Wiki » History » Version 8
Version 7 (Padraig Gleeson, 30 Apr 2014 14:57) → Version 8/18 (Padraig Gleeson, 30 Apr 2014 14:57)
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](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
===========================================
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
=================
Open neuroConstruct and open the Thalamocortical project; **File** ~~\> **Open Project**~~\> select <Git checkout dir>/Thalamocortical/Thalamocortical.ncx
Go to tab **Visualisation**, select **L23PyrFRB**, view 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. 3D…
To see the distribution of channels on the cell, select **Cell density mechanisms** in the lower right drop down box. More…
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, Run 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). single cell on NEURON…
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…**. More…
![](Thalamocortical_067.png)
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.
================================================
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
===========================================
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
=================
Open neuroConstruct and open the Thalamocortical project; **File** ~~\> **Open Project**~~\> select <Git checkout dir>/Thalamocortical/Thalamocortical.ncx
Go to tab **Visualisation**, select **L23PyrFRB**, view 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. 3D…
To see the distribution of channels on the cell, select **Cell density mechanisms** in the lower right drop down box. More…
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, Run 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). single cell on NEURON…
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…**. More…
![](Thalamocortical_067.png)
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.