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Stanford Works with XCT, Scalable Informatics to Build GPU-based Cluster for Computational Biology


Xtreme Compute Technologies this week said that it worked with informatics consulting firm Scalable Informatics to deploy a graphical processing unit-based cluster at Stanford University for initiatives including computational biology, molecular dynamics, and structural biology and chemical biology simulation.

XCT said that Stanford used its a-BriX servers, built with NVIDIA Tesla GPUs, as part of a new 50-node heterogeneous cluster called Numbercruncher. The system includes 100 Tesla C2050 GPUs, XCT said.

The company said that it worked with Vijay Pande, associate professor of chemistry, structural biology, and computer science at Stanford, to define the functional requirements and objectives for the cluster.

Pande, perhaps best known for leading the [email protected] protein-folding project, has long been a proponent of GPU-based biological computing. In 2009, he and his colleagues released OpenMM, a GPU-enabled implementation of the GROMACS molecular-dynamics package (BI 2/20/2009).

In addition to the a-BriX Tesla GPU servers, the cluster uses host servers based on AMD Magny-Cours multicore processors, Delta-V storage, and Bright Computing's Bright Cluster Manager software and Accelereyes' Jacket and GPU Engine software.

The Scan

For Better Odds

Bloomberg reports that a child has been born following polygenic risk score screening as an embryo.

Booster Decision Expected

The New York Times reports the US Food and Drug Administration is expected to authorize a booster dose of the Pfizer-BioNTech SARS-CoV-2 vaccine this week for individuals over 65 or at high risk.

Snipping HIV Out

The Philadelphia Inquirer reports Temple University researchers are to test a gene-editing approach for treating HIV.

PLOS Papers on Cancer Risk Scores, Typhoid Fever in Colombia, Streptococcus Protection

In PLOS this week: application of cancer polygenic risk scores across ancestries, genetic diversity of typhoid fever-causing Salmonella, and more.