From 134b47db90055f36a47539a539fec8a69723f581 Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Tue, 27 May 2025 16:54:54 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.html | 28 ---------------------------- README.md | 43 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 43 insertions(+), 28 deletions(-) delete mode 100644 README.html create mode 100644 README.md diff --git a/README.html b/README.html deleted file mode 100644 index 6f41428..0000000 --- a/README.html +++ /dev/null @@ -1,28 +0,0 @@ - - This is the readme for the NEURON and MATLAB code associated with the paper:

- Gold C, Henze DA, Koch C (2007) Using extracellular action potential recordings to constrain compartmental models. J Comput Neurosci 23:39-58
- http://dx.doi.org/10.1007/s10827-006-0018-2

- This code was contributed by Carl Gold.

-

- If you need extra help running the NEURON simulation please see:

- https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml

- Example use:
- ------------
- Either auto-launch from ModelDB if your browser is configured or, after downloading and extracting this archive, compiling the mod files in the mod folder with either "nrnivmodl mod" (unix), dragging and dropping the mod file on mknrndll (mac os), or using mknrndll on the mod folder and moving the nrnmech.dll up a level (mswin), start with "nrngui mosinit.hoc" (unix), drag and dropping the mosinit.hoc file onto nrngui (mac os), or double clicking mosinit.hoc in the file explorer (mswin).

- After the simulation is complete, exit NEURON and run the following scripts in the matlab command prompt after cd'ing to the mat sub-folder:

- addpaths
- zplane_eap_calc('line', [], [], 0.3, [-500 500 -150 150], 0, 50);
- plot_eap_grid('line', [], [], 0.3, [-500 500 -150 150], 0, 50);

- After a short while you should see a figure includes waveforms like those in Figure 8 in the paper:

- screenshot - -

See the "docs" folder for more instructions on using the -Extracellular Action Potential Simulation (EAPS) package. -

-

20190925 Model entry updated to include a mosinit.hoc file so autolaunch -will work (can also be used to easily start model). -

20190926 Model entry updated to include a screenshot and updates to the - readme and docs/index.html plus added temp folder to mat (matlab subfolder). -

20190927 Updated so that multiple runs would work when d151_params_X.hoc are - cp'd onto d151_params.hoc (see docs/index.html) for more info. - diff --git a/README.md b/README.md new file mode 100644 index 0000000..e13f1e3 --- /dev/null +++ b/README.md @@ -0,0 +1,43 @@ +# NEURON and MATLAB Code Readme + +This is the readme for the NEURON and MATLAB code associated with the paper: + +Gold C, Henze DA, Koch C (2007) Using extracellular action potential recordings to constrain compartmental models. *J Comput Neurosci* 23:39-58 +[http://dx.doi.org/10.1007/s10827-006-0018-2](http://dx.doi.org/10.1007/s10827-006-0018-2) + +This code was contributed by Carl Gold. + +If you need extra help running the NEURON simulation please see: +[https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml](https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml) + +## Example use: + +------------ + +Either auto-launch from ModelDB if your browser is configured or, after downloading and extracting this archive, compiling the mod files in the mod folder with either `nrnivmodl mod` (unix), dragging and dropping the mod file on mknrndll (mac os), or using mknrndll on the mod folder and moving the nrnmech.dll up a level (mswin), start with `nrngui mosinit.hoc` (unix), drag and dropping the mosinit.hoc file onto nrngui (mac os), or double clicking mosinit.hoc in the file explorer (mswin). + +After the simulation is complete, exit NEURON and run the following scripts in the matlab command prompt after cd'ing to the mat sub-folder: + +``` +addpaths +zplane_eap_calc('line', [], [], 0.3, [-500 500 -150 150], 0, 50); +plot_eap_grid('line', [], [], 0.3, [-500 500 -150 150], 0, 50); +``` + +After a short while you should see a figure includes waveforms like those in Figure 8 in the paper: + +![screenshot](./screenshot.png) + +See the "docs" folder for more instructions on using the Extracellular Action Potential Simulation (EAPS) package. + +--- + +### Changelog + +- 2019-09-25 Model entry updated to include a mosinit.hoc file so autolaunch will work (can also be used to easily start model). +- 2019-09-26 Model entry updated to include a screenshot and updates to the readme and docs/index.html plus added temp folder to mat (matlab subfolder). +- 2019-09-27 Updated so that multiple runs would work when d151_params_X.hoc are cp'd onto d151_params.hoc (see docs/index.html) for more info. + +--- + +2025-05-27 – Standardized to Markdown. \ No newline at end of file From e1c064d486bdc52330fbe773fae765dc8ab99a32 Mon Sep 17 00:00:00 2001 From: rsakai Date: Wed, 28 May 2025 12:27:16 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/README.md b/README.md index e13f1e3..f86cbaf 100644 --- a/README.md +++ b/README.md @@ -37,7 +37,4 @@ See the "docs" folder for more instructions on using the Extracellular Action Po - 2019-09-25 Model entry updated to include a mosinit.hoc file so autolaunch will work (can also be used to easily start model). - 2019-09-26 Model entry updated to include a screenshot and updates to the readme and docs/index.html plus added temp folder to mat (matlab subfolder). - 2019-09-27 Updated so that multiple runs would work when d151_params_X.hoc are cp'd onto d151_params.hoc (see docs/index.html) for more info. - ---- - -2025-05-27 – Standardized to Markdown. \ No newline at end of file +- 2025-05-27 – Standardized to Markdown.