[Comp-neuro] 'ACnet2' primary auditory cortex layer IV model

Dave Beeman dbeeman at Colorado.EDU
Wed Sep 4 01:32:22 CEST 2013


I would like to announce the release of the scripts and tutorial for the
'ACnet2' primary auditory cortex layer IV model that I presented at CNS
2013.  The documentation and links for download may be viewed at
http://genesis-sim.org/GENESIS/ACnet2-GENESIS/, with instructions for
reproducing the simulation results shown in Figure 1 of:

Beeman D (2013) A modeling study of cortical waves in primary auditory
cortex. BMC Neuroscience, 14(Suppl 1):P23 doi:10.1186/1471-2202-14-S1-P23.

In addition to their scientific purpose, these simulation scripts were
developed as a tutorial example for the construction of realistic cortical
networks.  The simulation scripts are designed to be run with GENESIS 2.3
and are extensively commented, easily customizable, and are designed for
extension to more detailed models, or conversion to other simulation
systems.  The model is slowly being implemented in GENESIS 3 (G-3) and a
conversion to neuroConstruct (http://www.neuroconstruct.org/) is planned.

The optional GUI for the simulation allows many experiments and
variations of the model to be carried out without modifications.

This package also contains both GENESIS and simulator-independent Python
tools for the visualization and analysis of network activity.

If you do not use the GENESIS simulator, and would like to try out the 
simulation, it is simplest to download the entire 'Ultimate GENESIS Tutorial 
Distribution' package with all source code, installation instructions, and the 
complete set of tutorials (about 50 MB) from 
http://genesis-sim.org/GENESIS/UGTD.html.  GENESIS usually installs without 
problems under modern versions of Linux.  Most questions related to 
installation have been answered in the archives of the 'genesis-sim-users' 
mailing list, which are available from the GENESIS 2 Sourceforge page at 
http://sourceforge.net/projects/genesis-sim/

The main documentation file 'ACnet2-docs.html' suggests experiments that may be 
tried with the many configurable options in the scripts, and ways to extend the 
model. It is my hope that this short tutorial and the example simulation 
scripts can provide a head start for a graduate student or postdoc who is 
beginning a cortical modeling project.

David Beeman
University of Colorado, Boulder


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