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Blue Gene, Biomedical Computing Centers, Spotfire, Partek, Genomatica, Teranode, Clinical Genomics, Tripos, FDA Issues Draft Guidance


IBM Says Blue Gene Surpasses Earth Simulator

IBM said last week that its Blue Gene/L supercomputer had surpassed NEC’s Earth Simulator based on the Linpack benchmark that determines the twice-yearly list of the world's top 500 fastest supercomputers.

The company said that Blue Gene/L attained a sustained performance of 36.01 teraflops, beating the 35.86-teraflop milestone that the Japanese Earth Simulator has held for three years.

IBM said it reached the milestone during internal testing at its production facility in Rochester, Minn., using an eight-rack prototype of a 64-rack system that the company plans to deliver to Lawrence Livermore National Laboratory early next year.

The LLNL system is expected to reach a peak performance of more than 300 teraflops.

NIH Awards $80M to Four Biomedical Computing Centers

The National Institutes of Health has awarded a total of $79.7 million in grants to four new National Centers for Biomedical Computing.

The centers, part of the National Institutes of Health’s Roadmap for Medical Research [BioInform 10-06-03], have been awarded five-year grants totaling $15.7 million in the first year.

Eric Jakobsson, director of the Center for Bioinformatics and Computational Biology at the National Institute of General Medical Sciences, will serve as principal leader for the NCBCs.

The four centers are:

  • The Physics-Based Simulation of Biological Structures Center, led by Russ Altman and Scott Delp of Stanford University, which will develop a simulation toolkit to model and simulate biological systems from single atoms to entire organisms (;
  • The National Alliance for Medical Image Computing, led by Ron Kikinis of Brigham and Women’s Hospital, which will develop software programs that integrate analysis and imaging data from a variety of sources, including MRI scans (;
  • The Computational Biology Center, led by Arthur Toga of the University of California, Los Angeles, which will join computational and mathematical approaches to study genes, cells, systems, and the brain (;
  • The Informatics for Integrating Biology and the Bedside Center, led by Isaac Kohane of Brigham and Women’s Hospital, which will develop computational tools that combine clinical and genomic data.

More information about the NCBCs is available at

Boehringer Expands DecisionSite License

Spotfire said last week that Boehringer Ingelheim will deploy its DecisionSite software worldwide across its R&D activities.

The agreement extends a narrower licensing agreement that Boehringer Ingelheim has had with Spotfire since 1997 to use the software in genomics, lead discovery, and medicinal chemistry.

NHLBI to Use Partek Pro

Partek said last week that the National Heart, Lung, and Blood Institute at the National Institutes of Health has signed a license agreement for its Partek Pro software.

The software will be used at NHLBI’s Bioinformatics Core Facility.

Financial terms of the agreement were not disclosed.

Genomatica Secures $750,000 SBIR Grant

Genomatica said last week that it has received a two-year, $750,000 Phase II Small Business Innovation Research grant to continue development of its SimPheny biological modeling platform.

The US Department of Energy awarded the grant under its Genomics: GtL Program.

The company said it plans to use the funding to expand SimPheny’s ability to support collaborative research efforts.

Teranode Partners with VWR

Teranode said last week that it has partnered with VWR International, a distributor of scientific supplies, to bundle its Design Suite software with computational hardware.

The agreement is part of the VWR In Silico Program, an initiative to provide an integrated software and hardware solution for life science researchers. VWR announced its first partners in the program, IBM and VizX Labs, in June [BioInform 06-28-04]. Teranode’s Design Suite includes two modeling solutions — one for computational systems biology and the other for laboratory protocols.

Cleveland Clinic to Use IBM’s Clinical Genomics Solution

IBM said last week that the Cleveland Clinic has agreed to become one of the first organizations to use its Clinical Genomics Solution, which includes IBM technology and services, along with applications available from IBM’s business partners.

Under the agreement announced last week, IBM and the Cleveland Clinic will develop a translational medicine platform that will use information from electronic medical records to support basic and genetic research.

In the first phase of the initiative, the Cleveland Clinic and IBM will build an information infrastructure to provide access to medical and genetic information involving patients with abdominal aortic aneurysms in a confidential, anonymous fashion. The infrastructure will provide methods to identify the cause of aneurysms and to predict those patients who will respond to various treatment options.

Tripos Extends Contract with Schering

Tripos said last week that it has expanded an ongoing contract with Schering to develop an Enterprise Chemical Information Management System.

“The expanded contract “now also includes the final development and deployment of the initial phase of the new system,” said John McAlister, president and CEO at Tripos. The extended deal “provides Tripos with increased incremental funding that we believe will adequately cover our cost to complete the project,” he said.

The new agreement includes scheduled development milestones. The project is expected to be complete by mid-2005.

FDA Issues Draft Guidance on Clinical Trials Software

The US Food and Drug Administration has issued a draft guidance document entitled, “Computerized Systems Used in Clinical Trials.”

The document, available at, “addresses how Agency expectations and regulatory requirements regarding data quality might be satisfied where computerized systems are being used to create, modify, maintain, archive, retrieve, or transmit clinical data,” the FDA said.

The primary focus of the guidance is on computerized systems used at clinical sites to collect data, but “the principles set forth may also be appropriate for computerized systems belonging to contract research organizations, data management centers, and sponsors,” according to the guidance document.

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