MAGINE

Mechanism of Action Generator involving Network Expansion

Installation

1. Install Anaconda

   Our recommended approach is to use `Anaconda`_, which is a distribution of Python containing most of the numeric and scientific software needed to get started. If you are a Mac or Linux user, have used Python before and are comfortable using pip to install software, you may want to skip this step and use your existing Python installation.

   Anaconda has a simple graphical installer which can be downloaded from https://www.continuum.io/downloads - select your operating system and download the Python 2.7 version. The default installer options are usually appropriate.

   Windows users: If you are unsure whether to use the 32-bit or

   64-bit installer, press the Windows Start button, search for “About your PC”, and under “System type” it will specify 32-bit operating system or 64-bit operating system

2. Open a terminal

   We will install most packages with conda:

   $ conda create -n magine_env python=2
   $ source activate magine_env
   $ conda config --add channels conda-forge
   $ conda install jinja2 statsmodels networkx graphviz
   $ conda install -c marufr python-igraph
   

3. Install MAGINE

   The installation is very straightforward with pip - type the following in a terminal:

    $ git clone https://github.com/LoLab-VU/magine
    $ cd magine
    $ pip install -r requirements.txt
    $ export PYTHONPATH=`pwd`:$PYTHONPATH
   
   **Mac users:** To open a terminal on a Mac, open Spotlight search
          (press command key and space), type ``terminal`` and press enter.
   

4. Start Python and MAGINE

   If you installed Python using `Anaconda`_ on Windows, search for and select IPython from your Start Menu (Windows). Otherwise, open a terminal and type python to get started (or ipython, if installed).

   You will then be at the Python prompt. Type import magine to try loading magine. If no error messages appear and the next Python prompt appears, you have succeeded in installing magine!

Documentation

The manual is available online at http://magine.readthedocs.io.