- If you need extra help running the NEURON simulation please see:
- https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide.cshtml - Example use:
-
- 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..f86cbaf --- /dev/null +++ b/README.md @@ -0,0 +1,40 @@ +# 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: + + + +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.