Erica Check Hayden at Nature News wrote this article about a Mozilla Science Lab effort to bring code review to scientific code. Code review is an important part of many open source, startup, and corporate software development cultures, and the goal of the Mozilla effort is to See What Happens …
read moreThere are comments.
Question: What do Nick Loman, Jared Simpson, Lex Nederbragt, and I all have in common?
Answer: We all spend way too much time thinking about assembly.
Question: What does Jonathan Eisen's lab do?
Answer: Sequence lots of really weird things that they'd like to assemble.
Motivated by …
There are comments.
We've just posted a new paper to arXiv: "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure." We'll be submitting it to PLoS One after we wait a few days for comments from the Twittersphere and/or on Haldane's Sieve.
The …
read moreThere are comments.
The paper Howison et al., 2013, just appeared in early form in Bioinformatics. Here is my first round review, which they handily addressed in their revisions; since I was quite positive I felt I might as well post the whole thing, though.
Note that a relevant paper from Mihai Pop …
read moreThere are comments.
Here's a draft PyCon '14 proposal. Comments and suggestions welcome!
Title: Data intensive biology in the cloud: instrumenting ALL the things
Description: (400 ch)
Cloud computing offers some great opportunities for science, but most cloud computing platforms are both I/O and memory limited, and hence are poor matches for …
read moreThere are comments.
So, we've been running this course on NGS data analysis. And it's been fun and all. But a lot of work.
About a year ago, I thought hard about whether or not I wanted to apply for renewal, and ended up applying again. You can see the final grant if …
read moreThere are comments.
Two papers on the Haemonchus contortus genome just came out (Schwarz et al. and Laing et al.), and I'm an author on one of them (Schwarz et al.). H. contortus, or Haemonch (as I affectionately called it) is a nasty parasitic nematode that feasts on the mucosal blood of ruminants …
read moreThere are comments.