The E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. Its latest version, E-Cell4, accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature. E-Cell4 is a free and open-source software licensed under the GNU General Public License version 3. The source code is available on GitHub (ecell4 and ecell4_base). This document is generated from ecell4_docs.
A Slack workspace is open for questions here.
.. toctree:: :maxdepth: 1 installation
- Single particle simulations, i.e. The enhanced Green's Function Reaction Dynamics (eGFRD) method, Spatiocyte (a lattice-based method), and the Reaction Brownian Dynamics (RBD) method
- Ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm (the next subvolume method)
- Rule-based modeling
- Python programmable
.. toctree:: :maxdepth: 1 top tutorials/index
.. toctree:: :maxdepth: 1 :caption: Examples examples/index
.. toctree:: :maxdepth: 1 :caption: Tests tests/index
.. toctree:: :maxdepth: 1 developers
If this package contributes to a project which leads to a scientific publication, I would appreciate a citation.
This product is licensed under the terms of the GNU General Public License v3. See also LICENSE for the software included in this product.
- Copyright (c) 2010-, RIKEN
All rights reserved.
.. toctree:: :maxdepth: 1 api/ecell4 api/ecell4_base api/index