Requirements

To execute this software you will need to have the following installed on your local machine or server:

• Python 2.7 for any platform (so far tested on Mac OS and RedHat Linux). Please note that python LSNM is NOT compatible with either Python 2.6 or Python 3.0.
• Python modules matplotlib, re, random, math, numpy, scipy, sys, PyQt4, pandas, and mayavi, among other scientific computation and visualization modules. My advice is to download Anaconda Python, freely available at http://continuum.io/downloads, which contains Python 2.7 and a full set of modules commonly used in scientific computation.
• The Virtual Brain Python modules, located at the TVB github repository at https://github.com/the-virtual-brain. You will need to clone the directories 'tvb-library' and 'tvb-data' and install it locally so that your Python installation is able to see the location of such modules. Please refer to the instructions provided in the github repository on how to cleanly install TVB. Also, refer to the 'Alternate installation: the user scheme' at https://docs.python.org/2/install/, for instructions on how to install python modules locally when you don't have 'write' permission to global-site packages (e.g., you are only a user in a Unix system an do not have a 'root' or 'su' password.

How to install The Virtual Brain Toolbox

1. Clone the required tvb code (along with data and surface simulations source code). I typed the following from a unix terminal:

git clone https://github.com/the-virtual-brain/tvb-data

git clone https://github.com/the-virtual-brain/tvb-geodesic

git clone https://github.com/the-virtual-brain/tvb-library

2. install the tvb toolboxes one by one by going into each individual directory (tvb-data, tvb-geodesic, tvb-library) by typing the following:

python setup.py install --user

3. start a python session (make sure you use Python 2.7.x) and tried importing tvb most commonly used toolboxes by typing the following:

from tvb.simulator.lab import *

Please note that there will be only one resulting ERROR. Something having to do with the Mayavi toolbox. Don't worry about that because you can use TVB without using any of the Mayavi tools (for plotting 3D surfaces). Maya does come with the Anaconda Python release but it is not automatically installed when you install Anaconda. If you are interested in installing Mayavi (useful for surface visualization), you have to install that separately by typing the following on a unix terminal:

conda install mayavi

Another thing to note is that if you install a personal python or conda environment to run LSNM/TVB simulations, you need to make sure to activate your environment using:

module load Anaconda

source activate /data/LSNM_TVB_Users/python/envs/python2.7.9

Also, make sure that you have created a file in your directory called ".condarc" that contains:

envs_dirs:

- /data/LSNM_TVB_Users/python/envs

Additionally, you need to define a PYTHONPATH in your ".bash_profile" (or equivalent):

PYTHONPATH=/data/LSNM_TVB_Users/python/envs/python2.7.9/lib/python2.7/site-packages

export PYTHONPATH

SVN_REVISION=7900

export SVN_REVISION

Finally, please note that you need to have a working installation of spicy and Cython to be able to install tvb.

Final Final note: You will need to copy the connectivity ZIP files (e.g., connectivity_998.zip) manually to tvb_data directory. ZIP connectivity data files need to be copied from "tvb-data-master/tvb_data/connectivity" to "...tvb_data-1.2-py2.7.egg/tvb_data/connectivity"