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Standardize readme #1

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0836a12
Standardized README to Markdown format
rsakai10 May 30, 2025
42b3bca
Update README.md
rsakai10 May 30, 2025
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52 changes: 28 additions & 24 deletions readme.html → README.md
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@@ -1,13 +1,12 @@
<html><pre>
This code reproduces the model published in Figure 8 of:

Chaudhuri, D., Issa, J.B., and Yue, D.T. (2007). �Elementary
Mechanisms Producing Facilitation of Cav2.1 (P/Q-type) Channels,�
J. Gen. Physiology 129, 385-401.
Chaudhuri, D., Issa, J.B., and Yue, D.T. (2007). “Elementary
Mechanisms Producing Facilitation of Cav2.1 (P/Q-type) Channels,”
*J. Gen. Physiology* 129, 385-401.

The model is run in Matlab. Run sc_gui.m to open the GUI from which
The model is run in Matlab. Run `sc_gui.m` to open the GUI from which
you can enter model parameter values and simulate results. The other
two m-files, setup_sc.m and camodel.m, are used to do the
two m-files, `setup_sc.m` and `camodel.m`, are used to do the
simulations. Euler integration is used to solve the differential
equations numerically.

Expand All @@ -24,32 +23,37 @@
The other text files contained are used to set the time axis for each
of the different measures.

Abbreviations:

po = channel open probability
poo = channel open probability with a delay t following a known first
opening transition
fl = first latency distribution (probability that first opening
occurred before time t)
ot = mean open time for a single channel opening
C2 fraction = fraction of channels that start in the 2nd closed state
for Ca++ as the charge carrier
hi po fraction = fraction of channels that start in the facilitated
state for EFa Ca++ with no prepulse
Ba C2 fraction = fraction of channels that start in the 2nd closed
state for Ba++ as the charge carrier
### Abbreviations:

- **po** = channel open probability
- **poo** = channel open probability with a delay t following a known first
opening transition
- **fl** = first latency distribution (probability that first opening
occurred before time t)
- **ot** = mean open time for a single channel opening
- **C2 fraction** = fraction of channels that start in the 2nd closed state
for Ca++ as the charge carrier
- **hi po fraction** = fraction of channels that start in the facilitated
state for EFa Ca++ with no prepulse
- **Ba C2 fraction** = fraction of channels that start in the 2nd closed
state for Ba++ as the charge carrier

Correction factors are used to scale the results to our data. These
values correct for blank sweeps in the data. They would all have a
value of 1 if there were no blank sweeps.

----

Running the model (in matlab command window type
run './sc_gui'
after cd'ing to the directory the files expanded into) (just press
`run './sc_gui'`
after `cd`'ing to the directory the files expanded into) (just press
the run button) should produce a graph similar to:

<img src="./screenshot.jpg" alt="screenshot image" width="600">
![screenshot image](./screenshot.jpg)

and the parameters in the GUI can be adjusted to produce graphs
similar to figs 3-6, 8.
</pre></html>

---

2025-05-30: Standardized to Markdown