We all know that biology (along with other sciences) is becoming ever more data intensive. Biologists (among other scientists) are not terribly well prepared for this, because of a lack of computational culture, lack of computational training, and a lack of tools. What do they need to know?
This question …
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(This blog post was mightily helped by Qingpeng Zhang, the first author of the paper; he wrote the pipeline. I just ran it a bunch :)
We have been benchmarking k-mer counters in a variety of ways, in preparation for an upcoming paper. As with the diginorm paper we are automating …
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Leslie Babonis, an attendee at the 2013 NGS course, posted the following on facebook. I'm reposting with permission. --titus
an ode to my lab bench...:
i've returned, my dear friend, after a fortnight away delighted to find you, in just the same way your tube racks still brilliant in hues …read more
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I just finished reading The Immortal Life of Henrietta Lacks, an excellent book about the HeLa cell line cultured from cancerous cells taken from Henrietta Lacks. In addition to raising some really interesting and astonishing questions about the appropriate (mis)use of patients' tissue samples, a section about George Gey …
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My advice to graduate students: blog! post garnered some interesting comments here and there. Most of the responses were positive, but then again, most anyone who reads blogs probably doesn't need to be convinced that blogging is useful. In particular, note that some of the comments at the bottom of …
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(with Adina Howe, James Tiedje, Titus Brown)
I have been working on the assembly of big shotgun metagenomic data from ARMO (Amazon Rain Forest Microbial Observatory) project. The biggest challenge is the huge data size, 2TB in fastq and more than 6 billions reads after read trimming. One lucky thing …
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Sometimes you've really got to wonder.
The Chronical of Higher Ed just posted this article on a collaboration between A. Sean Pue, Tracy K. Teal, and myself. It's about bringing bioinformatics (or, really, CS and computational linguistics) to the study of Urdu poetic meter.
The article has two interesting flaws …
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