E-Cell System is, a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell.

• Docker container for E-Cell System version4

  • Windows or Mac
  • Linux

• Installation

  • Requirements

    • Minimum requirements
    • Optional requirements
    • Build requirements

  • Windows

  • Mac

  • Linux

    • Ubuntu Linux 14.04
    • Building whl on Ubuntu or Debian
    • Linuxbrew

• How to open E-Cell4 Jupyter notebooks

• Simple examples

  • A reversible binding reaction
  • Particle tracking on a spherical surface

If you have docker environment, you can easily try E-Cell4. You can pull E-Cell4 container with docker pull ecell/ecell4.

After the following steps, you should see Jupyter Notebook up and running (and E-Cell4 tutorials) in your web browser.

1. Install Docker Toolbox.
2. Run Docker Quickstart Terminal.
3. Run docker run -d -p 443:8888 ecell/ecell4 in the terminal.
4. Open 192.168.99.100:443 with your web browser.

1. Install Docker.

2. Run the following commands in your terminal.

   sudo docker pull ecell/ecell4
   sudo docker run -d -p 443:8888 ecell/ecell4

3. Open localhost:443 with your web browser.

• Python 2.7 or 3.4(on Linux) 3.5(on Windows, Mac)
• pip

We strongly recommend that you run E-Cell4 with Jupyter Notebook. And some E-Cell4 functions (for visualization, datastore) optionaly depend on

• matplotlib (1.5.1 and later)
• ffmpeg or avconv
• hdf5
• pandas

If you build E-Cell4 from source code, you need to install these software.

• boost (1.59 and earlier)
• cmake
• gsl
• hdf5

Please use 32bit Python2.7 or 3.5, even if you use 64bit Windows. We have NOT supported 64bit Python yet.

• Install 32bit Miniconda for Windows from http://conda.pydata.org/miniconda.html

• Run the follwing commands on command prompt (if you use Python3.5, please replace the target of pip install to the whl for 3.5)

  conda update pip
  conda install hdf5 jupyter matplotlib
  pip install https://github.com/ecell/ecell4/releases/download/4.0.0/ecell-4.0.0-cp27-none-win32.whl

Although jupyter is optional, we strongly recommend that you run E-Cell4 with jupyter. If you use animated visualization for E-Cell4, please install ffmpeg windows build and add its path to your USER PATH enviromental variable.

Please run the following commands in your terminal.

# Please download E-Cell4 whl file for your Python version from https://github.com/ecell/ecell4/releases , here we downloaded a whl for Python27
pip install  --user ecell-4.0.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl

# Mac default matplotlib is too old for E-Cell4, you need to update it with the following options.
pip install -U --user matplotlib
pip install -U --user jupyter

# path config for --user installed Python packages
echo 'export PYTHONPATH=~/Library/Python/2.7/lib/python/site-packages:$PYTHONPATH' >> ~/.bashrc
echo 'export PATH=~/Library/Python/2.7/bin:$PATH' >> ~/.bashrc
source ~/.bashrc

# If you use animation support. (Install ffmpeg with homebrew)
brew install ffmpeg

We also have homebrew formula for E-Cell4 homebrew-ecell4. If you have trouble in above installation please try this instead.

We have tested the release whl files on Ubuntu Linux 14.04. Please run the following commands with root privilege.

# If you use Python3, replace python-pip to python3-pip
apt-get install libgsl0-dev libhdf5-dev python-pip
# If you use Python3 please replace the whl for Python3
pip install https://github.com/ecell/ecell4/releases/download/4.0.0/ecell-4.0.0-cp27-none-linux_x86_64.whl

# The latest matplotlib and jupyter
apt-get install python-dev libfreetype6-dev libpng-dev pkg-config python-numpy pandoc
pip install matplotlib jupyter

# Optional requirement (animation visualization)
apt-get install libav-tools

E-Cell4 homebrew formula also can be used for Linuxbrew. If you do not use Ubuntu (or Debian) and not have root privilege, please try Linuxbrew instead.

Please replace the CONDA_INSTALL_FOLDER with the folder you installed Miniconda. For example C:¥Miniconda27.

cd the CONDA_INSTALL_FOLDER
cd ecell4ipynb
jupyter-notebook

### in the case of Python27
~/Library/Python/2.7/ecell4ipynb
jupyter-notebook

cd /usr/local/ecell4ipynb
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("B.A.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)

This project is licensed under the terms of the GNU General Public License v2. See LICENSE for the project license.

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