importing data from clipboard into ChannelBuilderGateGUI

NMODL and the Channel Builder.
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declan
Posts: 2
Joined: Fri Jun 13, 2008 1:44 pm

importing data from clipboard into ChannelBuilderGateGUI

Post by declan »

Hi,
I am very new to NEURON and have been using the GUI for the last couple of weeks; I'm not the programmer type...yet. I would like to import x,y data from the clipboard into the ChannelBuilder GateGUI in the box labeled Equation Type, infh, KSChanTable. But I don't know how to get the x,y data onto the clipboard. Would anyone be able to help me out? The data deals with differing activation time constants at different voltages for an Na current.
Thanks!
ted
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Re: importing data from clipboard into ChannelBuilderGateGUI

Post by ted »

Suppose you have data for the time constant and steady state value of h at several membrane potentials. Put these data into two plain text files, one for time const and the other for steady state. Each file should consist of a series of lines with pairs of numerical values, e.g. the file that contains the steady state values for h might look like this
-100 1
-90 0.99
-80 0.97
. . . etc. . . .

Next use the ChannelBuilder to set up the equations that govern your channel.
Then on the "Properties" page of the ChannelBuildGateGUI tool:
In the top canvas, click on h.
In the bottom panel make sure that you are looking at the inf, tau equations.
You will know if you see something like
infh = algebraic stuff
tauh = other algebraic stuff
(If instead you are looking at the alpha, beta equations you will see
ah = stuff
bh = more stuff
This is not what you want--click on the EquationType button, drag the mouse onto the alpha, beta item,
and then over to the secondary menu to select inf, tau.)

You are now ready to read the tables into NEURON's clipboard and then into the ChannelBuilder.
Click on EquationType and scroll down to infh, then over to the secondary menu and down to KSChanTable.
The equation for infh, and the buttons for its parameters, will disappear. In its place you will see something like
infh = KSChanTable
Vector[20] from . . . stuff . . .
and a button labeled Fill.

But you don't have anything to fill the table with. Yet.

So in the NEURON Main Menu toolbar click on Vector / Retrieve from File
This brings up a file chooser that displays a list of the files in the current directory that end with the extension dat. If your data end with a different extension, e.g. inf, click in the "Filter" field of this tool and enter
*.inf
Then you will see a list of all the files that end in inf.
Double click on the name of the file that contains the steady state values for h.
Now you have read the data into NEURON's clipboard.
To paste them into the CellBuilder, click on the Fill button and select the "from Clipboard" item.

Do the same for tauh.

Much easier to do than to describe.
declan
Posts: 2
Joined: Fri Jun 13, 2008 1:44 pm

Re: importing data from clipboard into ChannelBuilderGateGUI

Post by declan »

Thanks so much. I'll give it a try.
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