jaxley-mech

A Jaxley-based library of ion channels and synapses for biophysical neuron models.

Installation

jaxley-mech is available on PyPI:

pip install jaxley-mech

or you can clone the repository and install it via pip's "editable" mode:

git clone git@github.com:jaxleyverse/jaxley-mech.git
pip install -e jaxley-mech

Usage

See the notebooks folder for usage examples.

First author last names and year abbreviations for the papers in which mechanism models are first described are used as the file names in cases where more than one mechanism is included or multiple implementations exist. For single mechanisms, e.g. the ribbon synapse model, the file is simply named ribbon.py.

To view available mechanisms and filter them by species, cell type, reference, etc., it is possible to run the following code:

import jaxley_mech as jm
print(jm.find_channel()) # shows metadata of the available channels
print(jm.find_channel(ion="K", species="rat")) # shows metadata of channels with these properties

all_synapses = jm.find_synapse()
print(all_synapses.reference) # shows the references of all synapses