Customizing Rate Equations In Channel Builder

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
Post Reply
Dmandel
Posts: 13
Joined: Wed Jul 08, 2015 2:32 pm

Customizing Rate Equations In Channel Builder

Post by Dmandel » Mon Jul 13, 2015 11:00 am

Hi,

I am attempting to model a Serotonergic Neuron of the Dorsal Raphe Nucleus.

I am using the CHANNEL BUILDER and I want to customize the K+ channel. How would I go about writing my own equations for N∞, IE

N∞ = 1 / 1 + e-(V-Vk)/k.

I also want to specify an equation for τn (tau), IE

τn = αk + βk / cosh((V-Vk2)/k2.

Thanks for the help!

ted
Site Admin
Posts: 5375
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Customizing Rate Equations In Channel Builder

Post by ted » Mon Jul 13, 2015 11:42 am

The Channel Builder limits your palette of equations to what is built into the Channel Builder. Furthermore, for HH-style gating, you must either use the alpha, beta or the inf, tau formulation--can't mix them.

That said, your formula for the steady state value of n is built into the Channel Builder, so the only problem is what to do about the time constant's voltage dependence. See
importing data from clipboard into ChannelBuilderGateGUI
http://www.neuron.yale.edu/phpbb/viewto ... =16&t=1291
After you have done that, try saving the ChannelBuilder to a ses file and see if the time constant data are preserved in that file.

Dmandel
Posts: 13
Joined: Wed Jul 08, 2015 2:32 pm

Re: Customizing Rate Equations In Channel Builder

Post by Dmandel » Mon Jul 13, 2015 5:29 pm

Thanks.

Dmandel
Posts: 13
Joined: Wed Jul 08, 2015 2:32 pm

How many points on the graph should I use?

Post by Dmandel » Tue Jul 14, 2015 9:58 am

I have successfully imported my x, y data but I don't understand how the KSchannel uses the data. Does it use the exact data points I import? Or does it make a calculation based on the data points?

ted
Site Admin
Posts: 5375
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Customizing Rate Equations In Channel Builder

Post by ted » Tue Jul 14, 2015 12:43 pm

Yes and yes. Think "piecewise linear approximation to a continuous function." Interpolation between breakpoints, and flat between -/+ inf and the first/last breakpoint.

Post Reply