Preface from Titus: this is an e-mail written by Deniz Kural of Seven Bridges Genomics in response to concerns and accusations about their patents and patent applications on genomics workflow engines and graph genome analysis techniques. It was sent to a closed list initially, and I asked Deniz if we …
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Over the last few months, I've been playing with hypothes.is and thinking about how to use it to further my scientific work. This resulted in some brainstorming with Jon Udell and Maryann Martone about, well, lots of things. And now we're putting in an open science prize entry!
tl …
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If you haven't seen mybinder.org, you should go check it out. It's a site that runs IPython/Jupyter Notebooks from GitHub for free, and I think it's a solution to publishing reproducible computational work.
For a really basic example, take a look at my demo Software Carpentry lesson. Clicking …
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CORRECTION: I mistakenly linked to Geoff Bilder, Jennifer Lin, and Cameron's piece on infrastructure in the first posted version, rather than Cameron's post on culture in data sharing. Both are worth reading but the latter is more relevant to this post, and I also wanted to make sure I correctly …
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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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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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