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DOE s INCITE, Blue Gene/L, University of Missouri, VizX Labs, Locus Pharmaceuticals

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Three Life Science Projects to Benefit from DOE's INCITE Scientific Computing Program

The US Department of Energy has awarded 18 million hours of supercomputing time to 15 teams for large-scale scientific computing under its Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, which is now in its third year.

Three of the awards are going to life science projects:

  • "Molecular dynamics of molecular motors," led by Martin Karplus at Harvard University, which was awarded 1.5 million processor hours on a Cray XT3 at Oak Ridge National Laboratory.
  • "High resolution protein structure prediction," led by David Baker at the University of Washington/Howard Hughes Medical Institute, which was awarded 5 million processor hours on an IBM Blue Gene at Argonne National Laboratory.
  • "Simulation and modeling of synuclein-based 'protofibril structures' as a means of understanding the molecular basis of Parkinson's disease," led by Igor Tsigelny at the University of California, San Diego, which was awarded 16,000 processor hours on an IBM Blue Gene at Argonne National Laboratory.

DOE said that 43 large-scale research proposals were submitted for the INCITE program.


Iowa State University to Use 5.7-Tflop Blue Gene/L for Maize Genome Project

Iowa State University has purchased a Blue Gene/L supercomputer with a peak performance of 5.7 teraflops from IBM for its work sequencing the corn genome, the university said this week.

The National Science Foundation awarded Iowa State's Srinivas Aluru $600,000 to purchase the $1.25 million supercomputer [BioInform 08-08-05], and the university paid the remaining $650,000 with allocations from the President's Office, the Office of the Vice Provost for Research, Information Technology Services and the Plant Sciences Institute.

The system, the university's first supercomputer, "will be a tremendous resource for our researchers involved in assembling the corn genome, studying protein networks, and other very important areas of computational biology," said Gregory Geoffroy, Iowa State president, in a statement.

The 2,048-processor supercomputer was delivered on Jan. 20. The system includes 11 trillion bytes of data storage and would rank No. 73 on the current Top 500 list of the world's fastest supercomputers.

The university will use the system to sequence the corn genome, which has proved difficult to assemble because it contains a very high number of repeats — around 65 percent to 80 percent of the genome.

Researchers at the university will also use the system to study protein-protein interactions.


University of Missouri Alumnus Provides $1M Gift for Bioinformatics Program

Paul Shumaker, an alumnus of the University of Missouri, Columbia, has donated $1 million to the university's bioinformatics program within its College of Engineering, the university said this week.

The gift will create the Shumaker Professorship of Bioinformatics in Computer Science. Chi-Ren Shyu, an assistant professor in the department of computer science, has been named to the position.

The gift also will create the Shumaker Fellows, a scholarship program for graduate students, and the Shumaker Lecture Series on Bioinformatics, a lecture series that will "draw on experts from all over the world, encouraging them to share their research with their peers," the university said.

Shumaker is a co-founder of Garmin International, a company that manufactures navigation and communication equipment for the US satellite network.


VizX Labs Sells 15-Seat GeneSifter License to NHGRI

VizX Labs said this week that the National Human Genome Research Institute has purchased a 15-seat site license of its GeneSifter Core Edition microarray data analysis system.

NHGRI will use the software in its Computational Genomics Unit.

Further details of the agreement were not provided.


Locus to Use In Silico Drug Design Platform in Collaboration with Eli Lilly

Locus Pharmaceuticals has entered into a research agreement with Eli Lilly to computationally design small molecule compounds with activity against a protein kinase target identified by Lilly.

Financial and other terms of the agreement were not disclosed.

Jeffrey Wiseman, vice president of technology and informatics at Locus, said in a statement that the company has already successfully applied its fragment-based approach to internal kinase programs that have reached the IND lead stage, and the company is "confident that our proprietary algorithms will allow us to design novel chemical classes of kinase inhibitors with predictably high potency and selectivity for Lilly."

Filed under

The Scan

Removal Inquiry

The Wall Street Journal reports that US lawmakers are seeking additional information about the request to remove SARS-CoV-2 sequence data from a database run by the National Institutes of Health.

Likely to End in Spring

Free lateral flow testing for SARS-CoV-2 may end in the UK by next spring, the head of Innova Medical Group says, according to the Financial Times.

Searching for More Codes

NPR reports that the US Department of Justice has accused an insurance and a data mining company of fraud.

Genome Biology Papers on GWAS Fine-Mapping Method, COVID-19 Susceptibility, Rheumatoid Arthritis

In Genome Biology this week: integrative fine-mapping approach, analysis of locus linked to COVID-19 susceptibility and severity, and more.