NMDA & GUI

Using the graphical user interface to build and exercise models. Includes customizing the GUI by writing a little bit of hoc.
ted
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Re: NMDA & GUI

Post by ted » Tue Apr 09, 2013 11:05 am

Martenzi wrote:Branco wrote this original code:

setpointer cNMDA[n].C, PRE[n].T_rel(0.5)
To reuse any bit of code written by anyone, you have to know something about what you're taking. Branco's code contained this setpointer statement because the cNMDA instance has a POINTER variable called C (look at the NEURON block), and he wanted this variable to have the value that belonged to something called T_rel at a particular location in a particular instance of the PRE class. For this setpointer statement

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setpointer cNMDA.vpre, soma.v(0.5)
to be appropriate, the cNMDA instance would have to have a POINTER variable called pre (does it?), there would have to be a presynaptic section called soma, and it would have to make sense for cNMDA's pre to be equal to the membrane potential at the middle of the soma.
Activating NMDA should that cause a noticable difference to the AMPA AlphaSynapse ?
I don't know anything your "AMPA AlphaSynapse". Does your model have an AlphaSynapse that is being used to represent AMPAergic synaptic transmission?

ted
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Re: NMDA & GUI

Post by ted » Tue Apr 09, 2013 11:28 am

Martenzi wrote:If you can help my figure out . . .
I guess you're not a computational modeler. If you're an experimentalist, think like an experimentalist.
Could you please explain if the NMDA mod file ought to have a major influence on the graph without the built in AlpaSynapse? Or is the effect very marginal and can be difficult to spot? How do I test whether my NMDA synapse is having effect?
Does an instance of the NMDA_Mg_T produce anything you can see? Look at the NEURON block in NMDA_Mg_T.mod, which declares the names of variables and parameters that are visible to hoc. In particular notice
RANGE g, gmax . . .
and
NONSPECIFIC_CURRENT i
If you have created an instance of NMDA_Mg_T with hoc statements like
objref foo
foo = new NMDA_Mg_T(0.5)
then you will probably want to see foo.g and foo.i, and you might be able to affect the current foo.i by changing the value of foo.gmax

To discover whether this is so, examine the BREAKPOINT block in NMDA_Mg_T.mod. The BREAKPOINT block contains statements that are executed at each time step. Notice

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BREAKPOINT {
        . . .
        g = gmax * O
        i = (1e-6) * g * (v - Erev)
}
so my guess was correct. You want to plot g and i vs. t. If foo.i is too small, you need to make foo.gmax bigger.

Or maybe you need to reduce foo's mg parameter. What is mg? Is it visible to hoc? If a particular synaptic mechanism is called foo in hoc, what would foo's mg parameter be called? Oops, that's a trick question because mg is declared GLOBAL. That means foo doesn't have it's own mg parameter (if it did have one, the parameter would be called foo.mg). Instead, there is a single mg paramter that affects every instance of the NMDA_Mg_T class, and its hoc name is mg_NMDA_Mg_T.

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