A Two-Neuron Chain

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ted
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Post by ted » Thu Jun 07, 2007 10:59 pm

Have you worked through the Network Builder tutorial at
http://www.neuron.yale.edu/neuron/docs
?

Actually you don't really need to add an axon--a single compartment model
with the HH mechanism would be sufficient.

ted
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Post by ted » Tue Jun 12, 2007 4:22 pm

This is a bit tricky when the target is a synapse on a biophysical model cell.

1. Click on the
Src -> Tar
button.

2. Click on the source cell, and while holding the mouse button down, drag the cursor over
to the target cell. If it is an artificial spiking cell, you should be able to release the mouse
button and a connection should remain.\

If it is a biophysical model cell, an expanded stick figure cartoon of the cell will appear on
the canvas, with target synapses indicated by labels and dots. Still holding the mouse
button down, drag the cursor over to the label (not the dot) of the target synapse that you
want. Now release the mouse button, and the connection should remain. For an example,
see the first two figures on this page:
http://www.neuron.yale.edu/neuron/stati ... .html#arch

ted
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Re: A Two-Neuron Chain

Post by ted » Sun Jul 01, 2007 7:49 pm

JoeA wrote:succeeded in making the connection, creating things, and making an AlphaSynapse for starting. The Voltage axis Graph gives me the action potential in soma0.
Excellent. A suggestion for future development: rather than an AlphaSynapse,
use a NetStim artificial spiking cell and a NetCon to deliver events to a
synaptic mechanism. This strategy makes it possible to apply arbitrary
temporal patterns of synaptic activation as input to a net.
The problem is, I can't get a plot for the Vm in soma1. In NetGUI[0] I chose a big Weight of 2, and clicked "NetVariables/Show Map". The Name window that popped up said that the real name of soma1 is soma_soma[1].
So the cell class is known to hoc as soma_soma. Specific instances of this
cell class will have hoc names soma_soma where i is an automatically-
generated "index" that distinguishes between individual instance of the same
class. The name of a section will be in the format
specificinstancename.sectionname
i.e. for your net it should be
soma_soma[1].soma
and any range variable that belongs to this section will be called
soma_soma[1].soma.rangevarname(range)
where 0 <= range <= 1 specifies the location along the length of soma
at which you want to know the value of rangevarname. Membrane potential
is called v,
so the fully qualified name for membrane potential at the middle of the
soma of your cell is
soma_soma[1].soma.v(0.5)
I right-clicked in the graph of a second graph from Graph/Voltage axis to get a "Plot what?" window, and typed soma_soma[1] in the field below "Enter symbol name:" I clicked Accept (nothing appeared to happen there).

Well, now you know the complete name to enter.
But you could also get Plot what? to construct that by clicking on its Show
button,
scrolling down to select Objects,
scrolling through the list in the left panel to find and select
soma_soma
then clicking on the 1 in the middle panel,
clicking on the name of the section (I think this appears in the
middle panel of Plot what? but the battery on this laptop is running down
and there's no outlet to recharge, so you'll have to discover for yourself),
and finally in the right panel clicking on v.
You may also have to manually edit the value of range that appears in the
paired parentheses--often it's something other than what one wants.

You're almost there, man. Keep at it!

blackaura11

Re: A Two-Neuron Chain

Post by blackaura11 » Sat Aug 27, 2011 1:17 pm

Hi,

I'm just getting to know NEURON so would it be possible to send that word file you have made to me??


Thank you,

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