Misc scribbles

Work

I have worked on a variety of bioinformatics applications including model organism databases, genome browsers, and data analysis pipelines. See my google scholar for publications. Our jbrowse 2 paper was recently published which I was proud to be first author of.

Awesome lists

I like to keep track of various awesome or odd or interesting things in these repos. Please add your favorites with PRs :)

Bioinformatics tools

  • secondary_rewriter - Adds SEQ/QUAL tags to secondary alignments in BAM/CRAM, written while learning Rust (2022)
  • vcfverifier - Checks that the REF field in VCF matches an underlying FASTA reference genome, written while learning Rust (2022)

Utilities

  • fml9000- A music player made using Rust and GTK4 (2022)

Visual art/code sketches

Memorial

Small projects

  • github burndown a shiny app to plot "burndown" style statistics on github issues (2021)
  • githubgraphjs visualize your Github Actions build times (2020)
  • travigraphjs visualize your travis-CI build times (2019)
  • tumblrgraph visualize tumblr reblogs with cytoscapejs (2017)
  • resort visualize sorting algorithms (2017)
  • ontograph visualize ontology (OBO) files (2016)

Setup

  • dotfiles - also has various other details on my setup

Games

  • gratiotquest multi-player websocket RPG where you are a pheasant running around a MS Paint world (2018)
  • slap happy retrofitted a arcade cabinet with a raspberry pi (2018)

Coursera classes

MAFViewer plugin for JBrowse 1 viewing multiple genome alignment of C. elegans

GWASViewer for JBrowse 1

Tumblrgraph showing the reblog graph

Ontograph showing gene ontology terms

Github burndown chart showing the closing of issues over time

A high-resolution export of the logistic map fractal from my logistic_chaos_map renderer (full res)