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National Institute on Deafness and Other Communication Disorders

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Large-Scale Neural Modeling software (LSNM)

Section on Brain Imaging and Modeling
Voice, Speech and Language Branch
National Institute on Deafness and Other Communication Disorders
National Institutes of Health

This README file was last modified on September 18, 2017.

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Python version of LSNM (Large-Scale Neural Modeling software).
This repository contains the following directories:

   * stimuli_creation: Scripts to create stimuli (visual and auditory) for simulation
   
   * simulation: LSNM Simulator source code
   
   * analysis: Scripts to analyze simulated neuronal and neuroimaging timeseries
   
   * visualization: Scripts to visualize simulated neuronal and neuroimaging data

   * auditory_model: Husain et al (2004)'s auditory model implemented using LSNM in python

   * visual_model: New version of Tagamets and Horwitz (1998)'s visual model using Ulloa and Horwitz (2016) framework
   
   * visual_model_with_forgetting: Slightly different version of "visual_model" above to allow decay in short-term 
   memory modules during a visual Delayed match-to-sample task


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, sys, and
     PyQt4, pandas, among other scientific computation modules. My
     advice is to download Anaconda Python, freely available
     from continuum.io, 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. If the ‘Alternate installation’ does not work, please
     refer to the “Installing Python modules” in the lsnm_in_python
     wiki page, at https://github.com/NIDCD/lsnm_in_python/wiki/Installing-Python-modules.