will use the MASI biological data warehouse developed by Insilico of Vienna, Austria.

RZPD said that it will integrate MASI with its material index so that researchers can cross-reference sources and identify research material offered by RZPD that matches their query.

MASI integrates information on RNA, DNA, proteins, and native tissues and cells. The database will be updated on a weekly basis.

Hitachi to Distribute GeneBio's Phenyx in Japan

Geneva Bioinformatics said last week that it has signed an agreement with Hitachi Software Engineering to distribute its Phenyx mass spec analysis platform within the Japanese market.

The agreement will "further solidify" GeneBio's existing business relationship with Hitachi Software, the company said. In December, the companies first agreed to work together via the Bioinformatics Institute for Global Good, a Hitachi business partner [ 12-06-04].

GeneBio opened a branch office in Japan last May [BioInform 05-17-04].

Under the terms of the current agreement, Hitachi Software Engineering "will further develop its existing distribution campaign for Phenyx in Japan in coordination with GeneBio's Japanese branch."

"We are confident that this collaboration will benefit GeneBio in terms of market penetration and also benefit Hitachi Software in terms of market acceptance in the area of mass spectrometry," said Yoichi Sakamoto, general manager of the life science division of Hitachi Software Engineering.

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