Adding Synapses (Excitatory and Inhibatory) - Staring Help

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nemomortus
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Joined: Fri Jan 08, 2016 11:05 pm

Adding Synapses (Excitatory and Inhibatory) - Staring Help

Post by nemomortus »

Hey guys,

I'm trying to understand how to add excitatory and inhibitory synapses to a simple cell and have been reading a lot of things online. I'm not really sure where to start, and I was wondering if anyone could point me in the right direction? I know in order to add these synapses, you have to use point processes and something about NetCon. Any help like tutorials or papers to read would be appreciated!
ted
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Re: Adding Synapses (Excitatory and Inhibatory) - Staring He

Post by ted »

Suggest you read chapter 9 of The NEURON Book. If you don't have the book, here's an early draft of that chapter
https://www.neuron.yale.edu/ftp/ted/boo ... xedref.pdf
You'll probably also find it interesting to read
Hines, M.L. and Carnevale, N.T.
Translating network models to parallel hardware in NEURON.
J. Neurosci. Methods 169:425-455, 2008
(preprint downloadable from http://www.neuron.yale.edu/neuron/nrnpubs)
and especially to examine the source code for the serial implementations of the ring and all-to-all network models (actual files are downloadable from https://senselab.med.yale.edu/modeldb/, but the printouts are included with the preprint).
nemomortus
Posts: 11
Joined: Fri Jan 08, 2016 11:05 pm

Re: Adding Synapses (Excitatory and Inhibatory) - Staring He

Post by nemomortus »

Thanks for your suggestion Ted! I have been reading and using the AlphaSynapse built in function in NEURON and was wondering a question. Can you put multiple AlphaSynapses in a cell model and have then both fire at different times?

I have used a simple model with soma, dend[2], and an axon. I placed AlphaSynapses on both dend, but when observing the output of the model, both AlphaSynapses does not seem to have an effect - only the last one placed does.

Here is the HOC code:

Code: Select all

load_file("nrngui.hoc")

ndend = 2

create soma, dend[ndend], axon
access soma

soma {
  nseg = 1
  diam = 18.8
  L = 18.8
  Ra = 123.0
  insert hh
  gnabar_hh = 0.25
  gl_hh = .0001666
  el_hh = -60.0
}

dend[0] {
    nseg = 5
    diam = 3.18
    L = 701.9
    Ra = 123
    insert pas
    g_pas = .0001666
    e_pas = -60.0
}

dend[1] {
    nseg = 5
    diam = 2.0
    L = 549.1
    Ra = 123
    insert pas
    g_pas = .0001666
    e_pas = -60.0
}

axon {
	nseg = 50
	diam = 10
	L = 20
	insert hh
}

// Connect things together
connect dend[0](0), soma(0)
connect dend[1](0), soma(1)
connect axon(1), 	soma(0)

dend[0] syn = new AlphaSynapse(0.5)	//places synapse near access point
syn.tau = 0.1				//ms
syn.onset = 100				//ms
syn.gmax = 150				//uohm
syn.e = 15					//mV

dend[1] syn = new AlphaSynapse(0.5)	//places synapse near access point
syn.tau = 0.1				//ms
syn.onset = 150				//ms
syn.gmax = 150				//uohm
syn.e = 15					//mV

tstop = 300

//======================= plot settings ============================
objref gV

gV = new Graph()
gV.size(0,tstop,-80,60)
graphList[0].append(gV)
gV.addvar("soma.v( 0.5 )", 2, 1, 0.8, 0.9, 2)

//----------------//
run()
Image
ted
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Re: Adding Synapses (Excitatory and Inhibatory) - Staring He

Post by ted »

First, a couple of questions.

When developing/debugging make run time short enough fo see the time course of interesting phenomena. Spikes and PSPs last only a few ms. What's the point of a 200 ms run time and waiting 100 ms to deliver an EPSP?

What is a good way to choose the value of nseg? Should nseg be even or odd?
nemomortus wrote:I placed AlphaSynapses on both dend, but when observing the output of the model, both AlphaSynapses does not seem to have an effect - only the last one placed does.

I didn't see a statement that declared syn to be an objref. Did I just miss that? A point process is an instance of an object class. Each point process needs to be referenced by its own objref. hoc treats each new name as a floating point variable unless the name is first declared to be an objref. Time to read the manual/book/one or more of the introductory article about NEURON--see the bibliography page at http://www.neuron.hale.edu. Also browse through the FAQ list--see link on the documentation page.
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