writing new equations in neuron

[MH]

Hello!
I am wanting to implement a set of equations into Neuron. Is it possible to write my own equations in Neuron or do all of the equations have to be of a certain form? Also, is there a tutorial that explains how to implement equations? I did the Channel Builder tutorial (from the documentation page) but I only saw that I could implement equations of a certain type there.
MH

[ted]

The Channel Builder is limited to equations that correspond to physically
realizable gating mechanisms--these include variations on the Boltzmann
equation, the Bose-Einstein equation, etc.. This is sufficient for most
published descriptions of the biophysical properties of voltage-gated
macroscopic currents, but occasionally some effort is required to
rearrange published equations into the same form as those that are
offered by the Channel Builder.

There is an entire universe of equations that one might be able to fit to
arbitrary experimental data, i.e. descriptive equations rather than
mechanistic equations. For these you have two options. One is to use the
arbitrary equations to generate tables of (voltage, rateconstant) and
(voltage, steadystatevalue)--actually Vectors--and then tell the Channel
Builder to use these Vectors as a set of lookup tables. There is no tutorial
on this yet, but it's not hard to do.

The other option is to resort to writing a model description in NMODL. The
NMODL programming language can be used to add general equations to
NEURON. Chapter 9 of The NEURON Book is the most up-to-date
documentation on NMODL, but there's a predecessor to it
Hines, M.L. and Carnevale, N.T. Expanding NEURON's repertoire
of mechanisms with NMODL. Neural Computation 12:995-1007, 2000.
that you can download from here
http://www.neuron.yale.edu/neuron/bib/nrnpubs.html

You'll also find a lot of information about NMODL in the Programmer's
Reference. Go to the "hierarchical index" to the Programmer's Reference
http://www.neuron.yale.edu/neuron/stati ... /hier.html
and check out these links

Code: Select all

      NMODL
         ModelDescriptionLanguage
            BasicNMODLStatements  GeneralParadigm  NMODLtoNEURON  
            ConnectingMechanismsTogether  Introduction

If you're using MSWin, you already have a copy of the Programmer's
Reference on your PC. Click on the
Documentation
item in the NEURON program group.