Introduction to using the Traub et al 2005 model

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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](http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=82894&file=\nrntraub\README)), and this has now been converted to NeuroML & neuroConstruct.

Install neuroConstruct & get latest project

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See the instructions [here](http://www.opensourcebrain.org/projects/neuroconstructprojects/wiki/Wiki) 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

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Open neuroConstruct and open the Thalamocortical project; **File** ~~\> **Open Project**~~\> select <Git checkout dir>/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**.

![](Thalamocortical_067.png)

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

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Assuming the simulator NEURON is installed, a simulation can be generated with just this cell. Go to tab **Generate** and select [Simulation Configuration](http://www.neuroconstruct.org/docs/Glossary_gen.html#Simulation%20Configuration): **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…**. Execute the simulation in NEURON using **Run Simulation**.

![](Thalamocortical_068.png)

This simulation can be loaded back into neuroConstruct. Go to tab **Visualisation**, click **View prev sims in 3D**, select the simulation and press **Load simulation**.

![](Thalamocortical_070.png)

To plot the data saved in the simulation, click on any part of the cell, and click **Plot selected**. This will list the locations recorded (soma and one point on axon).

To replay the simulation in the 3D view select **Replay**. This will give a time varying coloring to the cell based on membrane potential. Note that since only 2 locations are recorded, the majority of the cell will be coloured according to the membrane potential at the soma.

Generate synapse files

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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.