Condor-COPASI: high-throughput computing for biochemical networks

BMC Systems Biology

Pedro Mendes²  Stefan Hoops¹  Edward Kent³ 

[1] Virginia Bioinformatics Institute, Virginia Tech, Washington St 0477, Blacksburg, VA 24061, USA;School of Computer Science, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK;Doctoral Training Centre in Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK

关键词: Simulation;    Distributed computing;    High-throughput computing;    Computational modelling;    Systems biology;   

Others  :  1143752
DOI  :  10.1186/1752-0509-6-91

 received in 2012-02-10, accepted in 2012-07-12,  发布年份 2012

【 摘 要 】

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 athttp://code.google.com/p/condor-copasi/ webcite, along with full instructions on deployment and usage.

【 授权许可】

   
2012 Kent et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Kitano H: Systems biology: a brief overview. Science 2002, 295(5560):1662-4.
• [2]Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006, 34(Database issue):D689-91.
• [3]Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531.
• [4]Pahle J: Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Briefings Bioinf 2009, 10:53-64.
• [5]Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U: COPASI–a COmplex PAthway SImulator. Bioinformatics 2006, 22(24):3067-74.
• [6]Olivier BG, Snoep JL: Web-based kinetic modelling using JWS Online. Bioinformatics 2004, 20(13):2143-4.
• [7]Loew LM, Schaff JC: The Virtual Cell: a software environment for computational cell biology. Trends Biotechnol 2001, 19(10):401-6.
• [8]Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW: Systematic integration of experimental data and models in systems biology. BMC Bioinf 2010, 11:582.
• [9]Dada J, Mendes P: Design and architecture of web services for simulation of biochemical systems. In Data Integration in the, Life Sciences. Edited by Paton N, Missier P, Hedeler C. Berlin / Heidelberg: Springer; 2009:182-195.
• [10]Litzkow M, Livny M, Mutka M: Condor-a hunter of idle workstations. In Distributed Computing Systems, 1988., 8th International Conference on. IEEE; 1987:104-111.
• [11]Thain D, Tannenbaum T, Livny M: Distributed computing in practice: the Condor experience. Concurrency Comput: Pract and Experience 2005, 17(2-4):323-356.
• [12]Python Programming Language – Official Website [ http://python.org/ webcite]
• [13]Django The Web framework for perfectionists with deadlines [ http://www.djangoproject.com/ webcite]
• [14]matplotlib: python plotting [ http://matplotlib.sourceforge.net/ webcite]
• [15]Visualization: Motion Chart - Google Chart Tools - Google Code [ http://code.google.com/apis/chart/interactive/docs/gallery/motionchart.html webcite]
• [16]Sahle S, Mendes P, Hoops S, Kummer U: A new strategy for assessing sensitivities in biochemical models. Philos Trans R Soc A 2008, 366(1880):3619-3631.
• [17]Nash S: Newton-type minimization via the Lanczos method. SIAM J Numer Anal 1984, 21(4):770-788.
• [18]Kennedy J, Eberhart R: Particle swarm optimization. In Neural Networks, 1995. Proceedings., IEEE International Conference on, Volume 4. Perth, WA, Australia: IEEE; 1995:1942-1948.
• [19]Ashall L, Horton CA, Nelson DE, Paszek P, Harper CV, Sillitoe K, Ryan S, Spiller DG, Unitt JF, Broomhead DS, Kell DB, Rand DA, Sée V, White MRH: Pulsatile stimulation determines timing and specificity of NF-kappaB-dependent transcription. Science 2009, 324(5924):242-246.
• [20]Huang CY, Ferrell JE: Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Nat Acad Sci U S A 1996, 93(19):10078-10083.
• [21]Kummer U, Olsen LF, Dixon CJ, Green AK, Bomberg-Bauer E, Baier G: Switching from Simple to Complex Oscillations in Calcium Signaling. Biophys J 2000, 79(3):1188-1195.
• [22]Oracle Grid Engine http://www.oracle.com/us/products/tools/oracle-grid-engine-075549.html webcite
• [23]Maui Cluster Scheduler [ http://www.clusterresources.com/products/maui-cluster-scheduler.php webcite]
• [24]TORQUE Resource Manager [ http://www.adaptivecomputing.com/products/open-source/torque/ webcite]
• [25]PBS Works - Enabling On-Demand Computing [ http://www.pbsworks.com/ webcite]