Edit History

Wiki » History » Version 8

Padraig Gleeson, 30 Apr 2014 14:57

1 1 Padraig Gleeson
Introduction to using the Traub et al 2005 model
2 1 Padraig Gleeson
================================================
3 1 Padraig Gleeson
4 4 Padraig Gleeson
First, and most importantly, please remember that this is a **work in progress**!
5 1 Padraig Gleeson
6 6 Padraig Gleeson
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.
7 4 Padraig Gleeson
8 1 Padraig Gleeson
Install neuroConstruct & get latest project
9 7 Padraig Gleeson
===========================================
10 1 Padraig Gleeson
11 7 Padraig Gleeson
See the instructions [here](http://www.opensourcebrain.org/projects/neuroconstructprojects/wiki/Wiki) regarding obtaining the latest version of neuroConstruct.
12 4 Padraig Gleeson
13 4 Padraig Gleeson
Install NEURON, GENESIS or MOOSE (see project:simulators).
14 4 Padraig Gleeson
15 4 Padraig Gleeson
To get a local copy of the Thalamocortical project type:
16 4 Padraig Gleeson
17 6 Padraig Gleeson
`git clone git://github.com/OpenSourceBrain/Thalamocortical.git`
18 4 Padraig Gleeson
19 4 Padraig Gleeson
View a cell in 3D
20 7 Padraig Gleeson
=================
21 4 Padraig Gleeson
22 8 Padraig Gleeson
Open neuroConstruct and open the Thalamocortical project; **File** ~~\> **Open Project**~~\> select <Git checkout dir>/Thalamocortical/Thalamocortical.ncx
23 1 Padraig Gleeson
24 8 Padraig Gleeson
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**.
25 1 Padraig Gleeson
26 8 Padraig Gleeson
![](Thalamocortical_067.png)
27 8 Padraig Gleeson
28 8 Padraig Gleeson
To change the view so that all segments are drawn as solid cylinders select **All solid** in the lower left drop down box.
29 8 Padraig Gleeson
30 8 Padraig Gleeson
To see the distribution of channels on the cell, select **Cell density mechanisms** in the lower right drop down box.
31 8 Padraig Gleeson
32 8 Padraig Gleeson
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.
33 8 Padraig Gleeson
34 1 Padraig Gleeson
Test installation with single cell simulation
35 1 Padraig Gleeson
=============================================
36 1 Padraig Gleeson
37 8 Padraig Gleeson
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).
38 1 Padraig Gleeson
39 8 Padraig Gleeson
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…**.
40 7 Padraig Gleeson
41 1 Padraig Gleeson
Generate synapse files
42 7 Padraig Gleeson
======================
43 1 Padraig Gleeson
44 5 Padraig Gleeson
Currently the majority of the synapse models (ChannelML based synapses in **cellMechanism** folder) are not included in the project in the repository.
45 5 Padraig Gleeson
46 5 Padraig Gleeson
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).
47 5 Padraig Gleeson
48 5 Padraig Gleeson
This script (or **makeSyns.bat** on Windows) needs to be run once to generate files **cellMechanisms/Syn\_AMPA\_L4SS\_L4SS/ChannelMLSyn.xml** etc.