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Exercises and lectures on NEURON and NetPyNE (Salvador and Bill) for Lascon 2020

Software sources

Contents of this repo:

Talk pdfs

  • Day1Talk-NeuralCircuits.pdf General introduction to computational neuroscience + examples of neural circuits

  • Day2Talk-HopBrody.pdf Building a Hopfield-Brody network in NEURON (this talk contains additional slides that we did not get to in the time period)

  • Day3Talk-netpyne.pdf Introduction to netpyne

  • Day4Talk-MPI.pdf HPC, MPI and ParallelContext

Code

test0.py simple test of mpi mpiexec -n 4 --oversubscribe nrniv -python -mpi test0.py

HopBrod.py

presented on Day 2,4 -- Hopfield-Brody network using INVL ArtificialCell or HH cell (with useHHCell=True)

uses IClamp for HH cell rate randomization

mpirun() to run under MPI (using HHcell only)

invlfire.mod

NMODL source file for INVL ArtificialCell used by HopBrod.py

HopBrodNetPyNE.py

shortened and simplified version of netpyne/doc/source/code/tut7.py
uses HH with NetStims for HH cell rate randomization

Additional Exercises

  • Accessing and making github repos

    get a github account from http://github.com

    set up a repo for your LASCON project

    access github repos for NetPyNE and NEURON