I wrote the below in response to someone who e-mailed me about trying out our partitioning approach for metagenome assembly.
yes, the original partitioning approach worked only on low coverage data sets. The main reason is that highly connected regions (repeats, from biology; and some kinds of sequencing errors) are …
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A while back, Kai Blin (via Nick Loman) asked Michael Barton:
If we containerize all these things won't it just encourage worse software development practices; right now developers still need to consider someone other than themselves installing the software.
and Michael Barton's response, transcribed, was:
"It's a good point. Ultimately …read more
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We just finished the second day of a workshop on Docker at the Berkeley Institute for Data Science. I was invited to organize the workshop after some Berkeley folk couldn't make our Davis workshop in November, and so I trundled on down for two days to give it a try …
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Recently I was asked by someone at a funding organization about the term "hardening software"; I wrote a blog post asking others what they thought, and this got a number of great comments (as well as spurring Dan Katz to write a blog post of his own). I'd already written …
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I just received an e-mail from someone in the funding world who thinks a lot about software, and they were interested in any thoughts I might have on the term "software hardening", and its practice. To quote,
This is about making research software more robust, more easily usable and possibly …read more
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When I decided to move to UC Davis, I was also seizing the opportunity to dramatically expand my training efforts. At Davis, it was made clear to me that I could substitute skills training -- in whatever guise I chose -- for my for-credit teaching; in consequence, I'd asked for money for …
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On Friday, Emily Dolson, a doctoral student at Michigan State University in Charles Ofria's lab, walked a bunch of us through d3.js for data visualization. Crucially, she did this from Michigan, and in addition to a local classroom, taught three other classrooms -- one in Florida, one in Virginia, and …
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