At PyCon 2012, I took a tutorial on the IPython Notebook, which I'd already been using for a month or two (ever since Wes McKinney (the author of pandas) introduced me to it). The tutorial blew me away -- these guys have done a great job with the notebook so far …
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If you're like me, we pretend to care about the science in bioinformatics software. But what we really do is try to find reasons not to outright loathe the software -- because, lud knows, there are usually plenty of reasons to hate it.
In no particular order, here are the top …
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(updated to point to http://arxiv.org/).
Authors: Jason Pell, Arend Hintze, Rosangela Canino-Koning, Adina Howe, James M. Tiedje, C. Titus Brown
Abstract:
The memory requirements for de novo assembly of short-read shotgun sequencing data from complex microbial populations are an increasingly large practical barrier to environmental studies. Here we …read more
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I'm writing this on my way back from Stockholm, where I attended a workshop on the 4th Paradigm. This is the idea (so named by Jim Gray, I gather?) that data-intensive science is a distinct paradigm from the first three paradigms of scientific investigation -- theory, experiment, and simulation. I was …
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(and some related thoughts on reproducibility in computational science)
In a recent news article on the "data deluge" in biology, I was quoted as saying "It's not at all clear what you do with that data. Doing a comprehensive analysis of it is essentially impossible at the moment." So, naturally …
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This blog post was inspired by two recent events.
First, in response to a NY Times article about the "data deluge" affecting biologists, one of my Facebook friends said something like "stop whining about how hard it is to analyze the data and do some good experiments instead!" I vehemently …
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