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@@ -1,22 +1,19 @@
-
-Instructions how to use ModelDB entry which accompanies:
-
-Corey D. Acker and Srdjan D. Antic. Quantitative Assessment of the
+# Instructions how to use ModelDB entry which accompanies:
+
+Corey D. Acker and Srdjan D. Antic. Quantitative Assessment of the
Distributions of Membrane Conductances Involved in Action Potential
-Backpropagation Along Basal Dendrites. Journal of Neurophysiology,
+Backpropagation Along Basal Dendrites. *Journal of Neurophysiology*,
2008.
-- - - - - - - - - - - - - - - - -
+---
-The following simulations work well in NEURON 6.2. They do NOT work
-well in NEURON 5.6 and NEURON 5.8. Other versions of NEURON have not
+The following simulations work well in NEURON 6.2. They do NOT work
+well in NEURON 5.6 and NEURON 5.8. Other versions of NEURON have not
been tested.
+---
-- - - - - - - - - - - - - - - - -
-
-
- Setup (assuming Windows):
+## Setup (assuming Windows):
Either auto-launch from ModelDB and click buttons or:
@@ -27,7 +24,7 @@
- Compile the .mod files using the NEURON "mknrndll" command in the
"Model" directory. Make sure that mod files are compiled in the
-"Model" directory. If compiling was successful each mod file in the
+"Model" directory. If compiling was successful each mod file in the
Model directory must be accompanied by one .o file.
- Move the .dll file (nrnmech.dll) from the "Model" directory to the
@@ -39,52 +36,47 @@
- Double click on AckerAnticBasalBackprop.hoc. This will open 7
windows including the nrniv command console.
+---
-- - - - - - - - - - - - - - - - -
-
- REPRODUCING FIGURE 6B.
+## REPRODUCING FIGURE 6B
- To reproduce Fig. 6B use GUI (Best fit model). Hit RUN button. Wait
until the model finishes three sets of simulations (BLACK, RED, and
GREEN).
- BLACK = Control with all currents intact.
- RED = Block of sodium current with TTX.
- GREEN = Block of A-type current with 4-AP.
+ - BLACK = Control with all currents intact.
+ - RED = Block of sodium current with TTX.
+ - GREEN = Block of A-type current with 4-AP.
-
+
- Graph[0] plots the AP waveforms in the soma.
- Graph[1] plots the AP waveforms in the basal dendrite (indicated by
asterisk in Figure 6A).
-Graph[2] has a dual function.
+- Graph[2] has a dual function.
-(1)During the simulation Graph[2] is a space plot of AP waveforms
-along all basal dendrites considered in the model (BLACK motion).
+ 1. During the simulation Graph[2] is a space plot of AP waveforms
+ along all basal dendrites considered in the model (BLACK motion).
-(2)At the end of the entire set of experiments (CTR, TTX and 4-AP)
-Graph[2] plots peak AP amplitudes along all basal dendrites considered
-in the model (multiple locations). Each line corresponds to one basal
-dendrite. Each dendrite is analyzed in three conditions (CONTROL, TTX
-and 4-AP) and therefore each dendrite is represented with three lines
-at the end of simulations (BLACK, RED and GREEN).
+ 2. At the end of the entire set of experiments (CTR, TTX and 4-AP)
+ Graph[2] plots peak AP amplitudes along all basal dendrites considered
+ in the model (multiple locations). Each line corresponds to one basal
+ dendrite. Each dendrite is analyzed in three conditions (CONTROL, TTX
+ and 4-AP) and therefore each dendrite is represented with three lines
+ at the end of simulations (BLACK, RED and GREEN).
- Note: Duration is set to 15 ms. This can be changed in a hoc file by
changing tstop variable.
+---
-- - - - - - - - - - - - - - - - -
-
-
- TRIPLETS - REPRODUCING FIGURES 8B-2 and 10C
-
+## TRIPLETS - REPRODUCING FIGURES 8B-2 and 10C
- Double click on Triplets.hoc. This will open 9 windows.
-
- REPRODUCING FIGURE 8B-2
+### REPRODUCING FIGURE 8B-2
- Click "Run best fit model (Figure 8B)".
@@ -98,13 +90,12 @@
- Graph[2] plots the AP waveforms in the basal dendrite location
indicated by asterisk in Figure 8B-1.
-
- REPRODUCING FIGURE 10C
+### REPRODUCING FIGURE 10C
- Run special case dendrite (Figure 10C).
-- Same graphs, same recording locations, as in the previous exercise.
-
+- Same graphs, same recording locations, as in the previous exercise.
+
- Note that only one basal dendrite (Graph[2]) was endowed with
special case properties. The output from this dendrite is displayed in
Figure 10C - Right. Basal dendrite shown in Graph[0](red) is
@@ -115,12 +106,9 @@
otherwise all the amplitude boosting appears in the second action
potential and no further boosting appears in the third.
+---
-- - - - - - - - - - - - - - - - -
-
-
- LOCAL SPIKE SIMULATIONS (FIGURES 9 and 10)
-
+## LOCAL SPIKE SIMULATIONS (FIGURES 9 and 10)
- Double click on LocalSpikes.hoc. This will open 10 windows.
@@ -149,6 +137,8 @@
included higher sodium conductance and higher A-type conductance
(Special Case Dendrite A-Type Block).
+## Changelog
20120201 Cad.mod updated to use derivimplicit instead of euler as per
http://www.neuron.yale.edu/phpBB/viewtopic.php?f=28&t=592
-
+
+20250602 Converted README to Markdown.