COPASI is a biochemical systems simulator for building, simulating, and analyzing models of biochemical networks and their dynamics.
It’s a standalone application with a graphical interface and command line tools, and is designed for work with reaction-based models, SBML files, deterministic and stochastic simulations, parameter estimation, optimization, and systems biology analysis.
This is free and open source software.
Key Features
- Creates reaction-based biochemical network models with species, reactions, compartments, events, and user-defined functions.
- Imports and exports models using SBML, with additional export options including XPP, Berkeley Madonna, C code, LaTeX, and MathML.
- Offers deterministic, stochastic, and hybrid simulation algorithms including LSODA, RADAU5, Gillespie methods, tau-leap, and hybrid SSA approaches.
- Provides parameter scans, parameter sampling, repeated simulations, and complex simulation workflows.
- Includes analysis tools for stoichiometry, optimization, parameter estimation, sensitivity analysis, metabolic control analysis, time scale separation, and stochasticity.
- Visualizes results with network diagrams, arbitrary 2D plots, predefined plots, color-coded matrices, and 3D bar charts.
- Generates report files for exporting simulation and analysis output for use in other applications.
Website: copasi.org/Download/
Support:
Developer: COPASI team
License: Artistic License 2.0
COPASI is written in C++. Learn C++ with our recommended free books and free tutorials.
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