readme.txt

This code package was developed to generate and analyze simulated neuronal networks in which AMPAR conductance, connection density, and presynaptic current input were modified to simulate cypin overexpression.
Software Requirements: Python3.7; MATLAB2018a or later
Note: The Python scripts rely on Brian2, which can be downloaded at https://brian2.readthedocs.io/en/stable/introduction/install.html.

It includes, in order of appearance:
1. cypinOverexpression.py
2. cypinOverexpressionIO.py
3. cypinOverexpressionMain.m
4. cypinOverexpressionSpikeAnalysis.m
5. cypinOverexpressionNetworkAnalysis.m
6. cypinOverexpressionIOSpikeAnalysis.m
7. cypinOverexpressionIONetworkAnalysis.m
8. ISI.m
9. fanoFactor.m
10.INSI.m
11.functionalConnectivityMatrix.m
12.networkAnalysis.m
13.efficiency_wei.m
14.community_louvain.m
15.firingRatesIO.m 

The only files that need to be executed by the user are Files 1-3. Files 1&2 run the simulation and File 3 analyzes the simulations -- the rest are subfunctions.

This code can be accessed at https://www.seas.upenn.edu/~molneuro/

It was developed by Erin D. Anderson and Nicholas F. Vigilante. For questions, contact E. Anderson at anderin@seas.upenn.edu

Citation:
Rodriguez, et al., Cytosolic PSD-95 Interactor Regulates AMPA Receptor Signaling Independent of PSD-95 Binding. Network Neurosci, 2020.