E-Cell4
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 Molecule Positions
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 Simulations
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 ODEs
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
←
Welcome to E-Cell4 in...
1. Brief Tour of E-Cell4...
→