Hello E-Cell4

E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell.

from ecell4 import *

with reaction_rules():
    A + B == C | (0.01, 0.3)

run_simulation(10, {'A': 60, 'B': 60}, solver='gillespie')
gillespie

Features

Single particle simulations

This is a description about feature1. The enhanced Green's Function Reaction Dynamics (eGFRD) method, Spatiocyte, and the Reaction Brownian Dynamics (RBD) method.

Multi-algorithm support

This is a description about feature2.

Rule-based modeling

This is a description about feature3.

Python programmable

This is a description about feature4.

Interactive visualizations on Jupyter Notebook

This is a description about feature5.

Bioinformatics integration

Garuda gadget, data source, etc.

Examples

attractors

minde

This is a screenshot about example3.

notebook

attractors

For more tutorials and examples, see http://ecell4.readthedocs.io/.

License

This project is licensed under the terms of the GNU General Public License v2. See LICENSE.

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