Welcome to E-Cell4 in IPython Notebook!

E-Cell System, 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.

See README.md for how to install E-Cell4. Linux, Windows and Mac OSX are supported.

Tutorial

The Tutorial is divided in three sections: Basic, Topical and Advanced exercises. We recommend to try all Basic exercises to understand how to use E-Cell4. Each section contains several IPython notebooks with different exercises.

Get started with E-Cell4 by going through the tutorial.

Basic Exercises

There are three important components to understand E-Cell4: Model, World and Simulator classes. These components describe different concepts in a simulation.

Model, as its name suggests, describes the matter to simulate.
World describes the state. For example, initial state or a state of a time-point.
Simulator describes the solver and algorithm.

These three components are independent, but World is often dependent on a type of Simulator.

Topical Exercises

Advanced Exercises

Example

Here is an extremely simple example with a reversible binding reaction:



In [1]:

    
%matplotlib inline
import numpy
from ecell4 import *

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

y = run_simulation(
    numpy.linspace(0, 10, 100), {'A': 60, 'B': 60}, solver='ode')

More examples are available below:

MSD explains how to take statistics of trajectories of particles freely diffusing in three-dimensional space. This would be the best demonstration to explain the usage of FixedIntervalTrajectoryObserver.