# Wiki

Welcome to the lsnm_in_python wiki!

The lsnm_in_python repository contains Python scripts to simulate auditory and visual working memory experiments. The Python scripts in this repository are based on C and Matlab code originally developed by Malle Tagamets and Barry Horwitz to simulate a visual working memory experiment (see [Tagamets and Horwitz, 1998] (http://www.ncbi.nlm.nih.gov/pubmed/9651128) and [Horwitz and Tagamets, 1999](http://www.ncbi.nlm.nih.gov/pubmed/10524605)) and by Fatima Husain and Barry Horwitz to simulate an auditory working memory experiment (see [Husain et al, 2004] (http://www.ncbi.nlm.nih.gov/pubmed/15050592)). The Python scripts are also based on Barry Horwitz and Brent Warner's functional connectivity simulations (see [Horwitz et al, 2005] (http://www.ncbi.nlm.nih.gov/pubmed/16087450)).

The new large-scale neural simulator (LSNM) now uses a Graphic User Interface through which one specifies model, weights, and simulation script. The new LSNM simulator can also work with [The Virtual Brain Simulator] (https://github.com/the-virtual-brain), and it allows one to embed a neural model into a connectome to run whole-brain simulations ([Ulloa and Horwitz, 2016] (http://dx.doi.org/10.3389/fninf.2016.00032)).

The old set of programs written in C++ and Matlab to simulate auditory and visual working memory experiments is available at <https://github.com/NIDCD/lsnm>, but is no longer being updated. 

As a historical reference, the LSNM simulator was originally developed by Malle Tagamets and Barry Horwitz in the 1990's to simulate a visual working memory experiment (see [Tagamets and Horwitz, 1998](http://www.ncbi.nlm.nih.gov/pubmed/9651128)) and later adapted/modified by Fatima Husain to simulate an auditory working memory experiment (see [Husain et al, 2004] (http://www.ncbi.nlm.nih.gov/pubmed/15050592)). The system was significantly expanded around 2003 by Theresa Long and Barry Horwitz by adding batch processing and by Brent Warner and Barry Horwitz by adding functional connectivity simulations (see [Horwitz et al, 2005] (http://www.ncbi.nlm.nih.gov/pubmed/16087450)). Although the code was originally developed for simulating electrical neuronal activity and PET (Tagamets and Horwitz), extensions were added to the code to simulate fMRI ([Horwitz and Tagamets, 1999](http://www.ncbi.nlm.nih.gov/pubmed/10524605) and [Husain et al, 2004](http://www.ncbi.nlm.nih.gov/pubmed/15050592)) and MEG ([Banerjee et al, 2012](http://www.ncbi.nlm.nih.gov/pubmed/22291621)). 

In addition to the code described above, there were other branches of the code made over the years, such as the simulations of Transcranial Magnetic Stimulation (TMS) around 2001 (see [Husain et al, 2002] (http://www.ncbi.nlm.nih.gov/pubmed/11771974)),  the simulation of perceptual grouping around 2002 (see [Husain et al, 2005] (http://www.ncbi.nlm.nih.gov/pubmed/16197683)), the simulations of long-duration auditory stimuli around 2003 (see [Ulloa et al, 2008] (http://www.ncbi.nlm.nih.gov/pubmed/19132798), source code available at <https://github.com/NIDCD/lsnm_auditory_sequences>), and the simulation of a decision-making module around 2004 (see [Wen et al, 2008] (http://www.ncbi.nlm.nih.gov/pubmed/18496711), source code available at <https://github.com/NIDCD/lsnm_decision_making>).