/songburst

Package to construct network models of songbird nucleus HVC

Primary LanguagePythonMIT LicenseMIT

songburst

Package to construct models of songbird nucleus HVC

files

  1. neurons.py - basic package containing functions to generate post-synaptic currents, action potentials, implement LIF neurons etc.
  2. izneurons.py - package describing Izhikevich neurons and containing functions to evolve a single or a network of IZ neurons in time
  3. hvc.py - functions for implementing HVC neurons
  4. conductance.py - functions for analysing conductance model simulations
  5. networks.py - functions for simulating large networks of Izhikevich neurons
  6. poly.py - functions for constructing and evolving polychronous chains of neurons

Installing virtual environment

  1. Clone repo, navigate into folder
  2. If you don't already have poetry, install poetry. You may need to close command window and open a new one.
  3. Create conda environment: conda env create -f environment.yml
  4. Activate environment: conda activate songburst
  5. Make sure you are in the top folder of the cloned repo, then install dependencies: poetry install
  6. Setup the new environment as an ipython kernel: conda install -c anaconda ipykernel then python -m ipykernel install --user --name=songburst