E-Cell System, a software platform for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell.
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 Jupyter notebook and matplotlib
pip install -U jupyter pip install matplotlib
matplotlib depends on numpy. It takes some time to build numpy, please be patient.
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew tap ecell/ecell4
brew install ecell4 --HEADWe recommend you run E-Cell4 models from Jupyter notebook. Below is Jupyter notebook(and matplotlib) installation for Mac.
sudo python get-pip.py
sudo pip install -U matplotlib
sudo pip install -U jupyter# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-regex-dev libhdf5-dev cython
$ wget https://github.com/ecell/ecell4/archive/master.zip
$ unzip master.zip
$ cd ecell4-master
# By default install.sh tries to install E-Cell4 into /usr/local, in this case you need to use sudo.
# In the following command, we install E-Cell4 into $HOME/ecell4. In this case you do NOT need to use sudo.
$ PREFIX=$HOME/ecell4 ./install.sh py2# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-regex-dev libhdf5-dev cython3
$ wget https://github.com/ecell/ecell4/archive/master.zip
$ unzip master.zip
$ cd ecell4-master
# By default install.sh tries to install E-Cell4 into /usr/local, in this case you need to use sudo.
# In the following command, we install E-Cell4 into $HOME/ecell4. In this case you do NOT need to use sudo.
$ PREFIX=$HOME/ecell4 ./install.sh py3# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-regex-dev libhdf5-dev libatlas-base-dev python-dev python-pip
$ sudo pip install cython
$ wget https://github.com/ecell/ecell4/archive/master.zip
$ unzip master.zip
$ cd ecell4-master
# By default install.sh tries to install E-Cell4 into /usr/local, in this case you need to use sudo.
# In the following command, we install E-Cell4 into $HOME/ecell4. In this case you do NOT need to use sudo.
$ PREFIX=$HOME/ecell4 PYTHONPATH=/path/to/lib/python2.7/site-packages ./install.sh py2- run command prompt
- run Python
python
- run terminal
- run Python with PYTHONPATH
PYTHONPATH=/usr/local/Cellar/ecell4/HEAD/libexec/lib/python2.7/site-packages python
If you set PREFIX to $HOME/ecell4, run Python with
LD_LIBRARY_PATH=$HOME/ecell4/lib:$LD_LIBRARY_PATH PYTHONPATH=$HOME/ecell4/lib/python2.7/site-packages python
in case with Python3
LD_LIBRARY_PATH=$HOME/ecell4/lib:$LD_LIBRARY_PATH PYTHONPATH=$HOME/ecell4/lib/python3.4/site-packages python3
Here are two extremely simple examples, See http://ecell4.readthedocs.org/en/latest/tutorials/ 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 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')
If you use docker, you can easily try E-Cell4.
You can pull E-Cell4 container with docker pull ecell/ecell4
- Install Docker Toolbox
- Run Kitematic
- Search with ecell4, and create ecell4 container
- Open the ACCESS URL in IP & PORTS with your web browser
$ sudo docker pull ecell/ecell4
$ sudo docker run -d -p 443:8888 ecell/ecell4You'll now be able to E-Cell4 notebooks at https://THE_IP_RUNNING_DOCKER:443