Projects

2025-11-06

Note

This page mostly highlights funny side-projects that I do in my spare time as opposed to my work main work efforts

See my google scholar for publications

Simple bioinformatics tools

• 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 odd or interesting things or tool collections. Add your own to these lists!

• 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 dotfiles
• mysetup.nvim - My neovim setup

Coursera classes

• Experimental Genome Science, University of Pennsylvania 2013, statement of completion
• Computing for Data Analysis, Johns Hopkins 2013, statement of completion, with distinction

Visual art/code sketches

• chaosbot80 - A twitter bot to post fractals (2022)
• logistic map fractal viewer using Rust/WASM/React (2020)

Games/silly

• guygrrcounter - A raspberry pi device with a microphone that detects when someone says GRRRR nearby. also prints out daily star trek facts (2023)
• 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)

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 )