calcium point process

[srahim2]

Hi. I'm new to NEURON and I'm trying to visualize basic calcium diffusion. So far, I have the cell morphology and the file from the Hines/Carnevale book for calcium diffusion, however the model displays a zero concentration for calcium in the cell. Is there a way to inject calcium as a point process; further, are there more advanced tutorials anywhere for things like creating point processes or modeling second messenger systems?

Thanks for your help

[ted]

Good questions.

the file from the Hines/Carnevale book for calcium diffusion

Specificially which "file" do you mean? Listing number will suffice. This may have some
bearing on the following discussion.

the model displays a zero concentration for calcium in the cell.

How do you know this? From the appearance of a graph that shows cai vs. time? That
can be deceiving, because (1) cai tends to be very small (initially 5e-5, i.e. 50 nM, by
default in NEURON) so it is hard to distinguish from the x axis), and (2) if cai is constant
in your model, trying to rescale with the graph's "View = plot" will have no effect. So you'll
get a trace that seems to lie right on top of the x axis, i.e. looks like cai is 0.

Have you used that graph's "Crosshair" function to check the actual value at any plotted
point? (left click on the trace and drag the cursor back and forth; xy coords of each data
point will be displayed on the graph's canvas or--if you're using MSWin--on its drag bar).

Have you typed
cai
at the oc> prompt in the xterm? This will report the value of cai.

Is there a way to inject calcium as a point process

If you write one yourself. Why not use one of the calcium current mechanisms that
comes with NEURON? Go to the FAQ (Frequently Asked Questions) page at
NEURON's WWW site http://www.neuron.yale.edu/neuron/faq/general-questions
and look for the item
Where can I find examples of mod files?
Among the "examples" mod files you will find cacur.mod (a square pulse calcium current)
and cachan.mod (a voltage-gated channel). If you use cachan.mod, I'd suggest changing
SOLVE state METHOD euler
to
SOLVE state METHOD cnexp
before compiling it.

are there more advanced tutorials anywhere for things like creating point processes

Chapter 9 of The NEURON Book is as advanced as it gets.

or modeling second messenger systems?

No, but this is quite doable. Here
http://senselab.med.yale.edu/senselab/m ... odel=39949
are examples of two approaches for representing second messenger effects in models
of dopaminergic modulation of neuronal properties. For a third, see Example 10.5 on
pp. 281 et seq. of The NEURON Book. Depending on what you have in mind, there are
other approaches that may be more suitable. Messenger concentration can be
represented in a way that is purely "functional" (as in the model of dopamine effect),
or "mechanistic" (with a family of differential equations or kinetic schemes that describe
the processes that generate and regulate messenger conc).

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