Re: [Genesis-sim-users] Modified tabchannel objects in Vanier piriform cortex model

[Dave B. <db...@Co...>]

I think that the only way to understand the functions called in the
script code below would be to see Mike Vanier's C code for the
mod_tabchannel object and the function mod_setupalpha. These are
probably straightforward extensions of the src/olf tabchannel and
setupalpha code, and should contain the definition of INITREFCOUNT.
His code is usually pretty well documented, but I don't have these
files. It does not appear in the standard src/olf or newconn files.

Perhaps Simon O'Connor got these files from Mike.

Dave

On Thu, 28 May 2015, Christoph Metzner wrote:

> Hi all,
> 
> I am trying to use the cell models from the Vanier&Bower piriform cortex
> model. However, the model uses a modified version of Genesis 2.3 with
> several modified objects. One example is a modified version of the
> 'tabchannel' object, which I think allows for a modulation of the ion
> channels caused by neuromodulators. Since I am not interested in
> neuromodulation I wanted to 
> translate the channels to the standard tabchannel objects. However, the last
> line of the channel definition calls the action INITREFCOUNT (see code
> below) which is not an action of a standard tabchannel. Before I start
> diving into the Code behind the mod_tabchannel object, I was wondering  if
> anyone of you has an idea what this call does and how to translate it to
> standard tabchannel actions.
> 
> Thanks
> 
> Christoph
> 
> int pyr_std_xdivs = 4000
> 
> // ========================================================================
> //                Tabchannel Na Hippocampal cell channel
> // ========================================================================
> 
> function make_pyr_Na
>     if ({exists pyr_Na})
>         return
>     end
> 
>     create mod_tabchannel pyr_Na
>     setfield pyr_Na          \
>         Ek        {PYR_ENA}  \
>         Gbar      0          \
>         Ik        0          \
>         Gk        0          \
>         Xpower    2          \
>         Ypower    1          \
>         Zpower    0          \
>         mod_index 0
> 
>     float THRESHOLD_OFFSET = 0.025
> 
>     mod_setupalpha pyr_Na X  \
>             {320.0e3 * (0.0131 + PYR_EREST_ACT + THRESHOLD_OFFSET)}    \
>             -320.0e3                                                   \
>             -1.0                                                       \
>             {-1.0 * (0.0131 + PYR_EREST_ACT + THRESHOLD_OFFSET)}       \
>             -0.004                                                     \
>             {-280.0e3 * (0.0401 + PYR_EREST_ACT + THRESHOLD_OFFSET)}   \
>             280.0e3                                                    \
>             -1.0                                                       \
>             {-1.0 * (0.0401 + PYR_EREST_ACT + THRESHOLD_OFFSET)}       \
>             5.0e-3                                                     \
>             -size {pyr_std_xdivs} -range -0.1 0.1
> 
>     THRESHOLD_OFFSET = 0.025
> 
>     mod_setupalpha pyr_Na Y  \
>             128.0                                                      \
>             0.0                                                        \
>             0.0                                                        \
>             {-1.0 * (0.017 + PYR_EREST_ACT + THRESHOLD_OFFSET)}        \
>             0.018                                                      \
>             4.0e3                                                      \
>             0.0                                                        \
>             1.0                                                        \
>             {-1.0 * (0.040 + PYR_EREST_ACT + THRESHOLD_OFFSET)}        \
>             -5.0e-3                                                    \
>             -size {pyr_std_xdivs} -range -0.1 0.1
> 
>     call pyr_Na INITREFCOUNT
> end
> 
> --
> 
> Dr. Christoph Metzner, Dipl.-Math., B.Sc.
> 
> Wissenschaftlicher Mitarbeiter des Institutes für Robotik und Kognitive
> Systeme
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