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

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)

ytshuffle - An app to make a music library from multiple youtube channels (2023)
fml9000 - A music player made using Rust and GTK4 (2022)

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

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

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)

github burndown - A shiny app to plot "burndown" style statistics on github issues, also has CLI https://github.com/cmdcolin/github_burndown (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)

myloveydove.com - A serverless photo gallery for dixie code, using AWS lambda/S3 (2020)

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

gwasviewer plugin for JBrowse 1

github_burndown chart showing the closing of issues over time

high resolution export of the logistic map fractal from logistic_chaos_map (full res)