To begin

Hi

I’m Erik.

I am proud to be from the warm-hearted Commonwealth of Kentucky.

I grew up in the state’s tiny capital city, Frankfort. A childhood of exposure to government and psychology primed me to study society, which I did when I went to college. But I began to follow an unusual path. A persistent curiosity about computing led me to take a handful of computer science courses. I stated to write programs to enable my social science research. I installed Linux on my laptop and started learning everything I could about open source software. My thesis (since lost ಥل͟ಥ) focused on peer production in Wikipedia, reddit , and Linux and the ways that the pattern of communication that a technology enables affect the societies that use it.

After graduating I worked on an assortment of research projects as a contractor, programming with open source tools and writing free software.

The gig that caught my mind on fire was an idealistic but ill-fated attempt to bring the Polony sequencer to market as a the first fully open source DNA sequencing platform. After another job embedded in free software (at One Laptop Per Child), I found myself unemployed, making music and looking for a nice job. With a friend’s help I found my way back into biology, with a job focused on building computational techniques for handling sequencing data.

I still work in genomics. It has been an amazing experience to be part of front lines in the effort to observe the universe of DNA that defines life on our small planet. In these years the cost of observing DNA has fallen precipitously, and we have really extended our understanding of the biology of the world and ourselves. To a serious bio nerd, he only thing more cool than this is what happens next, as the need to make and refine microscopes wanes and we begin to focus ourselves on creating and changing things using the knowledge that genomics makes easy to come to.

I find it strange that I never really had a blog. I have been addicted to the internet since the web was unleashed on Prodigy in 1994. I spent years living with active bloggers and going to iron blogger parties they threw. I’ve run my own could host for ages. All that should matter, but until now I’ve not had much that I needed to explain that couldn’t be expressed in code and through direct communication.

This is changing. Today I live in England as a PhD student, and a big part of why I am here is that I want to focus on writing. I am also beginning to work on larger projects, and as these start to become more diffuse I find I am spending lots of time explaining ideas by text and email. Sometimes this format is the right way to share a small, clean idea. With enough care, a string of posts can become a paper or a book. I’d like to work in the open as much as possible. As time allows, I’ll try to do that here.

What will I write about? Eventually, everything! But first, I have interests in science, art, and communication which writing can help focus and I hope to explore here. More importantly, there are a pile of ideas that I want to unpack from the last half decade of effort. I’ve worked on applying Bayesian filters to detecting and genotyping genomic variation (known as variant calling). I’m also proud to have been part of the just-completed 1000 Genomes Project. I committed the last year to developing technology that uses the results of that project as a reference system in further analysis: variation graphs. With these we feed our knowledge of genomic variation back into the thing we align new reads to, which stands to make a huge array of problems in observing DNA vanish. More on that soon!