Models@Home: distributed computing in bioinformatics using a screensaver based approach.
BACKGROUND
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.
Krieger
Elmar
E
CMBI, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands. elmar.krieger@cmbi.kum.nl
Vriend
Gert
G
D019295:Computational Biology; D003195:Computer Communication Networks; D003198:Computer Simulation; D003199:Computer Systems; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry; D012984:Software; D013816:Thermodynamics
D011506:Proteins