Modeling of opioids in the Pre-Bötzinger complex

This repository uses the Brian 2 neural simulator (Python) to run simulations perturbing Pre-Bötzinger complex neuronal networks and analyze the resulting data. Published as:

GM Chou, NE Bush, RS Phillips, NA Baertsch, KD Harris. Modeling effects of variable preBötzinger complex network topology and cellular properties on opioid-induced respiratory depression and recovery. In press, eNeuro.

Subdirectories and files

• brian_utils/ - Utility functions to be used for postprocessing and analysis
• data/ - .pkl files of each experiment, which contain population monitors and spike monitors (refer to Brian docs). Note: these files are not on GitHub due to storage constraints.
• simulations/ - Subdirectories for each type of simulation. Each contains simulation scripts, network and burst statistics, and exploratory analyses
• figure_notebooks/ - Jupyter notebooks for generating the figures in the manuscript
• harris_eqs_oprmv1_gnap.yaml - Contains Hodgkin-Huxley style equations to be parsed by the experiment scripts
• harris_ns_oprmv1.yaml - Contains constant parameters

Disclaimer

• The filepaths specified in each script pertain to the WWU Computer Science Linux systems. To run our code on a different machine, you will need to modify filepaths and ensure that all the necessary packages are installed.