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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We're running three half-day workshops for your remote viewing pleasure! All three will be live-streamed via YouTube (well, Hangouts on Air).
Today 2/17, at 9:15am PT, Tiffany Timbers (Simon Fraser U.) is going to be going through regular expressions in Python - see the workshop description.
On Friday, 2 …
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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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Today at 9:15am PT, Raniere Silva will be giving a lesson on advanced git usage, including bisect, branches, pull requests, and rebasing.
This lesson will be broadcast via YouTube as a Hangout on Air - if you're interested in watching it, we will post the link on the workshop page …
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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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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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