From 7c7f9dd76381727264000eec0c9f15218118bfec Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Wed, 9 Jul 2025 16:10:29 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.html | 34 ---------------------------------- README.md | 36 ++++++++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+), 34 deletions(-) delete mode 100644 README.html create mode 100644 README.md diff --git a/README.html b/README.html deleted file mode 100644 index 7c54957..0000000 --- a/README.html +++ /dev/null @@ -1,34 +0,0 @@ -
-This is the readme for the model associated with the paper:
-
-Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles
-underlying optical stimulation of a channelrhodopsin-2 positive
-pyramidal neuron J Neurophysiol. 107(12):3235-45
-
-For best results, open directory in ipython notebook and load
-"Optical Stimulation". Otherwise, refer to "Optical Stimulation.py".
-
-On an ubuntu 13.10 we can cd to the expanded zip folder and then type
-ipython notebook.  Once the notebook starts in a browser you can
-select the "Optical Stimulation" notebook.  If you execute all the
-cells you shoud see an image at the end like:
-
-screenshot
-
--- Tom Foutz
-March 15, 2014
-
-20150518 Updates from Ted Carnevale:
-1.  The gbar parameters of the mechanisms specified by these files
-ca.mod kca.mod km.mod kv.mod na12.mod na16.mod na.mod are now the
-actual channel densities.  This eliminates a spurious temperature
-dependency of the effective channel density.
-2.  These same files are now threadsafe, and use efun rather than
-vtrap0 to deal with singularities.  See the mod files for more
-information.
-
-20150524 Update from Ted Carnevale: Changed integration method from
-euler to derivimplicit which is appropriate for simple ion
-accumulation mechanisms.  See Integration methods for SOLVE statements
-http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592
-
diff --git a/README.md b/README.md new file mode 100644 index 0000000..3d1aa39 --- /dev/null +++ b/README.md @@ -0,0 +1,36 @@ +This is the readme for the model associated with the paper: + +Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles +underlying optical stimulation of a channelrhodopsin-2 positive +pyramidal neuron *J Neurophysiol.* 107(12):3235-45 + +For best results, open directory in ipython notebook and load +"Optical Stimulation". Otherwise, refer to "Optical Stimulation.py". + +On an ubuntu 13.10 we can cd to the expanded zip folder and then type +ipython notebook. Once the notebook starts in a browser you can +select the "Optical Stimulation" notebook. If you execute all the +cells you should see an image at the end like: + +![screenshot](./screenshot.png) + +-- Tom Foutz +March 15, 2014 + +20150518 Updates from Ted Carnevale: +1. The gbar parameters of the mechanisms specified by these files +ca.mod kca.mod km.mod kv.mod na12.mod na16.mod na.mod are now the +actual channel densities. This eliminates a spurious temperature +dependency of the effective channel density. +2. These same files are now threadsafe, and use efun rather than +vtrap0 to deal with singularities. See the mod files for more +information. + +20150524 Update from Ted Carnevale: Changed integration method from +euler to derivimplicit which is appropriate for simple ion +accumulation mechanisms. See Integration methods for SOLVE statements +[http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592) + +--- + +2025-07-09: Converted README to Markdown. \ No newline at end of file From 6c712be51ca2dea88800c66634545bcf63e155de Mon Sep 17 00:00:00 2001 From: rsakai Date: Thu, 10 Jul 2025 15:26:07 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 32 +++++++++++++++----------------- 1 file changed, 15 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 3d1aa39..9a8f779 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,15 @@ This is the readme for the model associated with the paper: -Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles -underlying optical stimulation of a channelrhodopsin-2 positive +Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles +underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron *J Neurophysiol.* 107(12):3235-45 -For best results, open directory in ipython notebook and load +For best results, open directory in ipython notebook and load "Optical Stimulation". Otherwise, refer to "Optical Stimulation.py". -On an ubuntu 13.10 we can cd to the expanded zip folder and then type -ipython notebook. Once the notebook starts in a browser you can -select the "Optical Stimulation" notebook. If you execute all the +On an ubuntu 13.10 we can cd to the expanded zip folder and then type +ipython notebook. Once the notebook starts in a browser you can +select the "Optical Stimulation" notebook. If you execute all the cells you should see an image at the end like: ![screenshot](./screenshot.png) @@ -18,19 +18,17 @@ cells you should see an image at the end like: March 15, 2014 20150518 Updates from Ted Carnevale: -1. The gbar parameters of the mechanisms specified by these files -ca.mod kca.mod km.mod kv.mod na12.mod na16.mod na.mod are now the -actual channel densities. This eliminates a spurious temperature +1. The gbar parameters of the mechanisms specified by these files +ca.mod kca.mod km.mod kv.mod na12.mod na16.mod na.mod are now the +actual channel densities. This eliminates a spurious temperature dependency of the effective channel density. -2. These same files are now threadsafe, and use efun rather than -vtrap0 to deal with singularities. See the mod files for more +2. These same files are now threadsafe, and use efun rather than +vtrap0 to deal with singularities. See the mod files for more information. -20150524 Update from Ted Carnevale: Changed integration method from -euler to derivimplicit which is appropriate for simple ion -accumulation mechanisms. See Integration methods for SOLVE statements +20150524 Update from Ted Carnevale: Changed integration method from +euler to derivimplicit which is appropriate for simple ion +accumulation mechanisms. See Integration methods for SOLVE statements [http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592) ---- - -2025-07-09: Converted README to Markdown. \ No newline at end of file +20250709 Converted README to Markdown.