From 0cc1e7abbf8c210519151dea6b0f5b42cb99232c Mon Sep 17 00:00:00 2001 From: EnfxcFCb6 Date: Mon, 2 Jun 2025 17:41:55 -0400 Subject: [PATCH 1/2] Standardized README to Markdown format --- README.html | 54 ----------------------------------------------------- README.md | 24 ++++++++++++++++++++++++ 2 files changed, 24 insertions(+), 54 deletions(-) delete mode 100644 README.html create mode 100644 README.md diff --git a/README.html b/README.html deleted file mode 100644 index 90d777f..0000000 --- a/README.html +++ /dev/null @@ -1,54 +0,0 @@ -
-This is the readme for the model associated with paper:
-
-Publio R,  Oliveira RF,  Roque AC, 2009
-"A Computational Study on the Role of Gap Junctions and Rod Ih
-Conductance in the Enhancement of the Dynamic Range of the Retina".
-PLoS ONE 4(9): e6970. doi:10.1371/journal.pone.0006970  
-
-These NEURON model files were contributed by Rodrigo Publio.
-
-Recent works suggest that one of the roles of gap junctions in sensory
-systems is to enhance their dynamic range by avoiding early saturation
-in the first processing stages. In this work, we use a minimal
-conductance-based model of the ON rod pathways in the vertebrate
-retina to study the effects of electrical synaptic coupling via gap
-junctions among rods and among AII amacrine cells on the dynamic range
-of the retina. The model is also used to study the effects of the
-maximum conductance of rod hyperpolarization activated current Ih on
-the dynamic range of the retina, allowing a study of the
-interrelations between this intrinsic membrane parameter with those
-two retina connectivity characteristics. Our results show that for
-realistic values of Ih conductance the dynamic range is enhanced by
-rod-rod coupling, and that AII-AII coupling is less relevant to
-dynamic range amplification in comparison with receptor
-coupling. Furthermore, a plot of the retina output response versus
-input intensity for the optimal parameter configuration is well fitted
-by a power law with exponent ~0.5. The results are consistent with
-predictions of more theoretical works and suggest that the earliest
-expression of gap junctions along the rod pathways, together with
-appropriate values of rod Ih conductance, has the highest impact on
-vertebrate retina dynamic range enhancement.  ~
-
-Figures 1 of "A Computational Study on the Role of Gap Junctions and
-Rod Ih Conductance in the Enhancement of the Dynamic Range of the
-Retina" can be replicated with this code, for example:
-
-screenshot 1
-screenshot 2
-
-After compiling all MOD files load the appropriate HOC file (init.hoc)
-from the neuron main menu after starting nrngui or by either double
-clicking in mswin's window explorer, typing nrngui init.hoc in unix,
-or dragging and dropping the init.hoc file onto the nrngui icon in Mac
-OS X. Session files are called by the main HOC file.
-
-The network dimensions and synaptic convergence/divergence are
-specified at the parameters.hoc file. The cells are created from
-templates at the createcells.hoc while gap junctions and chemical
-synapses are created at netconnection.hoc.
-
-20120326 Bip_Cad.mod and Rod_Cad.mod solve methods updated from euler
-to derivimplicit as recommended in 
-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..5477aac --- /dev/null +++ b/README.md @@ -0,0 +1,24 @@ +# This is the readme for the model associated with paper: + +Publio R, Oliveira RF, Roque AC, 2009 +"A Computational Study on the Role of Gap Junctions and Rod Ih Conductance in the Enhancement of the Dynamic Range of the Retina". +*PLoS ONE* 4(9): e6970. doi:10.1371/journal.pone.0006970 + +These NEURON model files were contributed by Rodrigo Publio. + +Recent works suggest that one of the roles of gap junctions in sensory systems is to enhance their dynamic range by avoiding early saturation in the first processing stages. In this work, we use a minimal conductance-based model of the ON rod pathways in the vertebrate retina to study the effects of electrical synaptic coupling via gap junctions among rods and among AII amacrine cells on the dynamic range of the retina. The model is also used to study the effects of the maximum conductance of rod hyperpolarization activated current Ih on the dynamic range of the retina, allowing a study of the interrelations between this intrinsic membrane parameter with those two retina connectivity characteristics. Our results show that for realistic values of Ih conductance the dynamic range is enhanced by rod-rod coupling, and that AII-AII coupling is less relevant to dynamic range amplification in comparison with receptor coupling. Furthermore, a plot of the retina output response versus input intensity for the optimal parameter configuration is well fitted by a power law with exponent ~0.5. The results are consistent with predictions of more theoretical works and suggest that the earliest expression of gap junctions along the rod pathways, together with appropriate values of rod Ih conductance, has the highest impact on vertebrate retina dynamic range enhancement. + +Figures 1 of "A Computational Study on the Role of Gap Junctions and Rod Ih Conductance in the Enhancement of the Dynamic Range of the Retina" can be replicated with this code, for example: + +![screenshot 1](./screenshot1.jpg) +![screenshot 2](./screenshot2.jpg) + +After compiling all MOD files load the appropriate HOC file (`init.hoc`) from the neuron main menu after starting nrngui or by either double clicking in mswin's window explorer, typing `nrngui init.hoc` in unix, or dragging and dropping the `init.hoc` file onto the nrngui icon in Mac OS X. Session files are called by the main HOC file. + +The network dimensions and synaptic convergence/divergence are specified at the `parameters.hoc` file. The cells are created from templates at the `createcells.hoc` while gap junctions and chemical synapses are created at `netconnection.hoc`. + +20120326 Bip_Cad.mod and Rod_Cad.mod solve methods updated from euler to derivimplicit as recommended in [http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592) + +--- + +2025-06-02: Converted README to Markdown. \ No newline at end of file From fe7d253b7fb227cd4c19edbd6564e4bc0fc9abfb Mon Sep 17 00:00:00 2001 From: rsakai Date: Tue, 3 Jun 2025 15:22:17 -0400 Subject: [PATCH 2/2] Update README.md --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 5477aac..bc44fec 100644 --- a/README.md +++ b/README.md @@ -17,8 +17,7 @@ After compiling all MOD files load the appropriate HOC file (`init.hoc`) from th The network dimensions and synaptic convergence/divergence are specified at the `parameters.hoc` file. The cells are created from templates at the `createcells.hoc` while gap junctions and chemical synapses are created at `netconnection.hoc`. -20120326 Bip_Cad.mod and Rod_Cad.mod solve methods updated from euler to derivimplicit as recommended in [http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592) - --- +20120326 Bip_Cad.mod and Rod_Cad.mod solve methods updated from euler to derivimplicit as recommended in [http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592](http://www.neuron.yale.edu/phpbb/viewtopic.php?f=28&t=592) -2025-06-02: Converted README to Markdown. \ No newline at end of file +20250602 Converted README to Markdown.