From 0550311ab3601994a23853cea4e884c82168a981 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Wed, 9 Jul 2025 16:08:25 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.md | 43 +++++++++++++++++++++++++++++++++++++++++++ readme.txt | 33 --------------------------------- 2 files changed, 43 insertions(+), 33 deletions(-) create mode 100644 README.md delete mode 100644 readme.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..2a77ee9 --- /dev/null +++ b/README.md @@ -0,0 +1,43 @@ +This simulation was used in the following article: + +Eguchi A, Neymotin SA, Stringer SM. (2014) +Color opponent receptive fields self-organize in a biophysical model +of visual cortex via spike-timing dependent plasticity. +*Front. Neural Circuits* 8:16. doi: 10.3389/fncir.2014.00016 + +For questions email: akihiro dot eguchi at psy dot ox dot ac dot uk + +This simulation was tested/developed on LINUX systems, but may run on +Microsoft Windows or Mac OS. + +To run, you will need the NEURON simulator (available at +[http://www.neuron.yale.edu](http://www.neuron.yale.edu)) compiled with python enabled. To draw the +output you will need to have Matplotlib installed ([http://matplotlib.org/](http://matplotlib.org/)). + +### Instructions: + +- Unzip the contents of the zip file to a new directory. + +- Compile the mod files from the command line with: + + ``` + nrnivmodl *.mod + ``` + +The `nrnivmodl` command will produce an architecture-dependent folder +with a script called `special`. On 64 bit systems the folder is +`x86_64`. To run the simulation from the command line use: + +``` +python runMe.py +``` + +Various parameters used in the simulation are set in the python codes. +State of the networks are exported and saved every n iterations as +`Network_` + `str(itr)` + `.obj` format so that various analysis can be +applied to the network with specific point during the training using +`runMe2.py` script. + +--- + +2025-07-09: Converted README to Markdown. \ No newline at end of file diff --git a/readme.txt b/readme.txt deleted file mode 100644 index 81d4796..0000000 --- a/readme.txt +++ /dev/null @@ -1,33 +0,0 @@ -This simulation was used in the following article: - - Eguchi A, Neymotin SA, Stringer SM. (2014) - Color opponent receptive fields self-organize in a biophysical model - of visual cortex via spike-timing dependent plasticity. - Front. Neural Circuits 8:16. doi: 10.3389/fncir.2014.00016 - -For questions email: akihiro dot eguchi at psy dot ox dot ac dot uk - -This simulation was tested/developed on LINUX systems, but may run on -Microsoft Windows or Mac OS. - -To run, you will need the NEURON simulator (available at -http://www.neuron.yale.edu) compiled with python enabled. To draw the -output you will need to have Matplotlib installed ( -http://matplotlib.org/ ). - -Instructions: - Unzip the contents of the zip file to a new directory. - - compile the mod files from the command line with: - nrnivmodl *.mod - -The nrnivmodl command will produce an architecture-dependent folder -with a script called special. On 64 bit systems the folder is -x86_64. To run the simulation from the command line use: - python runMe.py - -Various parameters used in the simulation are set in the python codes. -State of the networks are exported and saved every n iterations as -"Network_"+str(itr)+".obj" format so that various analysis can be -applied to the network with specific point during the training using -runMe2.py script. From dae60830e1712d60b1b99c3ebdb5e578ae0efd21 Mon Sep 17 00:00:00 2001 From: rsakai Date: Thu, 10 Jul 2025 15:03:44 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 2a77ee9..a8b8ca0 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ This simulation was used in the following article: Eguchi A, Neymotin SA, Stringer SM. (2014) -Color opponent receptive fields self-organize in a biophysical model -of visual cortex via spike-timing dependent plasticity. +Color opponent receptive fields self-organize in a biophysical model +of visual cortex via spike-timing dependent plasticity. *Front. Neural Circuits* 8:16. doi: 10.3389/fncir.2014.00016 For questions email: akihiro dot eguchi at psy dot ox dot ac dot uk -This simulation was tested/developed on LINUX systems, but may run on +This simulation was tested/developed on LINUX systems, but may run on Microsoft Windows or Mac OS. -To run, you will need the NEURON simulator (available at -[http://www.neuron.yale.edu](http://www.neuron.yale.edu)) compiled with python enabled. To draw the +To run, you will need the NEURON simulator (available at +[http://www.neuron.yale.edu](http://www.neuron.yale.edu)) compiled with python enabled. To draw the output you will need to have Matplotlib installed ([http://matplotlib.org/](http://matplotlib.org/)). ### Instructions: @@ -24,20 +24,20 @@ output you will need to have Matplotlib installed ([http://matplotlib.org/](http nrnivmodl *.mod ``` -The `nrnivmodl` command will produce an architecture-dependent folder -with a script called `special`. On 64 bit systems the folder is +The `nrnivmodl` command will produce an architecture-dependent folder +with a script called `special`. On 64 bit systems the folder is `x86_64`. To run the simulation from the command line use: ``` python runMe.py ``` -Various parameters used in the simulation are set in the python codes. -State of the networks are exported and saved every n iterations as -`Network_` + `str(itr)` + `.obj` format so that various analysis can be -applied to the network with specific point during the training using +Various parameters used in the simulation are set in the python codes. +State of the networks are exported and saved every n iterations as +`Network_` + `str(itr)` + `.obj` format so that various analysis can be +applied to the network with specific point during the training using `runMe2.py` script. --- -2025-07-09: Converted README to Markdown. \ No newline at end of file +2025-07-09: Converted README to Markdown.