#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.
#Bioinformatics stuff
- maf2bed - A small rust command line tool to convert MAF to bedtabix, used along with mafviewer jbrowse plugin (2023)
- bam_index_visualizer - Visualize the structure of the binning index of BAI files (2023)
- secondary_rewriter - rust tool to add SEQ/QUAL tags to secondary alignments in BAM/CRAM (2022)
- vcfverifier - rust tool to check that a VCF matches an underlying FASTA reference genome using REF column (2022)
- sv blog post - My short guide about how SAM files store structural variant (SV) information (2022)
#Music players
- ytshuffle - An app to make a music library from multiple youtube channels (2023)
- fml9000- A music player made using Rust and GTK4 (2022)
#Awesome lists
I like to keep track of various awesome or odd or interesting things in these repos. Please add your favorites with PRs :)
- oddgenes - list of interesting genomics/bioinformatics trivia
- oddbiology - list of interesting more general biology/evolution trivia
- genomesignals - a list different types of 'signals' that exist in the genome
- awesome-jbrowse - list of jbrowse 1 instances
- awesome-jbrowse2 - list of jbrowse 2 instances
- technical-oddities - list of technical oddities
- awesome-genome-visualization - large list of genome visualization tools (681 github stars!)
- interesting gene names - list of gene names from different model organisms and what they stand for
#Setup
- dotfiles - My setup
#Coursera classes
- Experimental Genome Science, University of Pennsylvania 2013, statement of completion
- Computing for Data Analysis, John Hopkins 2013, statement of completion, with distinction
#Visual art/code sketches
- chaosbot80 - A twitter bot to post fractals (2022)
- sm u20 - A submarine inspired audio/visual page (2022)
- nightskies - An audio/visual webpage (2022)
- interaction shadow - An noise/visual webpage (2021)
- reclaimed space - A visual webpage (2021)
- spiralzone - A visual webpage (2021)
- logistic map fractal viewer using Rust/WASM/React (2020)
#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)
#Misc
- 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)
#Memorial
- myloveydove.com - A page for dixie code, using AWS lambda/S3 (2020)
#Gallery
mafviewer plugin for JBrowse 1 viewing multiple genome alignment of C. elegans
gwasviewer plugin for JBrowse 1
tumblrgraph showing the reblog graph
ontograph showing gene ontology terms
github_burndown chart showing the closing of issues over time
high resolution export of the logistic map fractal from logistic_chaos_map ( full res )
