Note: updated 2/18 with Benton Gravely's name -- he did the squid genome sequencing!
A few months back, I announced the khmer protocols project, an effort to write down an explicit, open protocol for transcriptome and metagenome assembly. This project was started during the summer of 2013 at the Woods …
read moreThere are comments.
This term, I'm once again teaching my upper-division CSE undergrad course in Web Dev here at MSU. For the second time, I'm requiring students to use github for their homework; unlike last year, I now understand pull requests and have integrated them into the process.
There are comments.
A few months back, we submitted a paper, These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure, to PLoS One. We got the (signed) reviews back in December, and I asked the reviewers if I could post their reviews publicly. They …
read moreThere are comments.
On January 27th, 2014, the MSU BEACON Center graduate students held a panel on how to review. The panel was organized by Emily Weigel (@choosy_female) and Jory Schossau, Bjorn Ostman (@CarnyEvolution), Kristin Parent, Rich Lenski (@RELenski), and Arend Hintze were panel members, together with me.
I put together the following …
read moreThere are comments.
I've just posted the narrative for a recently funded USDA grant on improving the quality of the chick genome assembly on the lab's research page. The issues are laid out in detail in the grant, but, basically, the question is: how can we improve the quality of the assembly? The …
read moreThere are comments.
Over the past year of PyCon, #sciox, and other gender imbalance/harassment/sexism discussions that I've seen on Twitter and blogging, I've run into a few posts on these matters that stood out to me in terms of clarity, logic, and/or good instruction for me. I'm sharing them below …
read moreThere are comments.
In 1947 a Bedouin shepherd found a bunch of ancient scrolls in a cave near the Dead Sea. These scrolls, now known as the Dead Sea scrolls, included some of the oldest known Biblical texts as well as other Jewish religious writing. Over the next few decades, these scrolls - of …
read moreThere are comments.