| Chapter | Title | nbviewer | Open in Colab |
|---|---|---|---|
| 1 | Brief Tour of E-Cell4 Simulations |  |
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| 2 | How to Build a Model | |
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| 3 | How to Setup the Initial Condition | |
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| 4 | How to Run a Simulation | |
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| 5 | How to Log and Visualize Simulations | |
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| 6 | How to Solve ODEs with Rate Law Functions | |
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| 7 | Introduction of Rule-based Modeling | |
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| 8 | More about 1. Brief Tour of E-Cell4 Simulations | |
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| 9 | Spatial Gillespie Method | |
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| 10 | Spatiocyte Simulations at Single-Molecule Resolution | |
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| Title | nbviewer | Open in Colab |
|---|---|---|
| Attractors | |
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| Drosophila Circadian Clock | |
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| Dual Phosphorylation Cycle | |
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| Simple EGFR model | |
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| A Simple Model of the Glycolysis of Human Erythrocytes | |
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| Hodgkin-Huxley Model | |
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| Lotka-Volterra 2D | |
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| MinDE System with Mesoscopic Simulator | |
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| MinDE System with Spatiocyte Simulator | |
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| Simple Equilibrium | |
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| Tyson1991 | |
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| How to use the unit system | |
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