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.

Important details of the process of conversion of the cell models to NeuroML, and matching cell behaviour acorss simulators is present in the [2010 NeuroML paper](http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000815).

### Install neuroConstruct & get latest project

See the instructions [here](http://www.opensourcebrain.org/projects/neuroconstructprojects/wiki/Wiki) regarding obtaining the latest version of neuroConstruct.

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

To get a local copy of the Thalamocortical project, [install Git](http://www.opensourcebrain.org/projects/gitintro/wiki/Wiki) and type:

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

### View a cell in 3D

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

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 (important!)

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.

### Generate a network model

Once the synapse mechanisms have been generated, it is possible to generate a 3D network model containing all 14 cell types from the original paper.

As this network example is quite large, it is wide to view the cells with only lines for neurites. Go to menu option **Settings** -\> **Project Properties** and **Soma solid, neurite lines** for the **Display** option. Press **Save** to exit.

Go to tab **Generate** and select [Simulation Configuration](http://www.neuroconstruct.org/docs/Glossary_gen.html#Simulation%20Configuration): **Demo3D** in the drop down box. This will generate a network with 14 cell groups. Go to tab **Visualisation**, select **Latest Generated Positions** and click **View**.

![](Thalamocortical_072.png)

Click on one of the cells (or select a cell group/cell number in the drpdown boxes) and click **Transparent mode** to better see the position of individual cells (and the somata of cells it’s connected to):

![](Thalamocortical_071.png)