chloride channel

NMODL and the Channel Builder.
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menica
Posts: 67
Joined: Wed Sep 02, 2015 11:02 am

chloride channel

Post by menica » Thu Dec 10, 2015 6:11 am

Hi,
I need to insert a chloride leak channel (CIC-2).
Where I could find this .mod mechanism implemented? I try to search on modelDB, but I found only the GABA receptors model.
I would like to insert also a potassium-chloride co-transporter (KCC2) and a sodium-potassium-chloride co-transporter (NKCC1).
Any suggestion?

Thanks!

ted
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Location: Yale University School of Medicine
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Re: chloride channel

Post by ted » Thu Dec 10, 2015 11:45 pm

menica wrote:I need to insert a chloride leak channel (CIC-2).
Where I could find this .mod mechanism implemented?
Using ModelDB's "advanced search" to look for NEURON models that involved various kinds of Cl current, I find an I Cl,Ca,
https://senselab.med.yale.edu/ModelDB/S ... odel=95870
plus 5 models that have an I Cl, leak
and 5 more models that have an I Chloride

Maybe one of those would be of interest to you.
To find them for yourself, click on ModelDB's
"advanced search" to bring up the "Database + Full Text Search" page,
then
click on the checkbox next to 6. Model Currents
and click on the adjacent Keywords button, then scroll down the menu to select one of the 3 kinds of Cl current that are in ModelDB.
Next click on the checkbox next to 10. Simulator software,
and click on the adjacent Keywords button, then scroll down the menu to find NEURON
Finally click on "Search"

To search for the other two Cl currents, click on "Change search parameters" and select the appropriate current to look for.
If you don't find what you want, you may need to implement one for yourself, or if you provide a mathematical description of it, I can create one for you in NMODL.
I would like to insert also a potassium-chloride co-transporter (KCC2) and a sodium-potassium-chloride co-transporter (NKCC1).
If you don't find them in ModelDB, it's probably not difficult to implement them with NMODL as long as you have a mathematical description of their properties and a solid grasp of NMODL syntax.

If it is important to keep track of chloride mass balance, you will also need a chloride accumulation mechanism. Be very careful about valence if you write your own, because it is easy to forget that icl > 0 means chloride is entering the cell (of course the same is true for bicarbonate). I have seen a user-written chloride accumulation mechanism that made the mistake of treating icl as if a positive value implied chloride efflux.

menica
Posts: 67
Joined: Wed Sep 02, 2015 11:02 am

Re: chloride channel

Post by menica » Thu Dec 17, 2015 8:32 am

Thanks!

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