diff --git a/README.md b/README.md new file mode 100644 index 0000000..5447d0f --- /dev/null +++ b/README.md @@ -0,0 +1,43 @@ +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. diff --git a/readme.html b/readme.html deleted file mode 100644 index 19fd37e..0000000 --- a/readme.html +++ /dev/null @@ -1,60 +0,0 @@ -
-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/
-
-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
-
-Running the following files similarly, leads to these images which
-correspond to the paper figures in parentheses:
-
-WBtonic.png: (fig 3)
-images/WBtonic.png
-
-ThetaTonic.ode: (fig 5)
-images/ThetaTonic.png
-
-WBperiodic.ode: (fig 6)
-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).
-
-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.
-