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Models@Home: distributed computing in bioinformatics using a screensaver based approach.

Elmar Krieger·Gert Vriend
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Abstract

MOTIVATION: Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. RESULTS: We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.

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Computational BiologyComputer Communication NetworksComputer SimulationComputer SystemsDatabases, ProteinProteinsSoftwareThermodynamicsJournal Article

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Elmar Krieger, Gert Vriend. 2002. Models@Home: distributed computing in bioinformatics using a screensaver based approach.. https://doi.org/10.1093/bioinformatics%2F18.2.315

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