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 2.7.9(32bit) https://www.python.org/ftp/python/2.7.9/python-2.7.9.msi or Python 3.4.3(32bit) https://www.python.org/ftp/python/3.4.3/python-3.4.3.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 (or C:\Python34, C:\Python34\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 IPython notebook. Below is IPython notebook(and matplotlib) installation for Windows.
pip install python-dateutil
pip install pyparsing
pip install "ipython[notebook]"
next, install matplotlib and numpy from
https://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.4.2/windows/matplotlib-1.4.2-cp27-none-win32.whl
http://sourceforge.net/projects/numpy/files/NumPy/1.9.1/numpy-1.9.1-win32-superpack-python2.7.exe/download
- homebrew
- hdf5
- pip
brew install homebrew/science/hdf5
brew install wget
wget https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
pip install https://github.com/ecell/ecell4/releases/download/4.0.0-beta2/ecell4-4.0.0b2-cp27-none-macosx_10_10_intel.whl --user
# if you are using Mountain Lion
# pip install https://github.com/ecell/ecell4/releases/download/4.0.0-beta2/ecell4-4.0.0b2-cp27-none-macosx_10_9_intel.whl --userWe recommend you run E-Cell4 models from IPython notebook. Below is IPython notebook(and matplotlib) installation for Mac.
pip install matplotlib --user
pip install "ipython[notebook]" --user
cd ~/Library/Python/2.7/ecell4ipynb
PYTHONPATH=~/Library/Python/2.7/lib/python/site-packages/ ipython notebooknow you can see IPython notebooks, please open index.ipynb to see E-Cell4 models.
# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-dev libboost-regex-dev libhdf5-dev cython
$ wget https://github.com/ecell/ecell4/archive/master.zip
$ unzip master.zip
$ cd ecell4-master
# in this case we install ecell4 to $HOME/ecell4
$ PREFIX=$HOME/ecell4 ./install.sh py2# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-dev libboost-regex-dev libhdf5-dev cython3 python3-pip
$ wget https://github.com/ecell/ecell4/archive/master.zip
$ unzip master.zip
$ cd ecell4-master
# in this case we install ecell4 to $HOME/ecell4
$ PREFIX=$HOME/ecell4 ./install.sh py3# dependent packages
$ sudo apt-get install cmake libgsl0-dev libboost-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
# in this case we install ecell4 to $HOME/ecell4
$ PREFIX=$HOME/ecell4 PYTHONPATH=/path/to/lib/python2.7/site-packages ./install.sh py2# If you set PREFIX to $HOME/ecell4, make sure to append $HOME/ecell4/lib to LD_LIBRARY_PATH
$ LD_LIBRARY_PATH=$HOME/ecell4/lib:$LD_LIBRARY_PATH PYTHONPATH=$HOME/ecell4/lib/python2.7/site-packages python
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
>>>
We support docker images too. If you use docker, you can easily test E-Cell4.
The latest version of boot2docker sets up a host only network adaptor which provides access to the container's ports.
$ boot2docker ssh
######## in boot2docker
docker@boot2docker:~$ docker pull ecell/ecell4:develop
docker@boot2docker:~$ docker run --rm -i -t -p 8888:8888 ecell/ecell4:developThen you should be able to access the E-Cell4 IPython notebook server using the IP address reported to you using:
$ boot2docker ipTypically, it is 192.168.59.103, then please open 192.168.59.103:8888 with your favorite browser. (But it could get changed by Virtualbox's DHCP implementation.)
$ sudo docker pull ecell4/ecell4:develop
$ sudo docker run --rm -i -t -p 8888:8888 ecell/ecell4:developOpen localhost:8888 with your favorite browser.
Please see http://nbviewer.ipython.org/github/ecell/ecell4/blob/develop/ipynb/index.ipynb