Introduction to using the Traub et al 2005 model¶

First, and most importantly, please remember that this is a work in progress!

The original Traub et al model was developed in FORTRAN, this was converted to NEURON by Tom Morse and Michael Hines, and this has now been converted to NeuroML & neuroConstruct.

Install neuroConstruct & get latest project¶

See the instructions here regarding obtaining the latest version of neuroConstruct.

Install NEURON, GENESIS or MOOSE (see project:simulators).

To get a local copy of the Thalamocortical project type:

hg clone http://www.opensourcebrain.org/hg/osb/models/cerebral_cortex/networks/Thalamocortical

View a cell in 3D¶

Open neuroConstruct and view a cell in 3D…

More…

Test installation with single cell simulation¶

Run a single cell on NEURON…

More…

Generate synapse files¶

Currently the majority of the synapse models (ChannelML based synapses in cellMechanism folder) are not included in the project in the repository.

These are generated by a script makeSyns.sh in pythonScripts/netbuild. This script was manually created from the info in teh Appendix of the original paper (it’s easier to check/update the values in makeSyns.sh than through the neuroConstruct GUI).

This script (or makeSyns.bat on Windows) needs to be run once to generate files cellMechanisms/Syn_AMPA_L4SS_L4SS/ChannelMLSyn.xml etc.