E-Cell System is, 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.
- Python (2.7 and 3.4, 3.5, 3.6 both major versions are supported [3.4 is supported only on Linux, Mac does not support 3.4 and 3.5])
- pip (8.1 or later)
- HDF5 (1.8.17, required only on Windows.)
We strongly recommend that you run E-Cell4 with Jupyter Notebook. Some E-Cell4 functions (for visualization, datastore) optionally depend on
- matplotlib (1.5.1 or later)
- ffmpeg
- pandas
We recommend that you install Miniconda to manage Python packages. Note that we do not support Python2.7 64bit for Windows.
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Install Miniconda for Windows from http://conda.pydata.org/miniconda.html
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Run the following commands on command prompt
conda install hdf5=1.8.17 conda install matplotlib notebook pip install ecell
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(Important) E-Cell4 for Windows needs
HDF5
version 1.8.17. If there's any problem, please run the following commands.conda uninstall hdf5 conda clean -a conda install hdf5=1.8.17
If you use animated visualization with E-Cell4, please install ffmpeg windows build and add its path to your USER PATH enviromental variable.
We recommend that you install Miniconda to manage Python packages. After installing Miniconda, run the following commands in your terminal.
(NOTICE for Mac users) We do not provide Python3.5 whl for Mac. Instead we provide Python3.6 whl for Mac. To use Python3.6 enviroment, please refer to http://conda.pydata.org/docs/py2or3.html . Continuum.io already offers Python3.6 conda packages.
# After installing Miniconda2 or Miniconda3 (Here we assume that you installed Miniconda3).
~/miniconda2/bin/conda install matplotlib notebook
# Download E-Cell4 whl file for your Python version from https://github.com/ecell/ecell4/releases before running this command.
~/miniconda2/bin/pip install ecell
# If you want animation support, install ffmpeg with homebrew
brew install ffmpeg
# or if you use Ubuntu Linux
# apt install ffmpeg
Here we download example notebooks from https://github.com/ecell/ecell4-notebooks 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 https://github.com/ecell/ecell4-notebooks/archive/master.zip -OutFile master.zip
Expand-Archive master.zip
.¥jupyter-notebook.exe .¥master¥ecell4-notebooks-master¥
Here we assume that you installed Miniconda(Python3.5) to ~/miniconda3
wget https://github.com/ecell/ecell4-notebooks/archive/master.zip
unzip master.zip
cd ecell4-notebooks-master
~/miniconda3/bin/jupyter-notebook
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
>>>
%matplotlib inline
import numpy
from ecell4 import *
with reaction_rules():
A + B == C | (0.01, 0.3)
y = run_simulation(
numpy.linspace(0, 10, 100), {'A': 60, 'B': 60}, solver='ode')
%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)
If you're familiar with Docker, the following commands should work in most cases:
docker pull ecell/ecell4
docker run -d -p 8888:8888 ecell/ecell4 start-notebook.sh --NotebookApp.token=''
and open a web browser to http://localhost:8888
.
Our Docker image is based on Minimal Jupyter Notebook Stack. See https://github.com/jupyter/docker-stacks/tree/master/base-notebook or Our Wiki page for more details on the Docker command options.
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.