Letter of resignation

Dear <chairs>, I am resigning my Assistant Professor position at Michigan State University effective January 2nd, 2015. Sincerely, CTB. Anticipated FAQ: Why? I’m moving to UC Davis. Do you have an employment contract with UC Davis?? Nope. But I’m starting there in January, anyway. Or that’s the plan. And yes, that’s how this kind of thing happen. …

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RFC: The khmer project: what are we, and what are our goals?

As we think about the next few years of khmer development, it is helpful to explore what khmer is, and what our goals for khmer development are. This can provide guiding principles for development, refactoring, extension, funding requests, and collaborations. Comments solicited! Links: khmer github repo: https://github.com/ged-lab/khmer/ khmer docs: http://khmer.readthedocs.org/ Definition khmer is an open …

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How good is MEGAHIT?

A few weeks back, Nick Loman (via Manoj Samanta) brought MEGAHIT to our attention on Twitter. MEGAHIT promised “an ultra-fast single-node solution for large and complex metagenome assembly” and they provided a preprint and some open source software. This is a topic near and dear to my heart (see Pell et al., 2012 and Howe …

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Estimate whether your sequencing has saturated your sample to a given coverage

This recipe provides a time-efficient way to determine whether you’ve saturated your sequencing depth, i.e. how much new information is likely to arrive with your next set of sequencing reads. It does so by using digital normalization to generate a “collector’s curve” of information collection. Uses for this recipe include evaluating whether or not you …

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Being a release manager for khmer

We just released khmer v1.1, a minor version update from khmer v1.0.1 (minor version update:220 commits, 370 files changed. Cancel that — _I_ just released khmer, because I’m the release manager for v1.1! As part of an effort to find holes in our documentation, “surface” any problematic assumptions we’re making, and generally increase the bus factor of the khmer project, …

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Software Carpentry trains the trainers

tl;dr? The Software Carpentry train-the-trainers workshop in Toronto this past M-W was just fantastic. I can’t recommend it enough. A bit of background: Software Carpentry is a project to teach scientists to use computing more effectively. Started by Greg Wilson about 16 years ago, the project has progressed through many different moults, including attempts to …

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A first science fair

So my daughter just participated in her first science fair, at the age of 6. (“Conclusion: science can be fun! and sticky!”) Over dinner, my wife and I came up with some ideas for her next fair. She was having trouble dissolving sugar in ice water, so we suggested maybe something where we measured the …

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Imagine…

Links, software, thoughts — all solicited! Send ’em to me, t@idyll.org. — Imagine… a rolling 48 hour hackathon, internationally teleconferenced, on reproducing analyses in preprints and papers. Each room of contributors could hack on things collaboratively while awake, then pass it on to others in overlapping timezones and go to sleep. The next day, they …

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Announcing khmer 1.0

The khmer team is pleased to announce the release of khmer version 1.0. khmer is our software for working efficiently with fixed length DNA words, or k-mers, for research and work in computational biology. Links: khmer documentation PyPI link Announcement ChangeLog Citation handle khmer v1.0 is the culmination of about 9 months of development work …

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The Story Behind “Tackling soil diversity with the assembly of large, complex metagenomes”

I’m pleased to announce the publication of “Tackling soil diversity with the assembly of large, complex metagenomes”, by Adina Howe, Janet Jansson, Stephanie Malfatti, Susannah Tringe, James Tiedje, and myself. The paper is openly available on the PNAS Web site here (open access). External links: Joint Genome Institute press release GenomeWeb article MSU press release …

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Loligo pealeii (squid) data dump

A few months back, I announced the khmer protocols project, an effort to write down an explicit, open protocol for transcriptome and metagenome assembly. This project was started during the summer of 2013 at the Woods Hole Marine Biological Lab, in collaboration with Joshua Rosenthal. I’d met Josh at the CephSeq meeting the year before, …

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Using github for homeworks

This term, I’m once again teaching my upper-division CSE undergrad course in Web Dev here at MSU. For the second time, I’m requiring students to use github for their homework; unlike last year, I now understand pull requests and have integrated them into the process. How does it work, basically? The instructions for handing in …

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