reopen cell builder

The basics of how to develop, test, and use models.
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Corinne
Posts: 38
Joined: Wed Feb 09, 2011 7:13 pm

reopen cell builder

Post by Corinne »

I am wondering if there is anyway to reopen a cell builder to an already built cell. For example, say "you" build a cell and run it. You are tweaking the parameters in the cell and rerunning to see what the effects are on the cell. Then you accidently close the cell builder and want to reopen it to continue where you left off. Is this possible? Or what if you built a model using hoc code and then want to change some of biophysics using the gui to see how they affect your model. Can you then open the current cell biophysics and all into the cell builder?

Thanks!
ted
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Re: reopen cell builder

Post by ted »

Corinne wrote:I am wondering if there is anyway to reopen a cell builder to an already built cell. For example, say "you" build a cell and run it. You are tweaking the parameters in the cell and rerunning to see what the effects are on the cell. Then you accidently close the cell builder
You're cooked. Exit NEURON and start again.
what if you built a model using hoc code and then want to change some of biophysics using the gui to see how they affect your model.
The CellBuilder can only import a 3d model specification. It cannot import SectionLists or biophysical properties or discretization strategy.

One can use a CellBuilder to create a complete model specification, make sure its Continuous Create button is ON, save the CellBuilder to a ses file, and exit NEURON.

Then one can come back later and use a program that does the following:
1. reads the ses file (this recreates the CellBuilder, which instantiates the model cell because Continuous Create is ON)
2. turns the CellBuilder's Continuous Create OFF
3. executes hoc statements that alter the model's properties ("posttranslational modification in silico")

A sample program that does this:

Code: Select all

load_file("nrngui.hoc")
load_file("cb.ses") // ses file that recreates a CellBuilder that has Continuous Create ON
// at this point there is a model cell
objref cb
cb = CellBuild[0]
cb.continuous = 0 // turns Continuous Create OFF
proc change_densities() {
  . . . code that changes channel densities . . .
}
change_densities()
// and now the model has been altered from what was specified in the CellBuilder
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