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454 Taps Myers, Gene Logic, Smallpox Grid Project, National Centers for Biomedical Computing


454 Taps Myers for Help on New Assembly Algorithm

CuraGen subsidiary 454 is collaborating with bioinformatics heavy hitter Gene Myers on a new assembly algorithm for the company’s high-throughput sequencing technology, according to a company spokesperson.

The company declined to provide further details on the collaboration or the assembly technology under development.

Myers, formerly vice president of informatics at Celera Genomics, led the assembly and analysis of Celera’s human genome sequencing project. He is currently a professor of computer science at the University of California, Berkeley, and is on the scientific advisory board of 454.

454 is developing a massively parallel method that sequences DNA fragments in hundreds of thousands of picoliter-scale wells. In September, the company raised an additional $20 million from CuraGen and shareholder Cooper Hill Partners to commercialize the technology.

Gene Logic Discontinues Use of TherImmune Name

Gene Logic last week said that following its acquisition of CRO TherImmune Research in April and “an internal examination of how best to achieve synergies from the combined enterprise,” it would discontinue use of the TherImmune name.

Going forward, the company’s combined bioinformatics, toxicogenomics, and contract research services will be marketed under the Gene Logic name.

UD, Accelrys, IBM, and Partners Deliver Results of Smallpox Grid Project

Accelrys, IBM, and United Devices took the stage with a number of technology and research partners last week to deliver the results of the Smallpox Research Grid project to representatives from the United States Department of Defense in an event hosted by the British Embassy in Washington, DC.

The project, which the collaborators began in February [BioInform 02-10-03], used distributed computing to screen 35 million potential drug molecules against nine models of the topoisomerase protein in the smallpox virus.

Volunteers from 195 countries donated spare CPU power from 2.5 million PCs to the project to contribute over 250,000 CPU-years of computing time, according to the project partners.

From 35 million inital molecules, the project ultimately selected 44 molecules that appeared to be the best candidates for blocking the function of the topoisomerase protein and 943 more that showed promise. The final data for smallpox fit on around 30 DVDs of 4 gigabytes each.

UD coordinated the project, which was funded by the United States Army Medical Research Institute of Infectious Diseases. IBM contributed a computing infrastructure based on eServer p690s and its DB2 database management software, and Accelrys provided its LigandFit docking software. Additional participants included Evotec OAI, the University of Oxford, Robarts Research Institute, the University of Western Ontario, Memorial Sloan-Kettering Cancer Center, and Essex University.

IBM’s general manager for global industry, Todd Ramsey, said that the grid of 2.5 million computers represents the world’s largest supercomputer right now, and is growing by 10,000-15,000 computers per week.

“Now that the grid exists, it can be exploited to decode any protein target,” said University of Oxford’s chairman of chemistry, Graham Richards — citing SARS, malaria, West Nile virus, tuberculosis, and bioterror threats such as ebola and botulinum toxin as future applications for the system.

NIH Roadmap Earmarks $14-17M in FY 2004 for New Biomedical Computing Centers

A national software engineering system in which “biologists, chemists, physicists, and computer scientists anywhere in the country will be able to tap into a supercomputing network to share and analyze data, using a common set of software tools” is among 28 initiatives that make up the National Institutes of Health’s new NIH Roadmap for Medical Research, which was introduced at a press conference held at the National Press Club in Washington, DC, last week.

The roadmap will be funded with $2.1 billion over the next five years, including $130 million in FY 2004, with $14 million to $17 million of the 2004 funding going to three or four new centers under the “National Centers for Biomedical Computing” (NCBC) initiative.

According to the program announcement, the NCBC centers will be devoted to “all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work.”

Letters of intent are due by Dec. 29, 2003, and applications are due by Jan. 23, 2004.

The complete program announcement is available at

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