PH_tutorial

An introductory tutorial for those looking to run persistent homology with Greg Henselman's Eirene software.

Day 1 tutorial

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.

Day 2 tutorial

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.

Further reading and helpful links

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