Parameter Searching paper

A Comparative Survey of Automated Parameter-Search Methods for Compartmental Neural Models

by Michael C. Vanier and James M. Bower Journal of Computational Neuroscience 7/2, pp. 149-171 (1999)
This paper describes a number of parameter-search algorithms that can be used to assign parameters to single-neuron models, and compares them with each other on several models, including very simple one-compartment spiking models, two passive dendrite models, and a moderately complex model of a layer II pyramidal cell in piriform (olfactory) cortex. The paper also makes specific recommendations about how to use the different methods and which ones are most suited for which kinds of tasks. We also make several general recommendations relating to parameter searching in neural models. The full text of the paper can be downloaded here. This is a preprint version, so it looks slightly different from the published version. The entire GENESIS parameter searching software package can be downloaded here. This contains:

  • The most recent version of the GENESIS parameter-searching library.
  • Documentation (GENESIS .doc files) for all GENESIS objects and functions included in this library, as well as for parameter searching in general.
  • Demo scripts for all five parameter-searching objects.
  • The source directory for the xplot program (originally written by Matt Wilson), which is useful for viewing the results of parameter searches.

    All of this will be included in the next release of GENESIS (except maybe for the xplot program; I don't know about that yet).

    This page also includes links to GENESIS scripts describing the ionic channels and the morphologies of the models described in the above paper.

  • Morphology of models 1 and 2
  • Channel descriptions for models 1 and 2
  • Morphology of model 3
  • Morphology of model 4
  • Channel descriptions for model 5
  • Morphology description for model 5

    If you do use the GENESIS parameter searching software, I'd be interested in hearing about your experiences with it, both good and bad. Please email me with your comments.

    Go back to my home page. Last updated April 11, 2017

    Mike Vanier (mvanier@cs.caltech.edu)