mod files: what they are, and how to use them

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ted
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mod files: what they are, and how to use them

Post by ted » Mon Feb 16, 2015 6:11 pm

"mod files" are instructions written in the NMODL programming language that are used to add new features to NEURON. Typically they are used to specify the properties of a biophysical mechanism such as a ligand- or voltage-gated ion channel, or an "ion accumulation mechanism" that tells NEURON how transmembrane and/or diffusional fluxes of an ionic species affect that ion's intra- and/or extracellular concentration (for examples, download and expand a recent gzipped tar file of NEURON source code from http://www.neuron.yale.edu/neuron/download/getstd, then descend into nrn/share/examples/nrniv/nmodl). mod files are also used to specify the properties of new kinds of synaptic mechanisms or of current or voltage sources like current or voltage clamps (e.g. https://www.neuron.yale.edu/ftp/ted/neu ... ynstdp.zip,, or basic_white_noise.zip or izap.zip at https://www.neuron.yale.edu/ftp/ted/neuron/). They can also be used for other purposes, e.g. to capture the local maximum and minimum of some variable during a simulation (see http://www.neuron.yale.edu/phpbb/viewto ... =15&t=1816)

mod files must be compiled in order to be incorporated into NEURON. It is most convenient to put all of the mod files that are relevant to a particular project into the same directory as the hoc, ses, and py files used by that project. Then you can compile them from the command line under Linux by using cd to go to that directory and executing
nrnivmodl
or, under OS X, by dragging and dropping that directory onto the mknrndll icon,
or, under MSWin, by double clicking on mknrndll and then using mknrndll's directory browser to navigate to the directory that contains the mod files. If compilation is successful, when you start NEURON in that directory it will automatically load the compiled mod files before doing anything else.

For more information, see chapter 9 in the NEURON Book, and also look at these items in the FAQ list url]http://www.neuron.yale.edu/neuron/faq[/url]
Where can I find examples of mod files?
How do I compile mod files?
I can't get mod files to compile.
I installed a new version of NEURON, and now I see error messages like this:
mechanisms fooba needs to be re-translated.
Is there a list of the functions that are built into NMODL?

And remember: if you update NEURON, you'll have to recompile you're mod files so that the new version of NEURON can use those mechanism.

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