Step 3. Specify subsets

The Subsets page is for grouping sections with similar features into subsets. This will make our job much easier when it comes time to assign biophysical properties.

This page is also for specifying rules, if any, that govern spatially inhomogeneous parameters that vary systematically with location. We'll use this feature in the second CellBuilder tutorial.

The gray panel in the middle of the Subsets page lists the names of all sets of sections. At first, the only set is "all", which contains every section in the model. We'll need this, so let's leave it alone.

Each of the apicals has identical active currents, so let's make a subset called apicals.

Click the Select Subtree radio button.

Then click on the root section of the apical tree (i.e. the section called ap).
Notice that the entire apical tree is red, and the unselected sections are black.

Also notice this message in the list of sets :

Now click on the New SectionList button (that's right, programmers--these "sets" are implemented with SectionLists).

Click in the edit field of the window that pops up.

Type the name of the new SectionList, and then click on Accept.

Notice the new item in the list of sets.

Quick, before we lose anything, save this CellBuilder to a session file!

Now think--do we need to create any more sets? The answer is no.

Also ask if we need to change the order of subsets. Sequence is important if a section appears in more than one set, because sequence determines the order in which Geometry and Biophysical properties are assigned. If a section appears in more than one set, earlier assignments may be overwritten by later assignments. So the order of sets should to go from general to specific.

The sequence we have here is fine.

We're ready to move on to geometry.

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