Wiki » History » Version 5
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 | 4 | Padraig Gleeson | The original Traub et al model was developed in FORTRAN, this was converted to NEURON by Tom Morse and Michael Hines, and this has now been converted to NeuroML & neuroConstruct. |
| 7 | 4 | Padraig Gleeson | |
| 8 | 1 | Padraig Gleeson | Install neuroConstruct & get latest project |
| 9 | 2 | Padraig Gleeson | ------------------------------------------- |
| 10 | 1 | Padraig Gleeson | |
| 11 | 1 | Padraig Gleeson | See the instructions [here](http://www.opensourcebrain.org:8080/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 | 4 | Padraig Gleeson | `hg clone http://www.opensourcebrain.org/hg/osb/models/cerebral_cortex/networks/Thalamocortical` |
| 18 | 4 | Padraig Gleeson | |
| 19 | 4 | Padraig Gleeson | View a cell in 3D |
| 20 | 4 | Padraig Gleeson | ----------------- |
| 21 | 4 | Padraig Gleeson | |
| 22 | 5 | Padraig Gleeson | Open neuroConstruct and view a cell in 3D… |
| 23 | 1 | Padraig Gleeson | |
| 24 | 5 | Padraig Gleeson | More… |
| 25 | 5 | Padraig Gleeson | |
| 26 | 4 | Padraig Gleeson | Test installation with single cell simulation |
| 27 | 1 | Padraig Gleeson | --------------------------------------------- |
| 28 | 4 | Padraig Gleeson | |
| 29 | 5 | Padraig Gleeson | Run a single cell on NEURON… |
| 30 | 1 | Padraig Gleeson | |
| 31 | 5 | Padraig Gleeson | More… |
| 32 | 5 | Padraig Gleeson | |
| 33 | 1 | Padraig Gleeson | Generate synapse files |
| 34 | 1 | Padraig Gleeson | ---------------------- |
| 35 | 1 | Padraig Gleeson | |
| 36 | 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. |
| 37 | 5 | Padraig Gleeson | |
| 38 | 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). |
| 39 | 5 | Padraig Gleeson | |
| 40 | 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. |