E-Cell System version 4¶
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.
Installation¶
Features¶
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
Tutorials¶
- Welcome to E-Cell4 in Jupyter Notebook!
- 1. Brief Tour of E-Cell4 Simulations
- 2. How to Build a Model
- 3. How to Setup the Initial Condition
- 4. How to Run a Simulation
- 5. How to Log and Visualize Simulations
- 6. How to Solve ODEs with Rate Law Functions
- 7. Introduction of Rule-based Modeling
- 8. More about 1. Brief Tour of E-Cell4 Simulations
- 9. Spatial Gillespie Method
- 10. Spatiocyte Simulations at Single-Molecule Resolution
Models¶
Examples
- Attractors
- Drosophila Circadian Clock
- Dual Phosphorylation Cycle
- Simple EGFR model
- Glycolysis Model and Metabolic Control Analysis
- Action Potentials in Neurons
- Lotka-Volterra 2D
- MinDE System with Mesoscopic Simulator
- MinDE System with Spatiocyte Simulator
- Simple Equilibrium
- Tyson1991
- How to Use the Unit System
- Multiary Complex Model of GPCR Signaling Activations
- The sGFRD Method
For Developers¶
Citation¶
If this package contributes to a project which leads to a scientific publication, I would appreciate a citation.
Licensing Terms¶
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.