Overview of the CellBuilder

The CellBuilder is a graphical tool for creating, editing, and managing models of nerve cells. It is probably most useful in two different settings.

The first, which you are exploring in this exercise, is when you need to build a model from scratch that will have only a few sections. If you need more than 5 - 10 sections, you might prefer to write an algorithm that creates the model under program control.

Later in this course you will encounter the second setting in which the CellBuilder is helpful: when you already have a model cell with a large number of sections, and you want to make targeted changes in its biophysical or anatomical properties without having to write any code.

The CellBuilder breaks the process of creating and managing a model of a cell into several tasks. These tasks are analogous to what you would do if you were writing a program in hoc. They are

setting up the topology (branching pattern) of the model
grouping sections into subsets. For example, it might make sense to group dendritic branches into subsets according to anatomical criteria (e.g. basilar, apical, oblique, spiny, aspiny), or biophysical criteria (passive, active).
assigning geometric properties to individual sections or subsets of sections (e.g. length, diameter)
assigning biophysical properties to individual sections or subsets of sections (e.g. cytoplasmic resistivity, membrane capacitance, ion channels, buffers, pumps)

Finally, the CellBuilder lets you save your model to a file for future use, or export it to NEURON's interpreter so you can run simulations with it immediately.

The CellBuilder can also import a model that already exists during a NEURON session. As you will see in a later exercise, this is particularly useful for dealing with complex models that are based on morphometric data.