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.
Project description
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
. orecell4-base-master/readthedocs/examples
- If you use Azure Notebooks, please go down to
readthedocs/tutorials
orreadthedocs/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.
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