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
ecell4
This provides pure Python libraries (Miscellaneous utility functions) for E-Cell System version 4.
Try online
You can try this package online with Google Colaboratory. Please refer to the https://github.com/ecell/ecell4_docs
Quick Start
Here are 3 extremely simple examples, See https://github.com/ecell/ecell4_docs or http://ecell4.readthedocs.org for more details.
(base) root@5e5b25d2363d:~# python
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from ecell4_base.core import *
>>> sp = Species("A.B.C")
>>> sp.serial()
'A.B.C'
>>>
Binding and unbinding reactions
Run this with Jupyter Notebook
%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
Run this with Jupyter Notebook
%matplotlib inline
from ecell4_base.core import *
from ecell4 import *
with species_attributes():
M | {'dimension': 2}
A | {'D': 1.0, 'location': 'M'}
surface = Sphere(ones() * 0.5, 0.49).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)
Installation
Please refer to https://github.com/ecell/ecell4_base#installation
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