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
), e.g. hhchannel.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
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
5. Double click on one of the numbers. The edit field of the Plot what? tool will
now contain the string
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
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
and the right panel will show a list of the parameters for the particular a,b or
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
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