Bioinformatics Vol. 18 no. 2 2002
Pages 315-318
© 2002 Oxford University Press
Models@Home: distributed computing in bioinformatics using a screensaver based approach
CMBI, Center for Molecular and Biomolecular Informatics, Toernooiveld 1, NL-6525 ED Nijmegen, The Netherlands
Received on June 14, 2001
; revised on August 28, 2001
; accepted on September 17, 2001
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.
Availability: Models@Home is freely available including source code and detailed instructions from http://www.cmbi.nl/models.
Contact: elmar.krieger{at}cmbi.kun.nl
* To whom correspondence should be addressed.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  T. M. Keane, T. J. Naughton, S. A. A. Travers, J. O. McInerney, and G. P. McCormack DPRml: distributed phylogeny reconstruction by maximum likelihood Bioinformatics, April 1, 2005; 21(7): 969 - 974. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Le Guezennec, G. Vriend, and H. G. Stunnenberg Molecular Determinants of the Interaction of Mad with the PAH2 Domain of mSin3 J. Biol. Chem., June 11, 2004; 279(24): 25823 - 25829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Shi, Z. Wei, and J. Song Dissection Study on the Severe Acute Respiratory Syndrome 3C-like Protease Reveals the Critical Role of the Extra Domain in Dimerization of the Enzyme: DEFINING THE EXTRA DOMAIN AS A NEW TARGET FOR DESIGN OF HIGHLY SPECIFIC PROTEASE INHIBITORS J. Biol. Chem., June 4, 2004; 279(23): 24765 - 24773. [Abstract] [Full Text] [PDF]
|
|