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Distributed and dynamical communication

Code for the paper "Distributed and dynamical communication: A mechanism for flexible cortico-cortical interactions and its functional roles in visual attention", Ni, S., Harris, B. & Gong, P., Commun Biol 7, 550 (2024)

Structure

analysis contains the functions and Python classes for data processing and analysis.
connection contains the functions and Python classes for generating spiking circuit model.
model contains the scripts for model simulation and data analysis.
model/spiking_circuit contains the scripts for the spiking circuit model. See the README.md in corresponding folders for instructions.
model/mathematical_model contains the scripts for the mathematical model.

  • The directories analysis and connection should be added to the PYTHONPATH environment variable so that Python can find these modules.

Required packages and software:

Python 3.7
Brian 2 (2.5) (https://brian2.readthedocs.io/en/stable/)
numpy
cython
scipy
pywavelets (https://pywavelets.readthedocs.io/en/latest/index.html)
scikit-learn
pylevy (https://github.com/josemiotto/pylevy)
JIDT (https://github.com/jlizier/jidt)
JPype
matplotlib
Matlab 2019b
MATLAB Engine API for Python (https://www.mathworks.com/help/matlab/matlab_external/install-the-matlab-engine-for-python.html)