- Project Leadership
- I've led multiple concurrent and successful small-team projects. I love working with customers to learn what they need, get the most out of their budget, and end with everyone happy.
- Software Practice
- I'm a big fan of developer responsibility, steady improvement, and sustainable codebases.
- Languages / Environments
2014 - present
Principal Software Engineer & Software Project Lead in High Performance Computing and Data Storage.
New gig! Looking forward to their fun challenges.
2005 - 2014
Principal Software Engineer in Analysis and Annotation Engineering in the Genome Sequencing and Analysis Program
(prev: Senior Software Engineer, Software Engineer)
Led design and development of Olive, a high-volume, low-cost web publishing platform for genomic data. It's simple, beautiful, and ridiculously automated and interconnected. Gathered requirements, designed the architecture, adjusted to changes in resources, participated in implementation. Published thousands of genomes in hundreds of projects, versioned correctly and packaged for general use.
Worked on a production Java/Jython pipeline that facilitated both manual and automated genome annotation and publication. This involved intricate applications with rapidly changing heuristic analyses, reading and writing arcane bioinformatics file formats, web design, automating the software whose execution case takes five pages to explain, database tuning — all using a big server farm. The system went from annotating and publishing four genomes per year to five thousand a year, with better quality and consistency. My work directly helped make that transition possible.
I worked directly with our geneticists customers in subjects from analysis to system budgets. I had friendly, productive relationships with people from vastly diverse backgrounds, each of whom was very, very smart and know where they want to be — but not how to get there with software. My job was not just to listen to what they say they wanted, but learning the nature of the goal and understanding what they needed. This was one of my favorite parts of that job.
The Broad Institute is a hotshot research lab, so it's hard to nail down departments. Teams, initiatives, and organizations are fluid. It's easier to describe the work I've been involved in:
- Genomic Sequencing Center for Infectious Diseases.
- Fungal Genome Initiative
- Human Microbiome Project
- Sequencing and annotation effort in response to the recent European E. coli outbreak
My software has assisted in annotating and publishing many horrible infectious diseases, including tuberculosis, malaria, influenza, the dengue virus, tuberculosis, Staphylococcus Aureus (of staph infection fame), HIV, and many more. Of course, I'm just working on their source code.
From my work in gene annotation (and naming), I've been published as a contributing author in a few journals, the most recent being in Nature magazine: "A framework for human microbiome research" and Science magazine: "A Catalog of Reference Genomes from the Human Microbiome", where I was part of the small army of people who worked on the Human Microbiome Project. I've also presented genomics work at the AGBT and Cold Spring Harbor Labs bioinformatics conferences. For better or worse, I'm also listed as part-author on more than twenty million genes.
The automated classification and tagging of coding DNA is challenging — I wrote Genepidgin, an open-source suite of Python tools to help with gene naming.
1998 - 2002
Software Group Leader
I worked in the tools and test group, eventually becoming a technical and project lead. The project's goal was to cause the company's shipping products to fail locally rather than during the on-site company installs. My proudest point in this group was to lead the development of the large, multiple-developer, readable Perl application which was used and extended by software testers who were not software engineers.
Our group was distributed across two major locations, and we had frequent collaborations with developers and testers around the world. I learned how to work and lead remotely.
2002 - 2005
Chief Software Pack Mule
I was a self-employed contractor who played backup infield for a few software projects. Every contract I worked on began thus: "This is behind schedule and we need to get something done." This wasn't the most interesting work I've ever done, but the lack of steady income was exciting.
1996 - 1998
M.E. / S.E
Began as a mechanical engineer, where I made sure that the given parts in radar and missile systems wouldn't corrode each other in surprising ways. I transitioned to being a software engineer, where I worked on a document repository system.
May of 2001: I received my MS in Computer Science from Worcester Polytechnic Institute. I enjoyed language design, trees, and parsing most of all. I went to school at night while I worked, and it took just short of five years.
May of 1996: I received my BS in Mechanical Engineering with a specialization in Material Science from Worcester Polytechnic Institute. I've largely forgotten the technical details, but I very clearly remember how the materials discovery process for every human implant seems to end in either a titanium alloy or polymethylmethacrylate.
My kids and family, books, software, games of all kinds, and fiction writing (not on this resume).
Available by request.