GitHub - ModelDBRepository/241240: Role of afferent-hair cell connectivity in determining spike train regularity (Holmes et al 2017)

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Name		Name	Last commit message	Last commit date
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H_HCNl.mod		H_HCNl.mod
Kv12.mod		Kv12.mod
Kv31.mod		Kv31.mod
Kv3s.mod		Kv3s.mod
Kv43A.mod		Kv43A.mod
Kv7M.mod		Kv7M.mod
Nav16.mod		Nav16.mod
README.html		README.html
SK.mod		SK.mod
Zone1s.hoc		Zone1s.hoc
Zone2s.hoc		Zone2s.hoc
Zone4_72.hoc		Zone4_72.hoc
Zone5s.hoc		Zone5s.hoc
ab4BK2.mod		ab4BK2.mod
afhcsyn_i0.mod		afhcsyn_i0.mod
caL.mod		caL.mod
cdp.mod		cdp.mod
cdp13.mod		cdp13.mod
hc1.mod		hc1.mod
i6s-hc.ses		i6s-hc.ses
i6s-tnew.ses		i6s-tnew.ses
main-i6s-hc.hoc		main-i6s-hc.hoc
main-i6s-tnew.hoc		main-i6s-tnew.hoc
main-i6sBKSK-hc.hoc		main-i6sBKSK-hc.hoc
main-i6sBKSK-tnew.hoc		main-i6sBKSK-tnew.hoc
mosinit.hoc		mosinit.hoc
random.mod		random.mod
ribbon1.mod		ribbon1.mod
run_ctrl.ses		run_ctrl.ses
screenshot.png		screenshot.png
screenshot1.png		screenshot1.png
screenshot2.png		screenshot2.png
screenshot3.png		screenshot3.png

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<html>
<p>These files form the basis of simulations in
</p><p>Holmes WR, Huwe JA, Williams B, Rowe MH, Peterson EH (2017) Models of
utricular bouton afferents: role of afferent-hair cell connectivity in
determining spike train regularity. J Neurophysiol 117:1969-1986
<a href="http://dx.doi.org/10.1152/jn.00895.2016">http://dx.doi.org/10.1152/jn.00895.2016<a/>
</p><p>A number of these files, including some of the more clever algorithms,
were adapted from work done by Jose Ambros-Ingerson for a different
project.  Morphology files for 4 vestibular bouton afferents,
reconstructed from turtle, are included.
</p><p>These scripts together with the simple GUI provided can be used
directly to reproduce voltage traces in Figs 3-5 and data points in
Figs 6-8 with only changing tstop, Poisson input rate and cell type.
Tstop = 1000 ms here which is sufficient to illustrate runs that
complete in a short amount of time.  For the paper it was necessary to
use tstop values of a few MINUTES in many cases in order to accumulate
a large enough number of spikes to allow cv to be computed accurately.
These simulations were run in batch mode and took days in some cases.
<p/>
Usage:<br/>
------<br/>
Compile the mod files in the method appropriate for your platform
(nrnivmodl on linux/unix, mknrndll on mswin/mac os x) and then run one
of the following which generate the graphs shown by default. If you
need more help consult the web page: <a href="https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide">https://senselab.med.yale.edu/ModelDB/NEURON_DwnldGuide</a>
<p/>
Once you start the program select Tools->RunControl and then click on
Init & Run.<br/>
To get cv results click on Parameters -> Run to get cv data<br/>
To get EPSPs for each synapse or Hair Cell activation click on Parameters -> Plot syn EPSPs (or Plot HC EPSPs)<br/>
</p>
<p>main-i6s-tnew.hoc <br/>
-- One hair cell to one afferent connectivity, synaptic conductance
</p><p>   constant or scaled by bouton diameter.  Runs produce data points
   for Figs 6A, 7A, 7C, 8
<p/><img src="./screenshot.png" alt="screenshot">
</p><p>main-i6s-hc.hoc  <br/>
--One hair cell to one or more afferents connectivity, synaptic
  conductance constant or scaled by bouton diameter.  Runs produce
  traces in Fig 5 and data points for Figs 6B, 7B, 7C, 8
<p/><img src="./screenshot1.png" alt="screenshot">
</p><p>main-i6sBKSK-tnew.hoc  <br/>
--Same as main-i6s-tnew.hoc but with BK and SK conductances added.
  Runs produce traces in Fig. 3 and data points for Fig 8
<p/><img src="./screenshot2.png" alt="screenshot">
</p><p>main-i6sBKSK-hc.hoc  <br/>
--Same as main-i6s-hc.hoc except BK and SK conductances added.  Runs
  produce traces in Fig 4 and data points for Figs. 6C and 8
<p/><img src="./screenshot.png" alt="screenshot">
</p>
<p>
<b>Changelog:</b><br>
2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.
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