Why I cannot use the GUI

Why I cannot use the GUI

Postby yk890406 » Wed Oct 26, 2011 3:30 am

After I click the insert. It shows "No accessed section: Can't start an insert.
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Re: Why I cannot use the GUI

Postby ted » Wed Oct 26, 2011 11:25 am

This happens when there is no default section.

At the oc> prompt in NEURON's xterm, type the command
forall print secname()
What is NEURON's reply to this command?
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Re: Why I cannot use the GUI

Postby yk890406 » Thu Oct 27, 2011 2:43 am

ted wrote:This happens when there is no default section.

At the oc> prompt in NEURON's xterm, type the command
forall print secname()
What is NEURON's reply to this command?

It shows" oc>for all print secname()
first instance of all
nrniv: syntax error
near line 8
for all print secname()
^"
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Re: Why I cannot use the GUI

Postby ted » Thu Oct 27, 2011 11:14 am

The command to try is
Code: Select all
forall print secname()
not
Code: Select all
for all . . .


Also, tell me what
print secname()
returns.
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Re: Why I cannot use the GUI

Postby yk890406 » Fri Oct 28, 2011 7:05 am

ted wrote:The command to try is
Code: Select all
forall print secname()
not
Code: Select all
for all . . .


Also, tell me what
print secname()
returns.

Thank you Ted, I have fixed the problem. Although I still cannot insert, I can use the GUI to build. That is good enough for me. I have a question that whether I can simulate the signal in a field such as magnetic field.
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Re: Why I cannot use the GUI

Postby yk890406 » Fri Oct 28, 2011 8:24 am

And can I simulate electric synapse with neuron?
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Re: Why I cannot use the GUI

Postby ted » Fri Oct 28, 2011 10:05 am

yk890406 wrote:Although I still cannot insert, I can use the GUI to build. That is good enough for me.
Well, it's not good enough for me, and if you don't mind, I'd like to identify whatever the problem is and make sure it has been fixed.

To diagnose the problem and figure out how to fix it, it is necessary to (1) confirm that there is no default section, and to (2) discover whether any sections exist. So if it isn't too much trouble for you, please tell me this: when you receive the error message you reported, what does NEURON do when you enter the command
Code: Select all
print secname()
at the oc> prompt, and what happens when you enter the command
Code: Select all
forall print secname()


I have a question that whether I can simulate the signal in a field such as magnetic field.
Alon Korngreen published a paper recently that describes how he did this--search PubMed for Korngreen and it will be one of the first 3 or 4 hits.
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Re: Why I cannot use the GUI

Postby ted » Fri Oct 28, 2011 10:06 am

yk890406 wrote:And can I simulate electric synapse with neuron?
Yes. What do you mean by electric synapse? Ephaptic interaction, or gap junction?
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Re: Why I cannot use the GUI

Postby yk890406 » Fri Oct 28, 2011 2:38 pm

oc>print secname()
nrniv: Section access unspecified
near line 3
print secname()
^
secname( )
oc>forall print secname()
oc>
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Re: Why I cannot use the GUI

Postby yk890406 » Fri Oct 28, 2011 2:45 pm

ted wrote:
yk890406 wrote:And can I simulate electric synapse with neuron?
Yes. What do you mean by electric synapse? Ephaptic interaction, or gap junction?

Sorry, I do not the term of it. It means there gap 2-3 nm between two nerve cells. The cell pass the signal without Neurotransmitter but with ions directly.
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Re: Why I cannot use the GUI

Postby ted » Fri Oct 28, 2011 10:47 pm

yk890406 wrote:
Code: Select all
oc>print secname()
nrniv: Section access unspecified
near line 3
print secname()
                ^
secname(        )
This confirms the fact that there is no default section. Many of NEURON's GUI tools assume that a default section exists, and will generate error messages if there is no default section.
Code: Select all
oc>forall print secname()
oc>
This shows that no sections exist. Not even one. How are you specifying the properties of your model cell--with a CellBuilder, or with hoc code?
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Re: Why I cannot use the GUI

Postby ted » Fri Oct 28, 2011 11:01 pm

yk890406 wrote:
ted wrote:What do you mean by electric synapse? Ephaptic interaction, or gap junction?

Sorry, I do not the term of it. It means there gap 2-3 nm between two nerve cells. The cell pass the signal without Neurotransmitter but with ions directly.
That's called a gap junction. With NEURON, gap junctions can be implemented in two different ways. One way is with a pair of point processes. The other way is with the LinearMechanism class. ModelDB contains examples of both approaches, but it's probably best to use the LinearMechanism class. Here's an example of that

M. Migliore, M. Hines and GM Shepherd
The role of distal dendritic gap junctions in synchronization of mitral cell axonal output
J. Comput. Neurosci., 18:151-161 (2005)
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=43039

and here's another

Minneci F, Janahmadi M, Migliore M, Dragicevic N, Avossa D, Cherubini E
Signaling properties of stratum oriens interneurons in the hippocampus of transgenic mice expressing EGFP in a subset of somatostatin-containing cells.
Hippocampus 17:538-53 (2007)
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=87546
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Re: Why I cannot use the GUI

Postby yk890406 » Sat Oct 29, 2011 3:24 pm

ted wrote:[quote="yk890406
Code: Select all
oc>forall print secname()
oc>
This shows that no sections exist. Not even one. How are you specifying the properties of your model cell--with a CellBuilder, or with hoc code?

I use CellBuilder.
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Re: Why I cannot use the GUI

Postby ted » Mon Oct 31, 2011 3:22 pm

Then I am forced to conclude that you have not worked through the CellBuilder tutorials at
http://www.neuron.yale.edu/neuron/docs
or maybe you didn't notice the part that said that the CellBuilder doesn't actually create any sections until you click on the "Continuous Create" button.
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Re: Why I cannot use the GUI

Postby yk890406 » Thu Nov 03, 2011 8:32 am

ted wrote:Then I am forced to conclude that you have not worked through the CellBuilder tutorials at
http://www.neuron.yale.edu/neuron/docs
or maybe you didn't notice the part that said that the CellBuilder doesn't actually create any sections until you click on the "Continuous Create" button.

Sure, I did not click on the "Continuous Create" button. Thank you!
Is there any way to shut down a single channel completely, such as increasing a single channel's Conductivity to infinite? I try to follow the NEURON's Channel Builder tutorials and change the gmax in Point Process Manager to infinite, but the current never change.
My plan is to simulate an abrupt interrupt when a signal passing through a neural cell. Is there any tutorals, models or articles I can follow?
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