CellBuilder doesn't affect a NetworkBuilder's cells

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tsa
Posts: 31
Joined: Mon Mar 26, 2007 12:44 pm

Post by tsa »

Hello,

Switching to GUIs per your advice I've used CellBuilder to create an intrinsically bursting cell which contains the currents I create. Using Network Builder I've set up a functioning model of 10 of these cells all synaptically connected to a NetSim artificel cell to view effects of the noisy point source input.

However when I attempt to change current parameters, either through Channel Builder or specification in Cell Builder nothing happens. Channel and Cell Builder switch to the new value but output graphs still show no change even if I switch all current values to zero.

Is there some sort of refresh action I need to complete for these changes to go into effect?

Thanks again.
tsa
Posts: 31
Joined: Mon Mar 26, 2007 12:44 pm

Post by tsa »

As a follow up....if I go into the command line and try looking at the parameters via forall psection(), as suggested above, it shows that the parameters I have changed in the GUI are unchanged.

If I now change the parameters through the command line then the parameters change both in viewing psection() and in voltage output but it's very cumbersome to do this for 10 cells individually each time I want to change one parameter.
ted
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Post by ted »

The cell and channel properties will be the ones that were specified just before you created
the network. Once the model net has been created, its cells and their channels do not
respond to the CellBuilder or Channel Builder.

The Network Builder is not designed to be used for interactive modeling. It is meant to be
used primarily as a means for prototyping small networks with just a very few cells, as a
preliminary step toward large scale network modeling. Once you have a toy net with a few
cells that works, you export the network to a hoc file, and then mine that file for reusable
pieces (e.g. cell class definitions) that you use to build a larger net in hoc. For an example
of this, see chapter 11 of The NEURON Book.

Managing the properties of cells in a network usually requires programming. That said, if
you are patient and careful, and don't need to change to many things, it is possible to
use the Network Builder for some exploratory modeling. When it comes time to run
simulations with a net that has different properties, you must first make sure that the
Network Builder's Create button is OFF (not checked). Then adjust the Channel Builder
and CellBuilder as you like--but don't destroy or rename any soma, and don't destroy any
section that has a synapse attached to it. Next save everything to a new session file and
exit NEURON. Finally, restart NEURON and reload the new session file. If your changes
didn't break anything, you will now be looking at a network that has the new properties.

It is also possible to use hoc code to adjust the properties of a Network-Builder-spawned
model net. You need to know the "real" names of the cells, not the short aliases that are
displayed on the canvas. To discover the real names, click on Net Variables and select
the item called "Provide NetGUI aliases". Then click on Net Variables and select the item
called "Show Map". The short aliases will be in the map's left column, and the corresponding
hoc names are in the right column. Knowing the names of the individual cell instances,
you can do whatever you like with a little programming.
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