COPASI[1] (COmplex PAthway SImulator) is an open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks, infectious diseases, and many others.
COPASI includes features to define models of biological processes, simulate and analyze these models, generate analysis reports, and import/export models in SBML format.
Model definition: Models are defined as chemical reactions between molecular species. The dynamics of the model is determined by Rate law associated with individual reactions. Models can also include compartments, events, and other global variables that can help specify the dynamics of the system.
Tasks: Tasks are different types of analysis that can be performed on a model. They include steady-state analysis, stoichiometric analysis, time course simulation using deterministic and stochastic simulation algorithms, metabolic control analysis, computation of Lyapunov exponent, time scale separation, parameter scans, optimization, and parameter estimation.
Importing and Exporting: COPASI can read models in SBML format as well as in Gepasi format. COPASI can write models in several different formats including the SBML, source code in the C programming language, Berkeley Madonna files, and XPPAUTArchived 18 April 2022 at the Wayback Machine files.
^Mendes, P. (1993). "GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems". Computer Applications in the Biosciences. 9 (5): 563–571. doi:10.1093/bioinformatics/9.5.563. PMID8293329.
