LFPy showcase

This Lab contains various examples on how LFPy (https://github.com/LFPy/LFPy, https://LFPy.rtfd.io) can be utilized in jupyter notebooks running on cloud infrastructure such as EBRAINS (https://wiki.ebrains.eu/bin/view/Collabs/), as well HPC infrastructure via EBRAINS and Unicore (https://www.unicore.eu/about-unicore/case-studies/the-human-brain-flagship/).

Collab URL:

https://wiki.ebrains.eu/bin/view/Collabs/lfpy-showcase

Using these files on EBRAINS:

We recommend choosing the kernel named EBRAINS_experimental_release, as this provides a virtual environment wherein LFPy and it's dependencies are already installed.

Installation of LFPy

In other environments where LFPy is not preinstalled such as Google Colab (https://colab.research.google.com), installation can be done by issuing in a notebook:

!pip install LFPy

After installation, the package can be imported as

import LFPy

The suite of unit tests can be executed by issuing

LFPy.run_tests()

Troubleshooting

In case a number of tests fail a likely cause is that NEURON NMODL (.mod) files were not compiled during installation because the NEURON-provided nrnivmodl script and other binaries was not in PATH. This issue may be fixed by restarting the kernel, updating PATH and reinstalling LFPy:

import os
import neuron
binpath = os.path.join(neuron.__path__[0].split('lib')[0], 'bin')
os.environ['PATH'] = f"{binpath}:{os.environ['PATH']}"

Followed by:

!pip install --upgrade --no-deps --force-reinstall --no-cache LFPy