E-Cell System version 4
What is E-Cell System?
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
If you have docker environment, you can try E-Cell4 easily.
You can pull E-Cell4 container with docker pull ecell/ecell4
For Windows or Mac
- Install Docker Toolbox
- Run Kitematic
- Search with ecell4, and create ecell4 container
- Open the ACCESS URL in IP & PORTS with your web browser
For Linux
$ 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
Native binary installation
Windows
Requirements
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
Jupyter for Windows
We recommend you run E-Cell4 models from Jupyter notebook. Below is Jupyter notebook(and matplotlib) installation for Windows.
-
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.
Mac or Linux
Please use homebrew-ecell4
Jupyter for Mac or Linux
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
Simple examples
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
A reversible binding reaction
%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')