Publications

The main publication to cite when you use COPASI in your research is:

• Hoops S., Sahle S., Gauges R., Lee C., Pahle J., Simus N., Singhal M., Xu L., Mendes P. and Kummer U. (2006). COPASI: a COmplex PAthway SImulator. Bioinformatics 22, 3067-74.
  Link | ISI Citations | Google Scholar Citations

Publications describing uses of COPASI in some detail:

• Mendes, P., Hoops, S., Sahle, S., Gauges, R., Dada, J.O. and Kummer, U. (2009). Computational Modeling of Biochemical Networks Using COPASI. Methods in Molecular Biology, Humana Press. 500: 17-59.
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• Mendes, P., Messiha, H., Malys, N. and Hoops, S. (2009). Enzyme Kinetics and Computational Modeling for Systems Biology. Methods in Enzymology 467: 583-599.
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• Sahle, S., Gauges, R. , Pahle, J., Simus, N., Kummer, U., Hoops, S., Lee, C., Singhal, M., Xu, L. and Mendes, P. (2006). Simulation of biochemical networks using COPASI: a complex pathway simulator. Proceedings of the 38th conference on Winter simulation. Monterey, California, Winter Simulation Conference. 1698-1706
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Research papers describing methods that are (or will be) used in COPASI:

• Challenger, J.D., McKane, A.J. and Pahle, J. (2012). Multi-compartment linear noise approximation. J. Stat. Mech. P11010.
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• Pahle, J., Challenger, J.D., Mendes, P. and McKane, A.J. (2012). Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6: 86.
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• Dada, J.O., Spasic, I., Paton, N.W. and Mendes, P. (2010). SBRML: a markup language for associating systems biology data with models. Bioinformatics 26: 932-938.
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• Surovtsova, I., Simus, N., Lorenz, T., König, A., Sahle, S. and Kummer, U. (2009). Accessible methods for the dynamic time-scale decomposition of biochemical systems. Bioinformatics 25: 2816-2823.
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• Pahle, J. (2009). Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Briefings in Bioinformatics 10: 53-64.
  Link | ISI Citations | Google Scholar Citations
• Sahle, S. Mendes, P., Hoops, S. and Kummer, U. (2008). A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A - Mathematical Physical and Engineering Sciences 366(1880): 3619-3631.
  Link | ISI Citations | Google Scholar Citations
• Pahle, J. (2008). Stochastic simulation and analysis of biochemical networks. PhD Thesis, Humboldt-Universität zu Berlin
  Link | Google Scholar Citations
• Kummer, U. (2007). Usage of Reaction Kinetics Data Stored in Databases - A Modeler's Point of View. In Silico Biology 7: 65-71.
  Link | Google Scholar Citations
• Gauges, R., Rost, U., Sahle, S. and Wegner, K. (2006). A model diagram layout extension for SBML. Bioinformatics 22: 1879-85.
  Link | ISI Citations | Google Scholar Citations

Publications describing other software applications that use COPASI:

• Kent E, Hoops S, Mendes P (2012). Condor-COPASI: High-Throughput Computing for Biochemical Networks. BMC Systems Biology 6:91 link
• Dada, J.O. and Mendes, P. (2009). Design and Architecture of Web Services for Simulation of Biochemical Systems. Data Integration in the Life Sciences; Lecture Notes in Computer Science, Springer, Berlin / Heidelberg. 5647: 182-195.
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• Schulz, M., Bakker, B.M., Klipp, E. (2009) TIde: a software for the systematic scanning of drug targets in kinetic network models BMC Bioinformatics : 10.
  Link | Google Scholar Citations
• Weidemann, A., Richter, S. , Stein, M., Sahle, S., Gauges, R., Gabdoulline, R., Surovtsova, I., Semmelrock, N., Besson, B., Rojas, I., Wade, R. and Kummer, U. (2008). SYCAMORE - a systems biology computational analysis and modeling research environment. Bioinformatics 24: 1463-1464.
  Link | ISI Citations | Google Scholar Citations
• Flötmann, M., Schaber, J., Hoops, S., Klipp, E. and Mendes, P. (2008). ModelMage: A Tool for Automatic Model Generation, Selection and Management. Genome Informatics 20: 52-63.
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