I'm at the 2014 Marine Microbes Gordon Conference right now, and at the end of my talk, I brought up the point that the function of most genes is unknown. It's not a controversial point in any community that does environmental sequencing, but I feel it should be mentioned at …
read moreThere are comments.
We just released khmer v1.1, a minor version update from khmer v1.0.1 (minor version update: 220 commits, 370 files changed).
Cancel that -- _I_ just released khmer, because I'm the release manager for v1.1!
As part of an effort to find holes in our documentation, "surface" any …
read moreThere are comments.
Eli Kintisch (@elikint) just wrote a very nice article on "Sharing in Science" for Science Careers; his article contained quotes from my MSU colleague Ian Dworkin as well as from me.
When Eli sent me an e-mail with some questions about open science, I responded at some length (hey, I …
read moreThere are comments.
As part of the 2-day Mozilla Science Labs hackathon in late July, the khmer project will be providing a "mentored open source contributathon" experience. This will provide an opportunity for people interested in trying out our instance of the "github flow" model, in which contributions are submitted for review using …
read moreThere are comments.
(or, What I Did For One Day Of My Summer Vacation.)
tl;dr? I played around with building a CountMin Sketch that is dynamic in size, based on a scalable Bloom Filter approach. I'm not sure it worked. Thoughts, suggestions, help?
In our research, we've made some hay …
There are comments.
About 10 days ago, I gave a talk in Manchester to Carole Goble's group, hosted by Aleksandra Pawlik. The talk title was "Six ways to Sunday: Approaches to computational reproducibility in non-model sequence analysis." I've posted the slides (here).
For the talk, I put together a list of five things …
read moreThere are comments.
I'm on a European trip that involves several plane flights accompanied by long airport stays, and I just used some of that time to do a bit of tedious coding on khmer.
The coding I did was to add proper exception handling to khmer's internal file loading routines (see the …
read moreThere are comments.