NMODL.md

NMODL

NMODL is a domain-specific programming language for describing chemical and protein reactions for neuroscience. NEUWON uses NMODL extensively. NMODL has been extended many times, and NEUWON further improves the file format.

Changes to the specification

• "USEION" statements now allows access all chemical species regardless of their electric charge, and their intracellular and extracellular concentrations can be read and written via the standardly named variables. Previously, accessing this data required a "POINTER" statement.

• "USEION" statements now provide WRITE access to conductance data.
  The syntax is "USEION x WRITE gx" and the units of gx are ???.
  Multiple mechanisms can write to the same species conductance without issue.

• "USEION" statements now provide a way to create nonspecific conductances, by assigning to the ion's equilibrium potential. Use the syntax "USEION x WRITE ex" and specify ex in your "PARAMETERS" block in units of mV.

• All mechanisms now have a magnitude and standard way of accessing it.

  • POINT_PROCESS ...
  • SUFFIX ...
  • Access other mechanisms magnitudes ...

• NMODL now exposes less information about the model's internal state to the simulator. These changes enabled significant performance optimizations.

  • "FUNCTION" and "PROCEDURE" blocks defined in NMODL can now only be called from within NMODL files. They are not accessible in NEUWON. The only methods accessible from NEUWON are to create, destroy, and advance the state of mechanisms.

  • "ASSIGNED" variables are now freed from memory at the end of the BREAKPOINT block, for improved memory consumption.

History of NMODL

NMODL is an extension of the model description language developed for SCoP; published in:

• A block organized model builder.
  Kohn, M. C., Hines, M. L., Kootsey, J. M., & Feezor, M. D. (1994).
  https://doi.org/10.1016/0895-7177(94)90190-2

The NEURON program extended the SCoP language with many neuroscience specific features to become NMODL.

• Expanding NEURON's repertoire of mechanisms with NMODL.
  Hines, M. L., & Carnevale, N. T. (2000).
  https://doi.org/10.1162/089976600300015475

Documentation

• NEURON's documentation on NMODL

• How to expand NEURON’s library of mechanisms
  Chapter 9 of The NEURON book.
  Carnevale, N. T., & Hines, M. L. (2006).

Where to find NMODL files?

• NEUWON
  [I intend to keep a fairly complete set of models in the project. I should state that my goal is to make a good toolkit, and the specific models are subject to change.]

• ModelDB

• ChannelPedia

• Automatic conversion from NeuroML