ecell4-base 1.0.dev2

A software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. E-Cell has multi-algorithm, multi-timescale and multi-spatial-representation as its central feature.

E-Cell System version 4
=======================

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[](https://circleci.com/gh/ecell/ecell4-base)
[](https://ci.appveyor.com/project/kaizu/ecell4)
[](http://ecell4.readthedocs.org/en/latest/?badge=latest)
[](https://pypi.python.org/pypi/ecell)
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[](https://ecell-project.herokuapp.com/)
<!---[](https://ecell-project.herokuapp.com/)--->

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.

Features
--------

- Single particle simulations, i.e. [The enhanced Green's Function Reaction Dynamics (eGFRD) method](http://gfrd.org), [Spatiocyte](http://spatiocyte.org) (a lattice-based method), and the Reaction Brownian Dynamics (RBD) method
- Ordinary differential equations, Gillespie algorithm (the direct method), and spatial Gillespie algorithm (the next subvolume method)
- Rule-based modeling
- Python programmable

Try online
----------

You can try this package online from the following links:

<a href="https://notebooks.azure.com/import/gh/ecell/ecell4"><img src="https://notebooks.azure.com/launch.png" /></a>
[](https://mybinder.org/v2/gh/ecell/ecell4/master?filepath=ecell4-master%2Freadthedocs)

- Code fragments that depend on ffmpeg will not work with Azure Notebooks. If you use movie export, please try Binder instead.
- If you use Binder, please go down to `tutorials` or `examples`.
- If you use Azure Notebooks, please go down to `readthedocs/tutorials` or `readthedocs/examples`.

Installation
-------------

Please see [INSTALL.md](https://github.com/ecell/ecell4-base/blob/master/INSTALL.md).
Basically you can install E-Cell4 on any OS just by running
```
pip install ecell
```

### Note about Windows
In Windows environment, all commands should be executed from **Anaconda Prompt** (Not from Command Prompt or PowerShell. You can run Anaconda Prompt from Windows Start Menu).
This in particular solves the problem of failing to load the DLL used from E-Cell4.


Tutorials
----------

Please see [tutorials](https://github.com/ecell/ecell4-base/tree/master/readthedocs/tutorials).

Examples
---------

Please see [examples](https://github.com/ecell/ecell4-base/tree/master/readthedocs/examples).

Simple examples
---------------

Here are two extremely simple examples, See http://ecell4.readthedocs.org 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()
A.B.C
>>>
```

### Binding and unbinding reactions

```python
%matplotlib inline
from ecell4 import *

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

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


### Diffusion on a spherical surface

```python
%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)
run_simulation(
0.4, y0={'A': 10}, structures={'M': surface},
solver='spatiocyte', observers=obs, return_type=None)

viz.plot_trajectory(obs, interactive=False)
```


Citation
========

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

[](https://zenodo.org/badge/latestdoi/6348303)

Licensing terms
===============

This product is licensed under the terms of the [GNU General Public License v2](https://github.com/ecell/ecell4/blob/master/licenses/LICENSE),
See [NOTICE](https://github.com/ecell/ecell4/blob/master/licenses/NOTICE.txt) for the software included in this product.

- Copyright (c) 2010-, RIKEN

All rights reserved.