NetGUI not refreshing?

[Js Lee]

Hello,

I have looked through the other posts on previous network topics and have not seen any individuals address problems relating to the NetGUI possibly not refreshing. I am currently using a modified version of the Butera, Rinzel, and Smith 1999 paper where I have added a full morphological data of the preBotzinger Complex. The morphological data was imported from Neurolucida.

When I had initially included this cell (and only this cell) in the NetGUI with 5 excitation cells and 5 inhibitory cells, the voltage spikes produced in the voltage graph by NEURON made sense and was expected. However, when I connected the same morphological cell to a dendrite existing in the already existing cell in the NetGUI, I did not see any changes in the voltage graph from the single neuron graph from where I started. Nevertheless, sometimes after running the simulation a multitude of times, the voltage graph did change into one that seemed to include both neuron cells.

Hence, I am not quite sure if this is a problem with me pressing on the "Create" button at a wrong time or why there might be a lag in the graph changing from one network to another. Any help/advice would be greatly appreciated, and thank you for you time!

Js Lee

[ted]

The NetGUI tool, unlike the CellBuilder, does not have a "Continuous Create" feature. After you click on NetGUI's Create button, you get whatever was specified in that tool prior to the button click. If you need to change the network, it is necessary to click on Create to clear the adjacent check box, and then you can make whatever changes you like. However, if you try to turn Create back on, a message box should appear that says
"Create" cannot be turned back on without exiting NEURON.
So you must save your GUI to a session file, then exit NEURON, and finally restart NEURON and load the new session file.

[Js Lee]

Hi Ted,

First of all, thank you for your response. I have tried what you had posted; however, I still receive the same voltage plot as the one with just one morphological neuron. The only time the graph changes is when I click on the CellBuilder functions. For instance, when I click on the Biophysics tab, a similar plot appears but the bursts have a longer duration. Also, when I touch the Geometry tab, the voltage just stabilizes to around -20mV and stays like that until the simulation ends. I am not quite sure why the CellBuilder has these effects. I am sorry if these problems might seem trivial, but I have tried changing many different things but they all seem to have no effect or only adverse effects.

Thank you,
Js Lee

[ted]

I need a clearer understanding of what you have done, your expectations of the consequences of those actions, and how the actual results deviated from your expectations.

When I had initially included this cell (and only this cell) in the NetGUI with 5 excitation cells and 5 inhibitory cells, the voltage spikes produced in the voltage graph by NEURON made sense and was expected. However, when I connected the same morphological cell to a dendrite existing in the already existing cell in the NetGUI

You may know what this means, and it might suffice if we were looking at the same computer monitor, but since this is not the case I will need to be able to reproduce your observations for myself. If you can zip up just those hoc, ses, and mod files that are necessary, along with a clear description of usage, and email them to me
ted dot carnevale at yale dot edu
I will let you know what I discover.

[ted]

There were many problems with the model implementation, ranging from issues with parameter values to the fact that a CellBuilder managed by a NetReadyCellGUI tool was in "continuous create mode" (which caused creation of a top level cell in addition to whatever cells might have been created by the Network Builder, resulting in confusion about which GUI tools were affecting which cell).

The implications for those who use the Network Builder suite of GUI tools to construct network models are:
1. Before constructing a network model, make sure that the cell class specifications are correct. Verify that parameters have the proper values, and that an instance of each cell class behaves properly in response to injected currents and synaptic inputs. Actually, this tip applies equally well to those who develop models entirely in programmer-written hoc or Python without resorting to the GUI.
2. Make sure that there is no check mark in the "Continuous Create" boxes of the CellBuilders that belong to your NetReadyCellGUI tools. This is especially important if you "imported" a CellBuilder into a NetReadyCellGUI (which is the typical situation in which people overlook the Continuous Create status of a CellBuilder).