COPASI

COPASI stands for COmplex PAthway SImulator. It is free, open-source software designed for the modeling, simulation, and analysis of biochemical networks. The program supports a range of methods for investigating dynamic behavior, including deterministic simulations of ordinary differential equations and stochastic simulations (such as Gillespie-type algorithms), as well as hybrid approaches that combine these methods.

Key features of COPASI include time-course simulations, steady-state analysis, parameter estimation and optimization, sensitivity analysis, and metabolic control analysis. It also supports design of experiments to help plan and interpret laboratory studies. In addition, COPASI provides extensive data output and visualization options for concentrations, fluxes, and control coefficients, aiding interpretation of model results.

Interoperability is a central concern: COPASI offers robust import and export of SBML (Systems Biology Markup Language) models, enabling integration with other tools and databases in the systems biology ecosystem. The software is accessible through a graphical user interface and a command-line interface, and it runs on major operating systems, including Windows, macOS, and Linux.

COPASI is implemented primarily in C++ with a Qt-based GUI. Its modular core library supports numerical solvers and model manipulation, making it suitable for researchers, educators, and students working on metabolic networks, signaling pathways, and other complex biological systems.

Development and use: COPASI is maintained by a community of researchers and users, with comprehensive documentation and tutorials available on its official website. It is widely used in academic settings for modeling, hypothesis testing, parameter fitting, and teaching concepts in systems biology.