Single Channel Simulation

NMODL and the Channel Builder.
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Kahlig

Single Channel Simulation

Post by Kahlig » Fri May 27, 2005 9:43 am

I have written a mod file for my channel of interest and I would like to test the single channel characteristics of this mod file using NEURON 5.7.159. When NEURON loads, I see "Allow single channel model for..." for my mechanism in the dialogue box, but I can not find where to simulate the single channel properties on my mechanism.

I am aware of the single channel simulator at
NEURON/Tools/Miscellaneous/Builders/Kinetic Scheme Builders
however, the rates must be entered by hand since I seem to be unable to load my mod file. This is very time consuming as I am trying to optimize my model to the microscopic as well as macroscopic properties of my channel.

Does NEURON alow for siingle channel simulations of a mod file and if not, will this be a feature that will be added sometime in the future?

hines
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Post by hines » Fri May 27, 2005 11:26 am

Single channel models can only be constructed with
NEURONMainMenu/Build/ChannelBuilder/Point
There can only be a single gate defined as a kinetic scheme raised to the first power. At that point you can select the
Properties/AllowSingleChannels
checkbox. For an example, launch the NEURONDEMO and select the "Stochastic Single channels: HH" demo.

Mod files cannot easily be used to construct single channel models and I need to remove the message about that long ago abandoned experimental implementation. I also should remove the NEURONMainMenu/Tools/Miscellaneous/Builders/KineticSchemeBuilder
since it has been made obsolete by the
ChannelBuilder. The only thing that keeps me from removing it is that it contains an interesting analysis method for single channel statistics.

hines
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Post by hines » Fri May 27, 2005 11:34 am

I should also mention that a PointProcess instance of a ChannelBuilder specification, when "Allow Single Channels" is selected, can be switched between macroscopic current mode and single channel mode by setting the value of Nsingle. When Nsingle has the value of 0 then it is a macroscopic current, any other value indicates the number of single channels for that PointProcess instance.

ted
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Re: Single Channel Simulation

Post by ted » Fri May 27, 2005 1:18 pm

Kahlig wrote:I am aware of the single channel simulator at
NEURON/Tools/Miscellaneous/Builders/Kinetic Scheme Builders
however, the rates must be entered by hand since I seem to be unable to load my mod file. This is very time consuming as I am trying to optimize my model to the microscopic as well as macroscopic properties of my channel.
Since you'll be using the Channel Builder, rather than the deprecated
Kinetic Scheme Builder, you'll need to know how to adjust the Channel
Builder's parameters from hoc--which is the only practcal way to optimize
a model current implemented with this graphical tool. The remainder of this
discussion assumes that you have completely specified the structure of
your channel model--whether it be HH-style or a reaction scheme--including
the equations that describe state transitions. It will be easiest to follow
these steps if you work through them with your own channel model, or with one
of the examples provided with the Channel Builder tutorial (get it from
http://www.neuron.yale.edu/neuron/docs), e.g. hhchannel.ses
or mykhh.ses

Click on the Properties button of the ChannelBuild window and turn
the "Provide transition aliases" item "on" (red check will appear next
to this item). This makes all of its parameters accessible from hoc.
It only remains to discover what these names are.

The easiest way to do that is to use the variable name browser that you
can get from a Graph. This is much more easily done than described.

1. Bring up a Graph.
NEURON Main Menu / Graph / State
will do nicely.

2. Bring up the Graph's Plot what? tool (click on the Graph's menu box,
then select Plot what? from the menu).

3. Click on the Plot what? tool's Show button and select Objects.
A list of object classes will appear in the left panel of the Plot what? tool.

4. Scroll through the list of object classes and double click on the ChannelBuild_ item.
The edit field of the Plot what? tool will now contain the string
ChannelBuild_
and the middle panel will show a list of numbers starting with 0.
Each of these numbers corresponds to one of the ChannelBuild windows that you
have opened.

5. Double click on one of the numbers. The edit field of the Plot what? tool will
now contain the string
ChannelBuild[n]
where n is the number you clicked on, and the middle panel will change
to a list of names. The first name is "aliases".

6. Double click on "aliases". The edit field of the Plot what? tool contains
ChannelBuild[n].aliases.
and the right panel will show a list of names that correspond to a,b variables
(rate constants) or inf,tau variables.
For the hhchannel.ses example, the names in the right panel are ah, am, bh, bm.

7. Double click on one of the names in the right panel. The edit field of the Plot what?
tool now contains
ChannelBuild[n].aliases.thenameyouclickedon.
and the right panel will show a list of the parameters for the particular a,b or
inf,tau variable.
For the hhchannel.ses example, ah=A*exp(k*(v-d)) so the right panel will contain
A, d, and k.

8. Double click on one of the names in the right panel, and the completed string
will appear in the edit field of Plot what? tool. This is the hoc name of the parameter
you selected.

So if you start NEURON, open hhchannel.ses, and work through these steps,
you will discover that the the parameters for ah are known to hoc as
ChannelBuild[0].aliases.ah.A
ChannelBuild[0].aliases.ah.d
ChannelBuild[0].aliases.ah.k

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