Home

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 and Horwitz and Tagamets, 1999) and by Fatima Husain and Barry Horwitz to simulate an auditory working memory experiment (see Husain et al, 2004). The Python scripts are also based on Barry Horwitz and Brent Warner's functional connectivity simulations (see Horwitz et al, 2005).

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, and it allows one to embed a neural model into a structural connectome to simulate whole-brain dynamics (Ulloa and Horwitz, 2016).

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Matlab to simulate auditory and visual working memory experiments is available at https://github.com/NIDCD/lsnm, but is no longer being updated.

As a historical reference, the LSNM simulator was originally developed by Malle Tagamets and Barry Horwitz in the 1990's to simulate a visual working memory experiment (see Tagamets and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) and later adapted/modified by Fatima Husain to simulate an auditory working memory experiment (see Husain et al, 2004). The system was significantly expanded around 2003 by Theresa Long and Barry Horwitz by adding multi-subject simulations and by Brent Warner and Barry Horwitz by adding functional connectivity simulations (see Horwitz et al, 2005). Although the code was originally developed for simulating electrical neuronal activity and PET (Tagamets and Horwitz, 1998), extensions were added to the code to simulate fMRI (Horwitz and Tagamets, 1999 and Husain et al, 2004), MEG (Banerjee et al, 2012), and laminar fMRI (Corbitt, Ulloa, and Horwitz, in preparation).

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),
• the simulation of perceptual grouping around 2002 (see Husain et al, 2005),
• the simulations of long-duration auditory stimuli around 2003 (see Ulloa et al, 2008), source code available at https://github.com/NIDCD/lsnm_auditory_sequences),
• the simulation of a decision-making module around 2004 (see Wen et al, 2008, source code available at https://github.com/NIDCD/lsnm_decision_making), and
• the simulation of multiple-item short-term memory (see Liu, Ulloa, and Horwitz, in press, source code will be available soon at https://github.com/NIDCD/lsnm-multiple-item-stm)