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Nature, Spotfire, Protein Data, National Institute of Biomedical Imaging and Bioengineering, Journal of Parallel and Distributed Computing


Nature Paper Gives [email protected] Scientific Street Cred

Stanford University scientists Christopher Snow and Vijay Pande are the proud authors of what they claim to be the first paper published in a scientific journal based on a distributed computing experiment.

In the online edition of Nature last week, their paper, “Absolute comparison of simulated and experimental protein-folding dynamics,” detailed their [email protected] distributed protein-folding project, which used 30,000 PCs to simulate the folding process of a 23-residue model protein, BBA5.

The authors’ findings were experimentally confirmed by co-authors Houbi Nguyen and Martin Gruebele from the University of Illinois at Urbana-Champaign.

Using the 30,000 computers, Pande and Snow performed 32,500 folding simulations over “several months” and accumulated 700 microseconds of folding data for two mutant forms of BBA5. These simulations tested the folding rate of the protein on a 5-, 10- and 20-nanosecond timescale under different temperatures. Using these data, the scientists were able to predict the folding rate and trajectory of the “average” molecule.

The computers predicted that one experimental protein would fold in 6 microseconds, while laboratory observations revealed an actual folding time of 7.5 microseconds.


Spotfire Claims 22 New Customers, Record Orders for 3Q

Spotfire said it signed 22 new customers for its DecisionSite product during the third quarter of 2002.

The company also noted in a statement that it saw “record orders” for its products during the quarter, but no further details were provided.

“Spotfire showed strong, continued growth over the quarter, even in markets where others were shaking their heads and wondering if it could get any worse,” said David Yoffie, a Harvard Business School professor who joined Spotfire’s board of directors during the quarter.

As a private company, Spotfire is not required to disclose its earnings. The last quarterly update the company provided was for the first quarter of 2002, in which it disclosed 23 new DecisionSite customers and a revenue increase of 107 percent over the year-ago period.


Protein Data Standards Emerge in Hinxton

A productive weekend gathering of researchers and database curators at the EBI’s Hinxton, UK, campus has paved the way for a universal standard for the exchange of protein-protein interaction data.

The 50-odd participants in the first meeting of the Proteomics Standards Initiative, held October 19-20, agreed upon a basic XML framework for exchanging protein interaction data.

The event was a “big step forward,” EBI researcher and meeting organizer Henning Hermjakob told BioInform’s sister publication ProteoMonitor. The attendees agreed on a multi-level data exchange standard, with the first level covering “all the common denominators.” The multi-level format will offer several options for researchers to submit their protein interaction information to a database. In addition, Henning and others hope they can convince a journal to adopt the standard, which would apply to any papers accepted for publication.

Specifically, the participants reached agreement on the general form of a “requirements document” mandating that the interchange format should include multiple levels of detail depending on the user’s requirements, represent pair-wise interactions and complexes but not small-molecule pathways, and that it should be able to describe posttranslational modifications, said Chris Hogue, a bioinformaticist at the University of Toronto and developer of the BIND database. In addition, the document states that the format should accommodate multiple experiments from a single paper in a record, and that the database curators should work together to create a standard vocabulary for representing their data, Hogue said.

“The consensus we agreed on is remarkable,” said Hogue. Some attendees said they were initially worried there would be some bickering over which database the standard should most closely resemble, but in the end the meeting “was one of the more successful meetings of its kind,” he added.

In addition to protein-protein interaction data standards, meeting attendees also discussed the potential for establishing standards for exchanging and creating a common repository for mass spectrometry data.

A full report on the meeting is available at: The next PSI meeting will be held November 21, as a satellite meeting of the first HUPO world congress in Paris.


NIH/NSF Sponsor Bioinformatics Summer School

The NSF and the NIH’s National Institute of Biomedical Imaging and Bioengineering have ponied up a total of $6 million over four years to support the Bioengineering and Bioinformatics Summer Institutes (BBSI) Program.

The BBSI program provides undergraduate and graduate students with interdisciplinary bioengineering or bioinformatics research and education experiences “that encourage the students to pursue biomedical careers,” according to the NIH.

Funded BBSIs are at California State University, Clemson University, Iowa State University, Massachusetts Institute of Technology, New Jersey Institute of Technology, Pennsylvania State University, University of Minnesota, University of Pittsburgh, and Virginia Commonwealth University.

The first institutes will be held during the summer of 2003. Further information is available at the NIBIB web site:


Computing Journal Seeks Papers for Special Biology Issue

The editors of the Journal of Parallel and Distributed Computing are seeking papers for a special issue on high-performance computational biology.

The issue will publish “important research in high-performance computing solutions as it relates to problems in molecular biology” according to the publisher, Academic Press, an Elsevier imprint.

Topics of interest include parallel algorithms, memory-efficient algorithms, large-scale data mining techniques, and high-performance software design for bioinformatics databases; DNA assembly, clustering, and mapping; gene expression and microarrays; molecular evolution; phylogeny reconstruction; and protein structure.

Authors should submit manuscripts to David Bader at the University of New Mexico ([email protected]) or Srinivas Aluru at Iowa State University ([email protected]) by November 15. Manuscript guidelines are available at

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