E-Cell4

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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

Attractors
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
MinDE System with Mesoscopic Simulator
MinDE System with Spatiocyte Simulator
Simple Equilibrium
Tyson1991

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

E-Cell4

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E-Cell4 gillespie API
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