[PYTHON] Try using E-Cell 4 on Windows 7 or Mac OS X

** The following information is outdated. Please refer to here for the latest information. ** **

How to install

__Note: E-Cell 4 is currently under development. Please note that it probably has a human pillar element. __

--Repository: https://github.com/ecell/ecell4 --Official documentation: http://ecell4.readthedocs.org/en/latest/

Installation of jupyter [notebook], numpy, matplotlib, etc. is really optional, but it's definitely better to use it.

For Windows

  1. Install the ** 32-bit version ** of Miniconda for Windows from http://conda.pydata.org/miniconda.html [^ 1 ].

[^ 1]: If you have plenty of space, you can save time by using Anaconda with all of them. Https://www.continuum.io/downloads

  1. Start the command prompt cmd and install other dependent Python libraries [^ 2].

conda update pip conda install hdf5 jupyter matplotlib

 [^ 2]: Not required for Anaconda.

 3. Continue to install E-Cell 4. For Python3, execute the lower part.

pip install https://github.com/ecell/ecell4/releases/download/4.0.0/ecell-4.0.0-cp27-none-win32.whl
# pip install https://github.com/ecell/ecell4/releases/download/4.0.0/ecell-4.0.0-cp35-none-win32.whl

Although it is an option, if you want to use the video display function, install FFmpeg from http://ffmpeg.zeranoe.com/builds/ and the path PATH Let through.

For Mac

For Mac OS X, E-Cell 4 itself can be installed with homebrew.

brew tap ecell/ecell4
brew install ecell4

install gsl with homebrew

ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
brew install gsl

Preparing the Python environment

Since Python, numpy and matplotlib are already included, install IPython Notebook using pip.

curl -O https://bootstrap.pypa.io/get-pip.py
sudo python get-pip.py
sudo pip install "ipython[notebook]"

E-Cell 4 installation

Next, install E-Cell 4. For Yosemite (10.10),

sudo pip install https://github.com/ecell/ecell4/releases/download/4.0.0-beta2/ecell4-4.0.0b2-cp27-none-macosx_10_10_intel.whl

For Mavericks (10.9),

sudo pip install https://github.com/ecell/ecell4/releases/download/4.0.0-beta2/ecell4-4.0.0b2-cp27-none-macosx_10_9_intel.whl

Can be installed with.

How to use

If you have IPython Notebook installed, launch it as follows. The browser should start and jump to the main page of IPython Notebook. Please note that problems may occur when using IE or Safari. Please.

ipython notebook

After creating a new notebook and running `` `% matplotlib inline``` on the first line, you can run the code below to display the simulation results as a graph.


%matplotlib inline
import numpy
from ecell4 import *

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

run_simulation(10, {'A': 60, 'B': 60})

The result should look like this:


Please refer to the following article for more detailed usage.

-Easy to use E-Cell 4 for beginners -Easy to use E-Cell 4 Intermediate -Easy to use E-Cell 4 Advanced Edition

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