Documentation for GillesPy2 1.5.0

GillesPy2 is an open-source Python package for stochastic simulation of biochemical systems. It offers an object-oriented approach for creating mathematical models of biological systems, as well as a variety of methods for performing time simulation of those models. The methods include the Gillespie direct method (SSA), several variant stochastic simulation methods including tau leaping, and numerical integration of ODEs. The solvers support a variety of user environments, with optimized code for C++, Cython, and NumPy. Models can also be read from files in SBML format.

Getting a copy of GillesPy2

The latest version of GillesPy2 can be found on PyPI. The source code is available on GitHub. GillesPy2 is licensed under the GNU General Public License version 3.

Please register as a user! GillesPy2's development is funded by NIH grant 2R01EB014877, and to continue support, we need to prove GillesPy2 has users. Please fill out our short registration form!

Getting help

If you find any problem with GillesPy2 or this documentation, please report it using the GitHub issue tracker for the project. You can also contact the main author, Dr. Brian Drawert, directly with questions and suggestions.

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