www.neuron.yale.edu

Awesome, thanks Robert! Do you think these could be moved to a "NEURON-tutorials" GitHub repo? Then I could git clone whatever was in there everytime I build my server for teaching, and also submit PRs if I see potential improvements. I could set it up and then transfer ownership if you'd ...

What is the status of this? I have students copying/pasting from https://neuron.yale.edu/neuron/static/d ... steps.html into Jupyter notebooks on our lab JupyterHub and it seems to work great. But just converting this directly to a notebook would be better. Has anyone done this?

I was using NEURON 7.5 so I don't think I had this functionality yet. It seems likely that I will be able to redirect stdout as needed entirely with Python calls in NEURON 7.6, since this commit https://github.com/neuronsimulator/nrn/commit/ef4da5dbf293580ee1bf86b3a94d3d2f80226f62 , which contains t...

When using NEURON from Python, I get lots of printed messages that I don't really want to see. If they originate from the NEURON python module, I am able to intercept them and redirect from stdout to another buffer that I can check later (if needed). But the ones coming from the C libraries I am hav...

If anyone gets here running NEURON with a miniconda installation, this is why it is happening and how to solve it: Your default gcc may be on the miniconda path (/path/to/miniconda/bin), and it will look in your miniconda path for libraries, too (/path/to/miniconda/lib). apt-get won't install the nc...

For simple NEURON scripts like the one in https://neuron.yale.edu/neuron/static/docs/neuronpython/firststeps.html , the instructions I gave seem to work, but for others I run into: dyld: Library not loaded: @rpath/libpython3.5m.dylib I can fix this with: sudo install_name_tool -change @rpath/libpyth...

I've created a minimal installation verified using Travis CI and tested against a simple example from the Neuron website.
https://github.com/rgerkin/neuron-python3-miniconda

Thanks, Ted. This is also probably a good idea since setting the PYTHONHOME environment variable, which I think NEURON needs for installation if not for execution, can screw up the version of python that it is not set to. Which means that in the example above Python2 can get screwed up and so best t...

Since the instructions on the webpage didn't work for me, I want to document here commands that allowed me to install NEURON 7.5 from source with Python 3 support on OSX 10.12.5. I hope this will be useful to someone. For simplicity, this installation excludes Interviews, MPI support, and everything...

On OSX (fresh installation of NEURON 7.5 but similar results with 7.4), but not on Linux, I observe the following problem with a python file LEMS_2007One_nrn.py (source here https://gist.github.com/rgerkin/e4867fbf22b455ca0f1517e9e2f88d2e ) import LEMS_2007One_nrn # runs fine however... def foo(): i...