title: Condor-COPASI: high-throughput computing for biochemical networks.
abstract: BACKGROUND
  Mathematical modelling has become a standard technique to improve our understanding of complex biological systems. As models become larger and more complex, simulations and analyses require increasing amounts of computational power. Clusters of computers in a high-throughput computing environment can help to provide the resources required for computationally expensive model analysis. However, exploiting such a system can be difficult for users without the necessary expertise.
  
  
  RESULTS
  We present Condor-COPASI, a server-based software tool that integrates COPASI, a biological pathway simulation tool, with Condor, a high-throughput computing environment. Condor-COPASI provides a web-based interface, which makes it extremely easy for a user to run a number of model simulation and analysis tasks in parallel. Tasks are transparently split into smaller parts, and submitted for execution on a Condor pool. Result output is presented to the user in a number of formats, including tables and interactive graphical displays.
  
  
  CONCLUSIONS
  Condor-COPASI can effectively use a Condor high-throughput computing environment to provide significant gains in performance for a number of model simulation and analysis tasks. Condor-COPASI is free, open source software, released under the Artistic License 2.0, and is suitable for use by any institution with access to a Condor pool. Source code is freely available for download at http://code.google.com/p/condor-copasi/, along with full instructions on deployment and usage.
authors: Doctoral Training Centre in Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
authors: Edward
authors: E
authors: Kent
authors: Stefan
authors: S
authors: Hoops
authors: Pedro
authors: P
authors: Mendes
mesh_terms: D000465:Algorithms; D020935:MAP Kinase Signaling System; D008954:Models, Biological; D012984:Software; D013269:Stochastic Processes; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors