#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.

#Small bioinformatics tools

• bam_index_visualizer - Visualize the structure of the binning index of BAI files (2023)
• 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)

#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
• genomesignals
• awesome-jbrowse and awesome-jbrowse2
• awesome-genome-visualization
• technical-oddities

#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

#Misc

See more stuff here

#Gallery

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 )