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I have 2 questions: How can I start RunControl panel from Python to avoid clicking each time on Tools->RunControl. Is it possible? How can I change size of the PlotShape window? I tried this: ps = h.PlotShape(True) ps.view(0,0,0,0,0,0,800,800) ps.show(0) But I'm not quite sure what view() params mea...

When I look closely to the NEURON Python I found package called gui2 which seems to work with JavaScript and HTML: https://github.com/neuronsimulator/nrn/tree/e5b6aa8bb504ec9c71c86b9abd49c3de3f98729e/share/lib/python/neuron/gui2 I also noticed that you have some Notebook tutorial which utilise the n...

It works straight forward. Thanks!

I would like to monitor "cai" variable across shape plot. After I execute this code it shows correctly what I want to monitor, except that it wont update with each steps: ps = h.PlotShape(True) ps.variable('cai') ps.scale(0, 0.01) ps.show(0) ps.exec_menu('Shape Plot') When I specify the sa...

Thanks for your help and comments, they are very valuable to me. I started with RxD and it works nice but I have 4 follow-up questions and one comment. Questions: if you don't specify geometry for the Region - it assumes the whole compartment's segment as a "single shell"? If I do specify ...

OK, so I would like to model Ca2+ radial diffusion from the top of the head of the dendritic spine -> through the neck -> to the dendrite (and in the dendrite radially and axially - as well, so Ca2+ may diffuse to the next spine). Basically I would like to model a whole-cell Ca2+ diffusion. EDIT: I ...

Hi, I want to use compartment's params (diam, L) inside my MODL mechanism "mymodl": NEURON { SUFFIX mymodl } UNITS { (um) = (micron) } ASSIGNED { diam (um) L (um) } STATE { my_diam (um) my_L (um) } BREAKPOINT { my_diam = diam my_L = L } hoc file looks like that: load_file("nrngui.hoc&...

You're right. After I carefully studied chapters 3 and 9 I got it. For those who may have similar questions - please read first: Compartment size in the section on Chemical reactions in Chapter 3 and then get back to the Chapter 9 . As to answer my questions (if anyone has similar problems): 1/4. CO...

From the Neuron Book, chapter 9. Ca2+ shells diffusion is defined as follows: KINETIC state { COMPARTMENT i, diam*diam*vol[ i ] {ca CaBuffer Buffer} } How does the COMPARTMENT statement work? Why there is diam^2? What is its relation to the volume? if shell_volume=diam*diam*vol[ i ] -> does the rate...

Thanks, indeed readline did the trick.

If anyone has the same problem in the future - this answer may help: https://askubuntu.com/questions/194523/ ... u-readline

Thanks for help. Unfortunatelly there is an error while I make nrnivmodl "/usr/local/nrn/share/nrn/libtool" --tag=CC --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath "/usr/local/nrn/x86_64/lib" cadif.lo mod_func.lo -L"/usr/local/nrn/x86_64/lib" -lnrnoc -loc -lmema...

Hi there, Is there any easy way to implement in NEURON a Calcium diffusion with shells similar in concept to the figure 6.8 from the Principles of Computational Modelling in Neuroscience, Sterrat et al. : https://drive.google.com/file/d/13YeDmGO26dwu-T63HEbbae_K6BQPVVdB/view (image) I would be very ...

Well obviously I did it after a fresh installation of NEURON Python couldn't find the neuron library, that's the problem. I use Anaconda, but it shouldn't be an issue. After I downloaded the source code from the github, compile it and then install nrnpython by hand - it finally started to work :) Bu...

Thank's for quick answer, but is there any supported way to use NEURON with Python? Well, at least according to this simple QuickStart: https://www.neuron.yale.edu/ftp/neuron/2019umn/neuron-quickstart.pdf after a fresh NEURON installation Python libs should just work, but not for me since I have: >>...

Hi there, I Try to install neuron for Python on Ubuntu 16.04 and Python 3.6 with command: pip install neuron but I received this error: Only Windows and 64-bit Linux currently supported by PyNEURON The error is strange since I have 64-bit Ubuntu. Then I tried with: pip install pyneuron and now the e...