On March 19th and 20th, the Center for Open Science hosted a small meeting in Charlottesville, VA, convened by COS and co-organized by Kaitlin Thaney (Mozilla Science Lab) and Titus Brown (UC Davis). People working across the open science ecosystem attended, including publishers, infrastructure non-profits, public policy experts, community builders …
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On a recent west coast speaking junket where I spoke at OSU, OHSU, and VanBUG (Brown PNW '15!), I put together a new talk that tried to connect our past work on scaling metagenome assembly with our future work on driving data sharing and data integration. As you can maybe …
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I'm returning from a small, excellent meeting on "Open Source, Open Science", held at the Center for Open Science in Charlottesville, VA. We'll post a brief meeting report soon, but I wanted to share my particular highlights --
First, I got a chance to really dig into what the Center for …
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Two weeks ago, I ran a workshop at UC Davis on mRNAseq analysis for semi-model organisms, which focused on building new gene models ab initio -- with a reference genome. This was a milestone for me - the first time I taught a workshop at UC Davis as a professor there! My …
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I've been putting together a streaming API for khmer that would let us use generators to do sequence analysis, and I'd be interested in thoughts on how to do it in a good Pythonic way.
Some background: a while back, Alex Jironkin asked us for high level APIs, which turned …
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A colleague who is starting their own computational lab just asked me for some advice on how to run software projects, and I wrote up the following. Comments welcome!
A brief summary of what we've converged on for our own needs is this:
everything's on github (you can have private …
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