GitHub - ModelDBRepository/182758: Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)

ModelDBRepository / 182758 Public

Notifications You must be signed in to change notification settings
Fork 3
Star 4

Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)

modeldb.science/182758

Notifications

Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
nrnfiles		nrnfiles
xppfiles		xppfiles
cluster.png		cluster.png
episodic.png		episodic.png
readme.html		readme.html
wave.png		wave.png

Repository files navigation

<html>

This is the readme for the models associated with the paper:
<p/> 
 Terman D, Rubin JE, Yew AC, Wilson CJ (2002)<br/> Activity patterns in a
 model for the subthalamopallidal network of the basal ganglia. <br/>
<a href="http://www.jneurosci.org/content/22/7/2963.full">J Neurosci</a> 22:2963-76

<p/> 
The xpp files were provided by David Terman, and the partial NEURON
implementation was provided by Taylor Malone.
<p/> 
xpp <a href="http://www.math.pitt.edu/~bard/xpp/xpp.html">http://www.math.pitt.edu/~bard/xpp/xpp.html</a>and NEURON <a href="https://neuron.yale.edu/neuron/">https://neuron.yale.edu/neuron/</a> simulation environments are each freely available.
<p/>
To run the xpp code, download and extract this archive.


Figure 3 was created with episodic.ode. Run with linux/unix commands like<br/>
xppaut episodic.ode<br/>
Then select File->Read set: episodic.ode.set<br/>
Then select Initial Conds.-> Go and you should see a graph like.<br/>
<img src="./episodic.png" alt="episodic"><br/>
which is similar to the STN cells in figure 3c.
<p/>

Figure 5 was created from cluster.ode. Run cluster with linux/unix commands like<br/>
xppaut cluster.ode<br/>
Then select File->Read set: cluster.ode.set<br/>
Then select Initial Conds.-> Go and you should see a graph like.<br/>
<img src="./cluster.png" alt="cluster"><br/>
which is similar to the GPe cells in figure 5c in the paper.
<p/>
Figure 7 was created from wave.ode. Run with linux/unix commands like<br/>
xppaut wave.ode<br/>
Then select File->Read set: wave.ode.set<br/>
Then select Initial Conds.-> Go and you should see a graph like.<br/>
<img src="./wave.png" alt="wave"><br/>
which is similar to the STN cells in figure 7c in the paper.
<p/>

The NEURON code was created by Taylor Malone.  Figures 1, 2, and 3c are reproduced however there are discrepancies with the network runs. We invite the modeling community to help us correct and/or finish the NEURON implementation.
<p/>
To run the NEURON implementation, compile the mod files (see <a href="https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml">https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml</a> for more help if necessary.
<p/>
In linux/unix, for example:<br/>
cd nrnfiles</br>
nrnivmodl<br/>
python -i Figures/Fig_1a.py<br/>
produces the graph<br/>
<img src="./nrnfiles/Figures/Figure 1A.png" alt="Fig 1a">
<br/>
20171112 update from David Terman: suggestion to use the ode.set files
</html>