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Open Job: How did the Gulf Oil Spill Affect the Ocean’s Microbiome?

Well, we’re not sure. But if you would like to find out, and you are on the market for an exciting postdoc position, this is the best way to go about it: Postdoctoral Position in Laboratory of Jack A. Gilbert. http://www.bio.anl.gov/PI/gilbert.html http://pondside.uchicago.edu/ecol-evol/people/gilbert.html The Macondo wellhead oil leak, also known as the Deepwater Horizon oil spill […]

DNA half life, and my dream of an Allosaurus Army

Let’s get this clear: Tyrannosaurus rex, the best selling figurine of class reptilia is not my favorite bad-ass top-of-the-food chain predator. Come on. Did you see its arms? I mean…   As a kid, I always thought the Allosaurus was much cooler. For one thing, it was on the cover of my favorite dinosaur book, “The […]

A Synopsis of Career Paths in Bioinformatics

My previous post on ROSALIND, a bioinformatics learning site, got picked up by the  Slashdot community. A discussion came up on careers in Bioinformatics, and the Slashdot user rockmulle made some interesting observations on career paths in bioinformatics, which I have copied here. While brief and therefore omitting many important details (research at a university […]

ROSALIND: an addictive bioinformatics learning site

  I just learned about this one: ROSALIND  is a really cool concept in learning bioinformatics. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once […]

Repost: the New Natural History

Today is the last day of the 19th Lake Arrowhead Microbial Genomics meeting. A great meeting of everything good: science, atmosphere, people and location. Good tweeter coverage too, at #LAMG12 The many genomic characterization talks in the meeting reminded me of a post I wrote three years ago. I decided to repost it, and dedicate […]

Announcement: a Competition to Improve Wikipedia Entries in Computational Biology

Improve wikipedia entries in computational biology, and you too can win cash prizes, a free membership to International Society of Computational Biology, or a dinner date with an ISCB officer  of your choice! OK, maybe not the last one, but definitely the first two. The ISCB is announcing a competition to improve Wikipedia entries that have to […]

Short note on getting students busy

I recently read this post about lacunae in  Bioinformatics.  One complaint was: I know that documentation is a thankless task. But some parts of the Bio[Java|Perl|Python] libraries are described only as an API? This became apparent to me when I had to teach the libraries to students. What does this module do and why does it do […]

Should research code be released as part of the peer review process?

So there have been a few reactions to my latest post on accountable research software, including a Tweeter kerfuffle (again). Ever notice how people come out really aggressive on Twitter? Must the the necessity to compress ideas into 140chars. You can’t just write “Interesting point you make there, sir. Don’t you think that your laudable goal would […]

Can we make accountable research software?

Preamble: this post is inspired by a series of tweets that took place over the past couple of days. I am indebted to Luis Pedro Coelho (@LuisPedroCoelho) and to Robert Buels (@rbuels) for a stimulating, 140-char-at-a-time discussion. Finally, my thanks (and yours, hopefully) to Ben Temperton for initiating the Bioinformatics Testing Consortium. Science is messing around with […]

ZomBee Watch, a new citizen-scientist project

“If the bee disappeared off the surface of the globe, man would have only four years to live”. — Albert Einstein No, there are no typos in the title. And, no, there is no zombie outbreak towards which people are being recruited to fight. (Well, yeah, that’s what “they” always say isn’t it?)  The ZomBee Watch […]

Postdocs in Genome-Scale Proteomics, Imaging-based Screening and Cancer Biology

  Three postdocs positions available at a great lab in Denmark. Read on:   We are seeking three Postdoctoral Fellows to The Cellular Signal Integration Group (C-SIG). The group is a network biology research group located at the Department of Systems Biology at the Technical University of Denmark (DTU). Our department represents one of the […]

ISMB 2012 Vignettes Pt. 3: Swag

Promotional materials are part of any conference. In scientific meetings, the swag usually comes from the booths of product promoters, science publishers, and scientific societies. It was a nice surprise to see a Federal funding agency, the US Department of Energy give away decks of cards. I’m a sucker for cards, so I took a […]

ISMB 2012 Vignettes Pt. 2: Phylogenomic Approaches to Function Prediction

I chaired the Automated Function Prediction meeting at ISMB this year. The meeting, held every year (almost) deals with the latest approaches to predicting protein function from genetic and genomic data, and also discussing the Critical Assessment of Function Annotation This year we were fortunate to have Jonathan Eisen as our keynote speaker. Ever wondered […]

Spaghetti Western Blot

This is simply brilliant. The best thing since Bad Project.

Intermission: two vids

Too busy with grant deadlines, and preparations for the looming ISMB 2012. (Including, of course, the Automated Function Prediction meeting.) So here are two nice vids to pass the time. Jennifer Gardy and Tom Scott made this great A-Z of bacteria video.  Guaranteed to freak out your kids, or yourself. So how many of those […]