A multi-algorithm, multi-timescale, multi-spatial-representation biochemical simulation environment.
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README.md

E-Cell System version 4

Build Status Build status Documentation Status PyPI License: GPL v2 Codacy Badge Slack Status

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 the cell. E-Cell has multi-algorithm, multi-timescale and multi-spatial-representation as its central feature.

Installation and usage

Installation

Requirements

Minimum requirements

  • 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.)

Optional requirements

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

Windows

We recommend that you install Miniconda to manage Python packages. Note that we do not support Python2.7 64bit for Windows.

  • Install Miniconda for Windows from http://conda.pydata.org/miniconda.html

  • Run the following commands on command prompt

    conda install hdf5=1.8.17
    conda install matplotlib notebook
    pip install ecell
  • (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.

Mac or Linux

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

How to try E-Cell4 examples

Here we download example notebooks from https://github.com/ecell/ecell4-notebooks and open it with Jupyter Notebook.

Windows

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¥

Mac or Linux

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

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
>>>

A reversible binding reaction

%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')

png

Particle tracking 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)

png

Docker image for E-Cell4

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.

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.