spontaneous gamma dynamics with a damped harmonic oscillator driven by noise

this is a repository for the paper:
"Spontaneous variability in gamma dynamics described by a damped harmonic oscillator driven by noise"
G Spyropoulos, M Saponati, JR Dowdall, ML Schölvinck, CA Bosman, B Lima, A Peter, I Onorato, J Klon-Lipok, R Roese, S Neuenschwander, W Singer, P Fries, M Vinck
(2022, Nature Communications) https://www.nature.com/articles/s41467-022-29674-x

dependencies

all the simulations use [Python 3.8]. The scripts require [numpy] and [matplotlib].

usage

the project has a pip-installable package. How to set it up:

• git clone the repository
• pip install -e .

structure

the modules of the package are in utils/.

• main
  (default args as in the paper, optional args: beta1, beta2, total number of timesteps time, the four elements of the affine transformation matrix A listed as a1,a2,a3,a4)
  python main {} {} {} {} {} {} {}
  
  outputs:
  results/num_solution_ar.npy: numerical solution of AR(2) model
  results/num_solution_ei.npy: numerical solution of (E,I) system obtained with the affine transformation

• scripts to replicate the results shown in the related figure:
  python suppfig_1 (optional arg: affine matrix A)
  python suppfig_2 (optional args: beta1, beta2, number of timesteps time, affine matrix A)
  python suppfig_3 (optional args: (optional args: beta1, beta2, number of timesteps time, affine matrix A)
  
  The plots are located in /plots

citation and credits

Spyropoulos, G., Saponati, M., Dowdall, J. R., Schölvinck, M. L., Bosman, C. A., Lima, B., ... & Vinck, M. (2022). Spontaneous variability in gamma dynamics described by a damped harmonic oscillator driven by noise. Nature communications, 13(1), 1-18.

@article{spyropoulos2022spontaneous,
  title={Spontaneous variability in gamma dynamics described by a damped harmonic oscillator driven by noise},
  author={Spyropoulos, Georgios and Saponati, Matteo and Dowdall, Jarrod Robert and Sch{\"o}lvinck, Marieke Louise and Bosman, Conrado Arturo and Lima, Bruss and Peter, Alina and Onorato, Irene and Klon-Lipok, Johanna and Roese, Rasmus and others},
  journal={Nature communications},
  volume={13},
  number={1},
  pages={1--18},
  year={2022},
  publisher={Nature Publishing Group}
}