E-Cell4 の Jupyter Notebook集へようこそ!

E-Cell Systemは、細胞のように複雑でマルチスケールなシステムのモデリング、シミュレーション、分析を行うためのソフトウェアプラットフォームです。 E-Cell4は、GNU General Public Licenseバージョン2の下でライセンスされたフリーでオープンソースのソフトウェアです。ソースコードはGitHubで入手可能です。

チュートリアル

Brief Tour of E-Cell4 Simulations local ipynb readthedocs
- Quick Demo
- Spatial Simulation and Visualization
How to Build a Model local ipynb readthedocs
- Species
- ReactionRule
- NetworkModel
- Python Utilities to Build a Model
How to Setup the Initial Condition local ipynb readthedocs
- Common APIs of World
- How to Get Positions of Molecules
- Lattice-based Coordinate
- Structure
- Random Number Generator
How to Run a Simulation local ipynb readthedocs
- How to Setup a Simulator
- Running Simulation
- Capsulizing Algorithm into a Factory Class
How to Log and Visualize Simulations local ipynb readthedocs
- Logging Simulations with Observers
- Visualization of Data Logged
How to Solve ODEs with Rate Law Functions local ipynb readthedocs
- ode.ODEReactionRule
- ode.ODERatelaw
- ode.ODENetworkModel
- References in a Rate Law
- More about ode
Introduction of Rule-based Modeling local ipynb readthedocs
- Species.count
- ReactionRule.count and generate
- NetfreeModel
- Differences between Species, ReactionRule and NetfreeModel
More about 1. Brief Tour of E-Cell4 Simulations local ipynb readthedocs
- Creating ODEWorld
- How to Use Real3
- Creating and Running ODESimulator
- Switching the Solver
Spatial Gillespie Method local ipynb readthedocs
- Spaces in E-Cell4
- Spatial Gillespie Method
- Defining Molecular Diffusion Coefficient
- Molecular localization
- Molecular initial location and the reaction
Spatiocyte Simulations at Single-Molecule Resolution local ipynb readthedocs
- Spatiocyte Lattice-based Method
- The Diffusion Movement of Single Molecule
- The Diffusion Coefficient and the Second-order Reaction
- The Structure in the Spatiocyte Method
- The structure and the reaction

例

極めて単純な可逆結合反応の例は下記になります



In [1]:

    
%matplotlib inline
from ecell4 import *

with reaction_rules():
    A + B == C | (0.01, 0.3)

run_simulation(10, {'A': 60, 'B': 60})

さらなる例は下記になります

Attractors local ipynb readthedocs
- Rössler attractor
- Modified Chua chaotic attractor
- Lorenz system
- Tamari attractor
- Moore-Spiegel attractor
Drosophila Circadian Clock local ipynb readthedocs
Dual Phosphorylation Cycle local ipynb readthedocs
Simple EGFR model local ipynb readthedocs
A Simple Model of the Glycolysis of Human Erythrocytes local ipynb readthedocs
Hodgkin-Huxley Model, FitzHugh–Nagumo Model local ipynb readthedocs
Lotka-Volterra 2D local ipynb readthedocs
- 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 local ipynb readthedocs
MinDE System with Spatiocyte Simulator local ipynb readthedocs
Simple Equilibrium local ipynb readthedocs
Tyson1991 local ipynb readthedocs



In [ ]: