Package: hybridLFPy
hybridLFPyPython module implementing a hybrid scheme for predictions of
extracellular potentials (local field potentials, LFPs) of spiking
neuron network simulations.Project StatusDevelopmentThe module hybridLFPy was mainly developed in the Computational Neuroscience
Group (http://compneuro.umb.no), Department of Mathemathical Sciences and
Technology (http://www.nmbu.no/imt), at the Norwegian University of Life
Sciences (http://www.nmbu.no), Aas, Norway, in collaboration with Institute of
Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6),
Juelich Research Centre and JARA, Juelich, Germany
(http://www.fz-juelich.de/inm/inm-6/EN/).CitationShould you findhybridLFPyuseful for your research, please cite the
following paper:Espen Hagen, David Dahmen, Maria L. Stavrinou, Henrik Lindén, Tom Tetzlaff,
Sacha J. van Albada, Sonja Grün, Markus Diesmann, Gaute T. Einevoll;
Hybrid Scheme for Modeling Local Field Potentials from Point-Neuron Networks,
Cerebral Cortex, Volume 26, Issue 12, 1 December 2016, Pages 4461–4496,
https://doi.org/10.1093/cercor/bhw237Bibtex source:@article{doi:10.1093/cercor/bhw237,
author = {Hagen, Espen and Dahmen, David and Stavrinou, Maria L. and Lindén,
  Henrik and Tetzlaff, Tom and van Albada, Sacha J. and Grün, Sonja and
  Diesmann, Markus and Einevoll, Gaute T.},
title = {Hybrid Scheme for Modeling Local Field Potentials from
  Point-Neuron Networks},
journal = {Cerebral Cortex},
volume = {26},
number = {12},
pages = {4461-4496},
year = {2016},
doi = {10.1093/cercor/bhw237},
URL = { + http://dx.doi.org/10.1093/cercor/bhw237},
eprint = {/oup/backfile/content_public/journal/cercor/26/12/10.1093_cercor_bhw237/2/bhw237.pdf}
}LicenseThis software is released under the General Public License (see theLICENSEfile).WarrantyThis software comes without any form of warranty.InstallationFirst download all thehybridLFPysource files usinggit(http://git-scm.com). Open a terminal window and type:cd $HOME/where/to/put/hybridLFPy
git clone https://github.com/INM-6/hybridLFPy.gitTo usehybridLFPyfrom any working folder without copying files, run:(sudo) pip install -e . (--user)Installing it is also possible, but not recommended as things might change with
future pulls from the repository:(sudo) pip install . (--user)examples folderSome example script(s) on how to use this moduledocs folderSource files for autogenerated documentation usingSphinx(https://www.sphinx-doc.org).To compile documentation source files in this directory using sphinx, use:sphinx-build -b html docs documentationDockerfileThe providedDockerfileprovides a Docker container recipe forx86_64hosts
with all dependencies required to run simulation files provided inexamples.
To build and run the container locally, get Docker fromhttps://www.docker.comand issue the following (replace<image-name>with a name of your choosing):docker build -t <image-name> -< Dockerfile
docker run -it -p 5000:5000 <image-name>:latestThe--mountoption can be used to mount a folder on the host to a target
folder as:docker run --mount type=bind,source="$(pwd)",target=/opt/hybridLFPy \
-it -p 5000:5000 <image-name>Then, code examples may be run as:cd /opt/hybridLFPy/examples
nrnivmodl  # compile local .mod (NMODL) files
mpirun --allow-run-as-root python3 example_brunel.pyOnline documentationThe sphinx-generated html documentation can be accessed athttps://hybridLFPy.readthedocs.io