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.
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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)
If this package contributes to a project which leads to a scientific publication, I would appreciate a citation.
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