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Standardized README to Markdown format #1

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43 changes: 21 additions & 22 deletions readme.html → README.md
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Original file line number Diff line number Diff line change
@@ -1,9 +1,7 @@
<html><pre>
This is the readme for the model associated with the paper
# This is the readme for the model associated with the paper

Rabinowitch I, Segev I (2006) The interplay between homeostatic
synaptic plasticity and functional dendritic compartments. J
Neurophysiol 96:276-83
synaptic plasticity and functional dendritic compartments. *J Neurophysiol* 96:276-83

These files were supplied by Dr Ithai Rabinowitch.

Expand All @@ -27,12 +25,11 @@
simulations in sequence (if you want to leave the computer to work
overnight and run different simulations one after the other).

Usage:
## Usage:

Download and extract the archive. Then under
Download and extract the archive. Then under

unix/linux:
-----------
### unix/linux:

cd main
nrnivmodl ../mechanisms
Expand All @@ -41,28 +38,28 @@
In the first selection window choose Spruston2 (not 3) and in the
Migliore2 Channel layout and Segment length 20.

<img src="./screenshot1.jpg" alt="screenshot 1">
![screenshot 1](./screenshot1.jpg)

Then click 'Done'.

You will be able to get 6 simulation configurations (RIP0: RDP0-5)
that do the following (the simulations are quite long):

RDP 0: runs in 'frozen' mode, i.e. no plasticity. This is used to get
a profile of the average membrane potential at each dendritic site (at
the end of the simulation choose Vavg in one of the two plot windows).
- **RDP 0**: runs in 'frozen' mode, i.e. no plasticity. This is used to get
a profile of the average membrane potential at each dendritic site (at
the end of the simulation choose Vavg in one of the two plot windows).

RDP 1: runs with plasticity so that at the end you also get gmax
values that are different from gmax0
- **RDP 1**: runs with plasticity so that at the end you also get gmax
values that are different from gmax0

RDP 2-5 start with the gmax distribution of RDP1 (since I have already
run this, their gmax0 is supposed to be stored).
- **RDP 2-5** start with the gmax distribution of RDP1 (since I have already
run this, their gmax0 is supposed to be stored).

RDP 2: local HSP RDP 3: frozen with the gmax0 obtained from RDP2's
final gmax.
- **RDP 2**: local HSP
- **RDP 3**: frozen with the gmax0 obtained from RDP2's final gmax.

RDP 4: global HSP RDP 5: frozen with the gmax0 obtained from RDP4's
final gmax.
- **RDP 4**: global HSP
- **RDP 5**: frozen with the gmax0 obtained from RDP4's final gmax.

---

Expand All @@ -71,7 +68,7 @@
distance -> vmax in the graph windows, then your simulation will look
like this:

<img src="./screenshot2.jpg" alt="screenshot 2">
![screenshot 2](./screenshot2.jpg)

I would suggest that you create a new RDP and just set a much shorter
simulation time (TSTOP under the RDP list). You can then run it to
Expand All @@ -83,4 +80,6 @@
the existing one) and change the time scale parameter in the synapse
parameter dialog box (just under the RIP list).

</pre></html>
---

2025-06-02: Standardized to Markdown.