Problems with Chapter 1 simulation

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2015shanbhvi

Problems with Chapter 1 simulation

Post by 2015shanbhvi » Fri Apr 22, 2016 9:37 pm

Has anyone else had trouble getting the first simulation in Chapter 1 to work using the NEURON GUI?
I followed the steps exactly, even entering the length and diameter of the for parts of the neuron.
Is there anything else that I need to keep in mind? Perhaps since the NEURON version is newer, there are some new parameters that need to be changed? Sorry, I am really new to this.
I've tried this several times. I would appreciate any tips. Thanks!

ted
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Re: Problems with Chapter 1 simulation

Post by ted » Fri Apr 22, 2016 10:55 pm

Exactly what symptom of failure are you encountering?

2015shanbhvi

Re: Problems with Chapter 1 simulation

Post by 2015shanbhvi » Sat Apr 23, 2016 11:17 am

There is no spike at all when I run the simulation.
I have placed the AlphaSynapse at the soma, and followed all the steps in the book, so I am thinking that I am missing some small parameter. I caught one mistake which was giving the length and diameter to each part of the cell. I added nseg but that didn't help either.
Thanks!

ted
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Re: Problems with Chapter 1 simulation

Post by ted » Sat Apr 23, 2016 7:07 pm

Suggest checking the following:
1. Does a model cell exist? At the oc> prompt execute the command
topology()
2. To what location on the cell is the IClamp attached? What are its parameters (delay, duration, amplitude)
3. Is Tstop correct?
4. Does the plot of soma v vs. time show anything at all? If there is no effective stimulus, v should remain constant during the simulation.
5. Is the specification of the model cell's properties correct? Check L, diam, nseg, and the biophysical properties of each section. At the oc> prompt execute the command
forall psection()

2015shanbhvi

Re: Problems with Chapter 1 simulation

Post by 2015shanbhvi » Sun Apr 24, 2016 1:03 pm

Thank you so much Ted!
It now works, although I am still confused as to why...
I entered the two commands that you suggested, which I found later in Chapter 6.3 (topology() and forall psection() )
I am now trying to narrow down what caused this to work.
The two aforementioned commands don't change any parameters, correct?
I think the graphs only show when I use Movie Run. Using Run Control and pressing Init Run only gives me a flat line.
Thanks again

ted
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Re: Problems with Chapter 1 simulation

Post by ted » Tue Apr 26, 2016 2:56 pm

2015shanbhvi wrote:the two commands that you suggested, which I found later in Chapter 6.3 (topology() and forall psection() )
Good that you looked those up. In the future try the the Programmers' Reference first--that will have the most up-to-date information.
The two aforementioned commands don't change any parameters, correct?
True.
I think the graphs only show when I use Movie Run. Using Run Control and pressing Init Run only gives me a flat line.
NEURONMainMenu/Graph/Voltage axis, Current axis, and State axis graphs all show dependent variables plotted vs. time and will update automatically during a simulation.

Space plots (dependent variable vs. distance along a path) and shape plots (dependent variable represented by color over the shape of a model cell) update only if you launch the simulation with the Movie Run tool, or control updating of those graphs with code similar to the example shown in the Programmers' Reference documentation of the Timer class--see
http://www.neuron.yale.edu/neuron/stati ... html#timer
This feature of NEURON's standard run system was introduced because shape plots and space plots take much more time to update than ordinary graphs do; it is often useful to be able to run a couple of quick simulations while adjusting parameters, then do a "movie run" while focusing on the spatiotemporal details revealed by shape or space plots. It's not described in the NEURON Book because it was introduced a few years after the book was published.

2015shanbhvi

Re: Problems with Chapter 1 simulation

Post by 2015shanbhvi » Fri May 27, 2016 5:56 pm

Ok thanks for your help Ted!

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