Defining new classes of artificial spiking cells.

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ted
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Defining new classes of artificial spiking cells.

Post by ted »

Amal Afzal Shaikh wrote:
i hv that the only way to add new classes of artificial spiking cells is to write a new model specification in NMODL, then compile that mod file. do i write the specfctn in a txt document and then save it as a mod file? hw do i compile a mod file?
It is not necessary to write new specifications in NMODL if the new classes are essentially
the same as the four built-in classes (IntFire1, IntFire2, IntFire4, or NetStim) except for
parameter changes.

For example, suppose you're making a network that has two kinds of IntFire1 cells: a
"fast" class with tau = 5 and refrac = 2, and a "slow" class with tau = 20 and refrac = 10.
1. First set up the "fast" class. Using the ArtCellGUI tool:
a. Select New / IntFire1. The list of Artificial Cell types will be
IntFire1
b. Click on Rename. A window pops up where you change the name from IntFire1 to FIF1.
c. Change tau to 5 and refrac to 2.
2. Next set up the "slow" class. Repeat steps 1a. The list of Artificial Cell types will be
FIF1
IntFire1
Make sure that the IntFire1 item in that list is selected, then repeat steps 1b and c, but
this time call the class SIF1, and set tau to 20 and refrac to 10.
If you now bring up a new Network Builder, you will see that its palette has two cell
classes called FIF1 and SIF1. After you build a network with these two cell classes,
you can export a hoc file and in that hoc file you will find class definitions for your fast
and slow integrate and fire cell classes.

The only reason to write new NMODL code is if you need a class that cannot be derived
trivially from one of the four built-in classes (NetStim, IntFire1, IntFire2, IntFire4), i.e. a
class that cannot be defined by merely changing a parameter of an existing class.
Developing and testing algorithms for predicting future firing times from the present
values of state variables is not trivial.
do i write the specfctn in a txt document and then save it as a mod file? hw do i compile a mod file?
See
Where can I find examples of mod files?
and
How do I compile mod files?
in the FAQ list http://www.neuron.yale.edu/neuron/faq/general-questions
Amal Afzal Shaikh

thanx

Post by Amal Afzal Shaikh »

thanx ted...
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