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README.md

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+This is the readme for the model associated with the paper
+
+Komek K, Bard Ermentrout G, Walker CP, Cho RY (2012) Dopamine and gamma band synchrony in schizophrenia--insights from computational and empirical studies. *Eur J Neurosci* 36:2146-55
+
+These xpp model files were contributed by Kubra Komek. xpp is free software by Bard Ermentrout available at [http://www.pitt.edu/~phase/](http://www.pitt.edu/~phase/)
+
+## Usage:
+
+You can start under uniz/linux with a command like xppaut ThetaPeriodic.ode
+
+If you then click on Initialconds -> (G)o and then Window/Zoom -> (F)it you should see a graph like (corresponds to paper fig 7)
+
+![images/ThetaPeriodic.png](./images/ThetaPeriodic.png)
+
+Running the following files similarly, leads to these images which correspond to the paper figures in parentheses:
+
+**WBtonic.png:** (fig 3)  
+![images/WBtonic.png](./images/WBtonic.png)
+
+**ThetaTonic.ode:** (fig 5)  
+![images/ThetaTonic.png](./images/ThetaTonic.png)
+
+**WBperiodic.ode:** (fig 6)  
+![images/WBperiodic.png](./images/WBperiodic.png)
+
+The procedure for the simulations was to run the code for 20 seconds, divide the results into 1 second bins, run FFT on LFP in Wang-Buzsaki model and on SE in the theta neuron model, then average across  
+those. Also I varied some parameters in each simulation as described in the paper. This meant running the code in batch mode for a range of the specified parameter as described in the paper.
+
+The neuron models that I used were Wang-Buzsaki neuron and theta neuron. Wang-Buzsaki neuron was modeled after their original paper, Wang XJ, Buzsaki G (1996) Gamma oscillation by synaptic inhibition in  
+a hippocampal interneuronal network model. *J. Neurosci.*, 16, 6402-6413. Theta neuron model is also known as the Ermentrout-Kopell canonical model (a link to the scholarpedia page describing it  
+[http://www.scholarpedia.org/article/Ermentrout-Kopell_canonical_model](http://www.scholarpedia.org/article/Ermentrout-Kopell_canonical_model)).
+
+An example batch file, BatchThetaTonic.ode, is identical to ThetaTonic.ode except that it has added lines (and added descriptions of those new lines) that control the running of the program in batch  
+mode. To run the batch file make sure you are in the same directory as the ode file and type
+
+xppaut BatchThetaTonic.ode -silent 
+
+on the command line. It runs without a GUI and will create 57 output files in the same directory starting with output.dat.0 and ending with output.dat.56 which indeed is the same as the first one. It takes  
+about 5 minutes to complete on a 2008 Dell Lattitude E6400 laptop.
+
+---
+
+2025-07-09: Converted README to Markdown.