An introductory tutorial for those looking to run persistent homology with Greg Henselman's Eirene software.
We'll be using data from https://world.openfoodfacts.org/ to practice running persistent homology.
To get set up for running the Day 1 tutorial, please add the following packages:
JLD
Plotly
Eirene
Combinatorics
SparseArrays
Plots
LightGraphs
GraphPlot
To install packages, either switch to the package handeler in julia with ']' and then type 'add PackageName' or load in the Pkg package handler with 'using Pkg' and then type 'Pkg.add("PackageName")' to add any package.
We'll use data from https://link.springer.com/article/10.1007/s10827-017-0672-6 to practice running persistent homology on actual brain data. These data are also available on the UPenn Complex Systems lab website.
Chad Giusti's topology in neuroscience webpage http://www.chadgiusti.com/bib.html
Barcodes: The persistent topology of data, Rob Ghrist
Roadmap for the computation of persistent homology, Nina Otter et al.
Eirene main page: https://github.com/Eetion/Eirene.jl
Importance of the whole: topological data analysis for the network neuroscientist, Sizemore et al.
Last updated 07.02.19