Jeremy Watson Graduate student in Computer Science


USB-C seems like such a great thing, then I read this. Now it seems like a high-risk/low-reward piece of technology, something that has the chance of making non-tech people, or really anyone who does not buy very carefully, frustrated in the extreme (and possibly out several thousand dollars of expensive equipment).

Seattle JW

De Bruijn graphs

Computational biology was my first interest related to computer science, so after taking a course in it I thought I'd try my hand at an implementation and visualization of a simple graph algorithm, the De Bruijn graph. Find it on the Algorithm Examples. It falls under the assembly category of algorithms, as scientists do not get full DNA sequences when using modern high throughput sequencing machines. Rather, they get small reads made up of anywhere from tens to thousands of base pairs, and must then align these reads together to create a single, whole genome.

The second part would be to implement something that converts reads in to a De Bruijn graph, rather than a simple sequence, and then finds a hamiltonian path in the graph. This more closely aligns to the actual problem of DNA assembly, but it isn't more interesting visually, and this was more an exercies in D3 and javascript.


First post

I'm expecting to keep this site pretty light, maybe showcase some photos or some code I've been working on. Social media links are in the sidebar, as are the permanent links to code. As of today I'm juggling a lot, so the site may be a bit haphazard for a while.

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