Using the CellBuilder

These tutorials show how to use the CellBuilder, a powerful and convenient tool for constructing and managing models of individual neurons. The CellBuilder is a "graphical form for specifying the properties of a model cell." It breaks the job of model specification into a sequence of tasks :
  1. Setting up model topology (branching pattern).
  2. Grouping sections with shared properties into subsets.
  3. Assigning geometric properties (length, diameter) to subsets or individual sections, and specifying a discretization strategy (i.e. how to set nseg).
  4. Assigning biophysical properties (Ra, cm, ion channels, buffers, pumps, etc.) to subsets or individual sections.
These are the same things we would have to do, and pretty much the same sequence we'd follow, in order to define a model by writing hoc code. However, the CellBuilder helps us keep it all nice and organized, and eliminates a lot of error-prone typgin  . . . ptyngi  . . . typing.

The Tutorials

Creating a stylized ("stick figure") model cell.
Given a conceptual model that has a simple branched topology, we implement a computational model. This introduces material that is helpful in the following tutorials.

Managing a model cell with complex anatomy.
We use the CellBuilder to specify the spatial grid (nseg) and biophysical properties of a model based on detailed morphometric data.

Specifying parameterized variation of biophysical properties.
How to make one or more biophysical properties vary systematically with position in space.

This link will get you a pkzipped collection of these html files and images.

Copyright © 1999-2006 by N.T. Carnevale and M.L. Hines, All Rights Reserved.