Vince Buffalo – Vince Buffalo

Disclosure: camdl is an open-source project I am developing at the Institute for Disease Modeling (Gates Foundation).

The Great Obsession of population geneticists, to borrow John Gillespie’s words, is genetic variation.

The last chapter of my dissertation with Graham Coop was recently published in PNAS (pdf , bioRxiv ) last week.

The last chapter of my dissertation with Graham Coop was recently published in PNAS (pdf , bioRxiv ) last week.

Heraldic snake from Flickr (CC Licensed).

An example of a present-day female's X material being broken up across her X ancestors in her X genealogy back through the generations.

I had a matrix (88662 loci x 2060 genotypes) of maize chromosome 1 genotypes, encoded as 0, 1, 2 (e.g. the number of alternate alleles).

I needed to work with the MD tag in BAM/SAM files for a recent project.

It’s hard not to fall in love with Unix as a bioinformatician.

Day to day bioinformatics involves interfacing and executing many programs to process data.

Note: I’ve been writing this essay in my head for a few months, but I felt it needed to be completed and released after the sad loss of Open Access advocate Aaron Swartz , a hacker and activist I admired. 21st Century Science and the Need for Open Data and

Scientists are learning programming at an unprecedented rate.

Simple Parallel Bioinformatics Pipelines with find, basename, and xargs Big-Ass Servers and Data Parallelism A routine operation in bioinformatics is to process a lot of files on a so-called “Big-Ass Server” .

Bioconductor is one of the open source projects of which I am most fond.

Git Notes These are updated by me periodically.

In talking with bioinformaticians, biologists, and other researchers, I’ve seen some worrying trends in computation in the sciences.

Hello, Julia Julia is an exciting new technical computing language.

In between refactoring some qrqc code this morning and looking at RNA-seq data, I grabbed some cold brew coffee and caught up on some missed tweets.

Recently a coworker showed me a FASTQ file from an Illumina HiSeq run (which will be packaged in the new release of my Bioconductor package qrqc ) that was severely contaminated.

Please developers, don’t be dicks.