ecell4-base 2.0.0b1

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

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, Spatiocyte (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:

• 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 ecell4-base-master/readthedocs/tutorials. or ecell4-base-master/readthedocs/examples
• If you use Azure Notebooks, please go down to readthedocs/tutorials or readthedocs/examples.

Installation

Please see INSTALL.md. Basically you can install E-Cell4 on any OS just by running

pip install ecell4

Tutorials

Please see tutorials.

Examples

Please see 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

%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

%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.

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.