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PUBLIC DOMAIN NOTICE

National Institute on Deafness and Other Communication Disorders

This software/database is a "United States Government Work"

under the terms of the United States Copyright Act. It was

written as part of the author's official duties as a United

States Government employee and thus cannot be copyrighted.

This software/database is freely available to the public for

use. The NIDCD and the U.S. Government have not placed any

restriction on its use or reproduction.

Although all reasonable efforts have been taken to ensure

the accuracy and reliability of the software and data, the

NIDCD and the U.S. Government do not and cannot warrant the

performance or results that may be obtained by using this

software or data. The NIDCD and the U.S. Government disclaim

all warranties, express or implied, including warranties of

performance, merchantability or fitness for any particular

purpose.

Please cite the author in any work or product based on this

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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.