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 (for important information on this see here), 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:

git clone git://github.com/OpenSourceBrain/Thalamocortical.git

View a cell in 3D¶

Open neuroConstruct and open the Thalamocortical project; File > Open Project> select /Thalamocortical/Thalamocortical.ncx

Go to tab Visualisation, select L23PyrFRB, a Fast Regular Bursting Layer 2/3 Pyramidal cell, in the drop down box (or any other cell of your choosing) and click View.

To change the view so that all segments are drawn as solid cylinders select All solid in the lower left drop down box.

To see the distribution of channels on the cell, select Cell density mechanisms in the lower right drop down box.

To get more details on the properties of this cell, go to tab Cell Types, select L23PyrFRB, and a summary of the biophysical properties and structure of the cell is given.

Test installation with single cell simulation¶

Assuming the simulator NEURON is installed, a simulation can be generated with just this cell. Go to tab Generate and select Simulation Configuration: Cell2-suppyrFRB-FigA1FRB in the drop down box. This will generate a network with one L23PyrFRB and current clamp input (hyperpolarising followed by depolarising).

Go to tab Export, sub tab NEURON, and click Create hoc simulation. This generates the HOC and MOD files specific to NEURON for this cell & network steup. These files can be viewed using View….

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.