Using the CellBuilder

Bringing up the CellBuilder

This exercise assumes you are starting in the course/ballstk directory from an xterm or DOS window. Enter the command line
	nrngui
This makes NEURON open a hoc file that loads and starts the graphical user interface ($NEURONHOME/lib/hoc/nrngui.hoc). However, no sections are created.

Once you see the Main Panel, invoke the CellBuilder with the command Miscellaneous/Builders/CellBuilder

Tips for Using the CellBuilder

Across the top of the CellBuilder is a row of radio buttons that let you select any of the CellBuilder's different pages. There is also a checkbox for "Continuous Create" ; leave this box unchecked for now.
  1. The "About" page.
    Scan this information, but don't worry if everything isn't immediately obvious. You can reread this material any time you want.
  2. The "Topology" page. Use this to add a dendrite to the cell.
    Select "Make Section" from the list of actions, and then L click in the graph panel. Use the other actions as necessary to make your model look like the figure in this exercise.
  3. The "Subsets" page. Subsets can simplify management of models that have many sections. For this simple model, there is no need to define subsets, so just look briefly at this page. Note the subset "all," which was generated automatically.
  4. The "Geometry" page. This is where you set the dimensions and spatial grid (nseg) of the soma and dendrite.
    1. Make sure the Specify Strategy button is checked.
      Choose soma from the list of subsets and section names, and then select L, diam, and nseg.
      Repeat for dend.
      Note: choosing nseg means you will be able to use the CellBuilder to set the number of segments manually. The CellBuilder also offers you the option of automatically adjusting nseg according to one of two built-in compartmentalization strategies; we will return to this later.
    2. Clear the Specify Strategy button.
      Using the list of section names to select the soma and dendrite individually, enter the desired dimensions in the numeric fields for L and diam.
      For now leave nseg = 1.
  5. The "Biophysics" page.
    Use this to endow the sections with biophysical properties (ionic currents, pumps, buffers etc.).
    1. Specify Strategy. This is for inserting biophysical mechanisms into the sections of your model (Ra and cm for "all," hh for the soma, and pas for the dend section).
    2. Clear the Specify Strategy button, and you will see a new list that lets you adjust the parameters of the mechanisms that you inserted.
  6. The "Management" page.
    Choose the "Export" radio button.
    Verify that all four boxes (Topology, Subsets, Geometry, Biophysics) are checked, and then click on the large grey Export button. Save the cell to a file called ballstk.hoc in the same directory where you started NEURON (e.g. the directory that contains hhcable.hoc). This is an ordinary text file that contains hoc commands.

When you have exported your model to ballstk.hoc, exit NEURON.


NEURON summer course
Copyright © 1998, 1999 by N.T. Carnevale and M.L. Hines, all rights reserved.