Condor-COPASI: high-throughput computing for biochemical networks

Kent, Edward; Hoops, Stefan; Mendes, Pedro

Condor-COPASI: high-throughput computing for biochemical networks

dc.contributor.author	Kent, Edward	en
dc.contributor.author	Hoops, Stefan	en
dc.contributor.author	Mendes, Pedro	en
dc.date.accessioned	2012-12-20T16:08:24Z	en
dc.date.available	2012-12-20T16:08:24Z	en
dc.date.issued	2012-07-26	en
dc.date.updated	2012-12-20T16:08:24Z	en
dc.description.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.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	BMC Systems Biology. 2012 Jul 26;6(1):91	en
dc.identifier.doi	https://doi.org/10.1186/1752-0509-6-91	en
dc.identifier.uri	http://hdl.handle.net/10919/19098	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Edward Kent et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Condor-COPASI: high-throughput computing for biochemical networks	en
dc.title.serial	BMC Systems Biology	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en