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Questions tagged [neuron-simulator]

NEURON simulator is a spiking neural network simulator developed in Yale University in collaboration with Human Brain Project.

NEURON simulator is a spiking neural network simulator developed in Yale University in collaboration with Human Brain Project. http://neuron.yale.edu/neuron/

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Allen Brain Institute - brain observatory example

I'm trying to follow the example of brain observatory ipython notebook. However, I became stuck loading the nwb file like below. from allensdk.core.brain_observatory_cache import BrainObservatoryCache boc =…
Hyunsu Lee
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Singularity behaviour: shell vs exec

So I'm trying to debug an error I got on an HPC setup I have access to. I won't go into details about the error since it's package specific and I'm pretty sure this is an environment variable kind of problem. That said the package is neuron, and if…
bidby
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Storing output from Python function necessary despite not using output

I am trying to understand why I must store the output of a Python function (regardless of the name of the variable I use, and regardless of whether I subsequently use that variable). I think this is more general to Python and not specifically to the…
CodeGuy
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Debugging NEURON MOD files?

What are some useful ways to debug NEURON simulator .MOD files? In other languages one can usually use print() statements to see the variable values. Is there something like a print() statement in .MOD files?
Justas
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Easy way to list NEURON section properties/information?

In NEURON simulator, is there an easier way to list properties of a section other than iterating over each property individually?
Justas
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How would I do tuple unpacking such that the returned variables are paired based on being the nearest neighbor in a 2-D grid?

I am exploring neural network simulations between these "neurons" that you see in the figure below. The difficulty I have is connecting each neuron to its nearest neighbor. I first figured that I could do it by tuple unpacking, but it has become…
KNutellaZ
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How to create a synapse in NEURON?

How can I create a synapse in the NEURON simulator using its Python interface? I would like to create 2 Sections and connect them with a synapse, but there aren't any functions for it on the Section API or in the Section docs: from neuron import…
Robin De Schepper
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Why does mounting the home directory in singularity container break a python import?

I've been building a singularity container to run some python code, and despite reading the singularity docs, I can't understand the errors/behavior. Firstly the container is Ubuntu18.04 bootstrapped from docker, ie, : Bootstrap: docker From:…
bidby
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Visual Studio 2019, Python and Neuron simulator

I have Visual Studio Community 2019 up and running. I am attempting to use Python with NEURON(7.2.536.15) package. I have the neuron package in my Python 3.7 (64 bit) environment. How do I load the neuron simulator into my Python Application? The…
Seti Net
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MAC NEURON-Python: Error A newer Command Line Tools release is available. Update them from Software Update in the App Store

When trying to install NEURON with Python support (eg. can run python -c "import neuron"), using instructions from the Human Brain Project portal website. After: brew install neuron I get the following (misleading) error: Error: A newer Command Line…
Justas
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NEURON python Graph() is blank

When using python interface for NEURON, when I create a g=h.Graph() object in python, with g.addvar(...) to plot a variable, clicking Init & Run results in an empty Graph:
Justas
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Show GUI when running nrniv?

How do you open the GUI when running NEURON simulator using the nrniv command?
Justas
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Opening .hoc files in neuron simulator + "not a mechanism" problem

I am trying to run a NEURON simulation via python. I got all the libraries in order and am able to run some simple simulations, but am experiencing some troubles with a more complicated code. If you have any idea how to help I will appreciate it…
Daniel Atad
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SyntaxError: Invalid Syntax without solution

It's my first request here, I hope you'll could help me. I try to explain this particular situation. Files that use are bases for launch a neuronal simulation and they were for Python 2. Using an Atom's plug-in, I fixed manually any Indent errors…
SimoneT
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On neuron No such file or directory?

I am using neuron, a simulation software on OS. However, when I open nrngui I see the following error. ls: /usr/local/bin/../lib/libpython*.dylib: No such file or directory :114: SyntaxWarning: "is not" with a literal. Did you mean…
Edward
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