Music Wheel

Programming · Art

Back in my day, the word “theory” meant something. So, in all my attempts to learn music theory, I was stymied by suggestions of memorizing seemingly unrelated collections of patterns, facts, and rediculous nomenclature. With dedication, books, wiki pages, and a good instructor (Ed Dee of Corvallis), though, I was able to make some progress. To help, I wrote a little program for exploring scales, notes, chords, and temperament.

NOTE: An updated, web-based version of this application is described at Interval.

Timelapse Thing

Programming · Art · Photography

TimelapseThing is a Python script that includes a number of tools for working with timelapse image series (in JPG format). It can be used to deflicker images (if some images in the series are mildy under- or over-exposed), merge a series of JPGs into a video, batch crop and resize, expand a series into a longer series, and lighten/darken/median merge using a sliding window approach (see below) for artistic effect and artifact removal (such as someone walking across your timelapse and getting caught in a frame). The heavy lifting is done using ImageMagick’s convert tool, and ffmpeg for video creation, so these tools are required.

Glass Beads

Art · Glass

Work in borosilicate glass, mostly done between 2011 and 2013 at the University of Notre Dame Glass Club.

Transcriptomics

February, 2013 · 207 words · 1 minute read

Research · Programming

Assessing the quality and completeness of transcriptome assemblies is a challenge. For this problem, we developed a measure of gene assembly known as the “ortholog hit ratio.” First we associate each assembled gene with its closest match in a related organism. Then we compare the length of the matching region to the total length of the related gene. (Comparing the length of only the matching region ignores untranslated regions on the ends that are not considered part of the gene.) When this ratio is near 1, the sequence is likely to be completely assembled. This measure has since been adopted by other research groups. (Paper.)

A Statistical Analysis of Nerf Blasters and Darts

Data · Nerf

By Shawn O’Neil and Katie Drueen.

Algorithmic Haplotyping

April, 2012 · 241 words · 2 minute read

Research · Theory · Programming

When working with sequencing datasets of ecological interest, an interesting problem is how to tease out the genetic diversity present in the population being sequenced. Usually, assembly software simply aligns the short read sequences, and determines the consensus sequence based on the majority vote of each position. However, we may wish to seperately assemble each haplotype (version) of each gene.

We formulate this as a graph problem, where short reads that overlap are considered nodes in a graph that share an edge if they should go in different haplotypes. We then need to minimally “color” the graph (assign a minimum number of colors to nodes such that connected nodes always get different colors, upper right). This normally NP-Hard problem is solvable in cubic time given the linear input data.