E-Cell System version 4 API reference

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

E-Cell4 is a free and open-source software licensed under the GNU General Public License version 2. The source code is available on GitHub.

Please refer to https://github.com/ecell/ecell4 for information about installation instructions.

Tutorials

• 1. Brief Tour of E-Cell4 Simulations
  • 1.1. Quick Demo
  • 1.2. Spatial Simulation and Visualization
• 2. How to Build a Model
  • 2.1. Species
  • 2.2. ReactionRule
  • 2.3. NetworkModel
  • 2.4. Python Utilities to Build a Model
• 3. How to Setup the Initial Condition
  • 3.1. Common APIs of World
  • 3.2. How to Get Positions of Molecules
  • 3.3. Lattice-based Coordinate
  • 3.4 Structure
  • 3.5. Random Number Generator
• 4. How to Run a Simulation
  • 4.1. How to Setup a Simulator
  • 4.2. Running Simulation
  • 4.3. Capsulizing Algorithm into a Factory Class
• 5. How to Log and Visualize Simulations
  • 5.1. Logging Simulations with Observers
  • 5.2. Visualization of Data Logged
• 6. How to Solve ODEs with Rate Law Functions
  • 6.1. ReactionRuleDescriptor
  • 6.2. ReactionRuleDescriptorPyFunc
  • 6.3. NetworkModel
  • 6.4. References in a Rate Law
  • 6.5. More about ode
• 7. Introduction of Rule-based Modeling
  • 7.1. count_species_matches
  • 7.2. ReactionRule.count and generate
  • 7.3. NetfreeModel
  • 7.4. Differences between Species, ReactionRule and NetfreeModel
• 8. More about 1. Brief Tour of E-Cell4 Simulations
  • 8.1. Creating ODEWorld
  • 8.2. How to Use Real3
  • 8.3. Creating and Running ODE Simulator
  • 8.4. Switching the Solver
• 9. Spatial Gillespie Method
  • 9.1. Spaces in E-Cell4
  • 9.2. Spatial Gillespie Method
  • 9.3. Defining Molecular Diffusion Coefficient
  • 9.4. Molecular localization
  • 9.5. Molecular initial location and the reaction
• 10. Spatiocyte Simulations at Single-Molecule Resolution
  • 10.1. Spatiocyte Lattice-based Method
  • 10.2. The Diffusion Movement of Single Molecule
  • 10.3 The Diffusion Coefficient and the Second-order Reaction
  • 10.4. The Structure in the Spatiocyte Method
  • 10.5 The structure and the reaction

Examples

• Attractors
  • Rössler attractor
  • Modified Chua chaotic attractor
  • Lorenz system
  • Tamari attractor
  • Moore-Spiegel attractor
• Drosophila Circadian Clock
• Dual Phosphorylation Cycle
• Simple EGFR model
• A Simple Model of the Glycolysis of Human Erythrocytes
• Hodgkin-Huxley Model
• FitzHugh–Nagumo Model
• Lotka-Volterra 2D
  • The Original Model in Ordinary Differential Equations
  • The Modified Model Decomposed into Elementary Reactions
  • A Lotka-Volterra-like Model in 2D
• MinDE System with Mesoscopic Simulator
• MinDE System with Spatiocyte Simulator
• Simple Equilibrium
• Tyson1991

API

• E-Cell4 core API
• E-Cell4 gillespie API
• E-Cell4 ode API
• E-Cell4 meso API
• E-Cell4 spatiocyte API
• E-Cell4 bd API
• E-Cell4 egfrd API