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Standardized README to Markdown format
rsakai10 Jun 2, 2025
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Update README.md
rsakai10 Jun 2, 2025
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82 changes: 36 additions & 46 deletions readme.html → README.md
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@@ -1,22 +1,19 @@
<html><pre>
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:

Expand All @@ -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
Expand All @@ -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.

<img src="./screenshot.jpg" alt="screenshot">
![screenshot](./screenshot.jpg)

- 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)".

Expand All @@ -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
Expand All @@ -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.

Expand Down Expand Up @@ -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
</pre></html>

20250602 Converted README to Markdown.