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E-Cell System version 4

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What is E-Cell System?

E-Cell System is a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like a cell.

E-Cell4 accepts multi-algorithms, multi-timescales and multi-spatial-representations as its central feature.


Try online

You can try this package online from the following links:

<a href=""><img src="" /></a>

  • Code fragments that depend on ffmpeg will not work with Azure Notebooks. If you use movie export, please try binder instead.
  • If you use Azure Notebooks, please move readthedocs/tutorials or readthedocs/examples. There are several Jupyter Notebooks.


Please see

How to try E-Cell4 examples

Here we download example notebooks from and open it with Jupyter Notebook.


Open powershell and run these commands.
Here we assume that you installed Miniconda(Python3.5) to C:¥Miniconda3

cd C:¥Miniconda3¥Scripts
wget -OutFile
.¥jupyter-notebook.exe .¥master¥ecell4-notebooks-master¥

Mac or Linux

Here we assume that you installed Miniconda(Python3.5) to ~/miniconda3

cd ecell4-notebooks-master

Simple examples

Here are two extremely simple examples, See for more details on running E-Cell4.

Python 2.7.6 (default, Mar 22 2014, 22:59:56)
[GCC 4.8.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from ecell4.core import *
>>> sp = Species("A.B.C")
>>> print sp.serial()

Binding and unbinding reactions

%matplotlib inline
from ecell4 import *

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

run_simulation(100, {'A': 60, 'B': 60})

Diffusion on a spherical surface

%matplotlib inline
from ecell4 import *

with species_attributes():
    A | {'D': '1', 'location': 'M'}

surface = Sphere(ones() * 0.5, 0.5).surface()
obs = FixedIntervalTrajectoryObserver(1e-4)
    0.4, y0={'A': 10}, structures={'M': surface},
    solver='spatiocyte', observers=obs, return_type=None)

viz.plot_trajectory(obs, interactive=False)


If this package contributes to a project which leads to a scientific publication, I would appreciate a citation.

Licensing terms

This product is licensed under the terms of the GNU General Public License v2,
See NOTICE for the software included in this product.

  • Copyright (c) 2010-, RIKEN

All rights reserved.

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