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

• Dockerized E-Cell4 Jupyter notebooks

  • For Windows or Mac
  • For Linux

• Native binary installation

  • Windows
  • Mac or Linux

• Simple examples

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

1. Install Docker Toolbox
2. Run Kitematic
3. Search with ecell4, and create ecell4 container

4. Open the ACCESS URL in IP & PORTS with your web browser

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

You'll be able to E-Cell4 notebooks at http://THE_IP_RUNNING_DOCKER:443

Please use 32bit Python, even if you use 64bit Windows. We don't support 64bit Python.

• Python 2.7.10(32bit) https://www.python.org/ftp/python/2.7.10/python-2.7.10.msi
• HDF5-1.8.14 Pre-built Binary(32-bit) http://www.hdfgroup.org/ftp/HDF5/current/bin/windows/extra/hdf5-1.8.14-win32-vs2008-shared.zip

Please add C:\Python27, C:\Python27\Scripts and C:\Program Files (x86)\HDF_Group\HDF5\1.8.14\bin to your PATH enviromental variable.

And run following command with command prompt.

pip install https://github.com/ecell/ecell4/releases/download/4.0.0-beta2/ecell4-4.0.0b2-cp27-none-win32.whl

We recommend you run E-Cell4 models from Jupyter notebook. Below is Jupyter notebook(and matplotlib) installation for Windows.

• Install Visual C++ Compiler for Python 2.7

• Install Jupyter notebook and matplotlib

  pip install jupyter
  pip install matplotlib
  

matplotlib depends on numpy. It takes some time to build numpy, please be patient.

Please use homebrew-ecell4

We recommend you run E-Cell4 models from Jupyter notebook. Below is Jupyter notebook(and matplotlib) installation for Mac or Linux.

sudo python get-pip.py
sudo pip install matplotlib
sudo pip install jupyter

Here are two extremely simple examples. Please see http://ecell4.readthedocs.org for more details.

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 import *
>>> sp = Species("B.A.C")
>>> print(sp.serial())
B.A.C
>>> print(unique_serial(sp))
A.B.C

%matplotlib inline
import numpy
from ecell4 import *

with reaction_rules():
    A + B == C | (0.01, 0.3)

run_simulation(
    numpy.linspace(0, 10, 100), {'A': 60, 'B': 60}, solver='ode')