cochlear_nucleus

A Python package implementing computational models of the globular bushy cells (GBCs) in the mammalian ventral cochlear nucleus. Phenomenological models of endbulbs of Held with with short term synaptic depressions are also included.

Usage

Look for examples in the examples directory (e.g. nrn_gbc_demo.py and nrn_gbc_demo_with_default_weights.py). Note that some examples require cochlea to be installed.

Installation

Install the dependencies:

• Python 2.7
• Numpy
• NEURON (with Python bindings): http://neuron.yale.edu/neuron/
• Brian: http://briansimulator.org/

Clone the git repo with:

git clone https://github.com/mrkrd/cochlear_nucleus.git
cd cochlear_nucleus

Compile NEURON's models:

make

or manually:

cd cochlear_nucleus/nrn && nrnivmodl
cd -

Install the package itself:

python setup.py develop --user

Citing

Rudnicki M. and Hemmert W. (2017). High entrainment constrains synaptic depression levels of an in vivo globular bushy cell model. Frontiers in Computational Neuroscience, Frontiers Media SA, 2017, 11, pp. 1-11. doi:10.3389/fncom.2017.00016 https://www.frontiersin.org/articles/10.3389/fncom.2017.00016/full

BibTeX entry:

@Article{Rudnicki2017,
  author    = {Marek Rudnicki and Werner Hemmert},
  title     = {High Entrainment Constrains Synaptic Depression Levels of an In vivo Globular Bushy Cell Model},
  journal   = {Frontiers in Computational Neuroscience},
  year      = {2017},
  volume    = {11},
  pages     = {1--11},
  month     = {mar},
  doi       = {10.3389/fncom.2017.00016},
  publisher = {Frontiers Media {SA}},
  url       = {https://www.frontiersin.org/articles/10.3389/fncom.2017.00016/full},
}

Acknowledgments

This work was supported by the German Research Foundation (DFG) within the Priority Program “Ultrafast and temporally precise information processing: normal and dysfunctional hearing” SPP 1608 (HE6713), the Technische Universität München within the funding programme Open Access Publishing, and the German Federal Ministry of Education and Research within the Munich Bernstein Center for Computational Neuroscience (reference number 01GQ1004B).

License

The project is licensed under the GNU General Public License v3 or later (GPLv3+).