## Starting the CellBuilder

There are several ways to do this.

- Under UNIX, go to the working directory of your choice and enter the command line `nrngui` This makes NEURON open a hoc file that loads the graphical user interface ($NEURONHOME/lib/hoc/nrngui.hoc) and brings up the NEURON Main Menu.
- Under MSWin it is easiest to double-click the nrngui icon on the desktop. Take a look at NEURONMainMenu / File / recent dir. If your desired location appears in the menu list, select it. Otherwise, use NEURONMainMenu / File / working dir to bring up a directory browser that you can use to navigate to the desired location.

Then select NEURONMainMenu / Build / Cell Builder to start the CellBuilder.

## Using the CellBuilder

Across the top of the CellBuilder there is a row of radio buttons, plus a checkbox labeled "Continuous Create". For now you should leave the checkbox empty.

Use the radio buttons to select the following pages.

About
  Scan this information, but don't worry if everything isn't immediately obvious. You can reread it any time you want.

Topology
  This is where you change the branching architecture of the cell.
  Select "Make Section" from the list of actions, and then L click in the graph panel on a blank space to the right of the soma. Use the other actions as necessary to make your model look like the figure in this exercise.

Subsets
  Subsets can simplify management of models that have many sections. The CellBuilder automatically creates the "all" subset, which contains every section in the model. There is no need to define subsets for the ball and stick model, so just skip this page.

Geometry
  This is for setting 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 lets you set the number of segments manually. The CellBuilder also offers you the option of automatically adjusting nseg according to one of its built-in compartmentalization strategies; we will return to this later.
  2. Clear the Specify Strategy button.
     Use the list of section names to select the soma and dendrite individually, and enter the desired dimensions in the numeric fields for L and diam.
     For now leave nseg = 1.

Biophysics
  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. To examine and adjust the parameters of the mechanisms that you inserted, clear the Specify Strategy button.

Management
  This panel is not used in the ballstick exercise.

When you are done, the CellBuilder will contain a complete specification of your model cell. However, no sections will actually exist until you click on the CellBuilder's Continuous Create button.

At this point you should turn Continuous Create ON, because many of NEURON's GUI tools require sections to exist before they can be used (e.g. the PointProcessManager).

## Saving your work

This took a lot of effort and you don't want to have to do it again. So save the completed CellBuilder to a session file called ballstk.ses in the working directory course/ballstk.

To do this, start a NEURONMainMenu / Window / GroupManager. In the WindowGroupManager create a new group and change its name to Ball Stick Model.

The CellBuilder appears as the item CellBuild[0] in the list of ungrouped windows in the right panel of the WindowGroupManager. Click on CellBuild[0] to add it to the "Ball Stick Model" group.

Then save the "Ball Stick Model" group to a session file (call it ballstk.ses) with the "Save Group" button, and close the WindowGroupManager.

Why didn't we just tell you to use NEURONMainMenu / File / SaveSession?

### Checking what you saved

Retrieve ballstk.ses with NEURONMainMenu / File / load session. A new CellBuilder window called CellBuild[1] will appear. Since Continuous Create is ON, this new CellBuilder forces the creation of new sections that will replace any pre-existing sections with the same names. NEURON's interpreter announces that this happened :

    oc>Previously existing soma[0] points to a section which is being deleted
    Previously existing dend[0] points to a section which is being deleted

Check Topology, Geometry, and Biophysics. When you are sure they are correct, exit NEURON.

NEURON hands-on course
Copyright © 1998-2001 by N.T. Carnevale and M.L. Hines, all rights reserved.