From e7f889897621fd6272cb48d2bee75b9ff2b9f4ef Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Wed, 9 Jul 2025 11:43:10 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- readme.html => README.md | 78 ++++++++++++++++++++-------------------- 1 file changed, 40 insertions(+), 38 deletions(-) rename readme.html => README.md (59%) diff --git a/readme.html b/README.md similarity index 59% rename from readme.html rename to README.md index 19fd37e..9fed828 100644 --- a/readme.html +++ b/README.md @@ -1,60 +1,62 @@ -
 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
+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/
+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:
+## Usage:
 
-You can start under uniz/linux with a command like
+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 ->
+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](./images/ThetaPeriodic.png)
 
-Running the following files similarly, leads to these images which
+Running the following files similarly, leads to these images which  
 correspond to the paper figures in parentheses:
 
-WBtonic.png: (fig 3)
-images/WBtonic.png
+**WBtonic.png:** (fig 3)  
+![images/WBtonic.png](./images/WBtonic.png)
 
-ThetaTonic.ode: (fig 5)
-images/ThetaTonic.png
+**ThetaTonic.ode:** (fig 5)  
+![images/ThetaTonic.png](./images/ThetaTonic.png)
 
-WBperiodic.ode: (fig 6)
-images/WBperiodic.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 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 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
+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. \ No newline at end of file From 3da64adf1cf1f50fa900e3864172365007f75213 Mon Sep 17 00:00:00 2001 From: rsakai Date: Wed, 9 Jul 2025 15:13:53 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 47 ++++++++++++++--------------------------------- 1 file changed, 14 insertions(+), 33 deletions(-) diff --git a/README.md b/README.md index 9fed828..5447d0f 100644 --- a/README.md +++ b/README.md @@ -1,24 +1,18 @@ 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 +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/) +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 +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) +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: +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) @@ -29,34 +23,21 @@ correspond to the paper figures in parentheses: **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 +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 +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 +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. \ No newline at end of file +2025-07-09: Converted README to Markdown.