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Science

Group review of papers?

So I’ve been catching up on my paper reviewing duties this weekend. To those outside the Ivory Outhouse, “reviewing a paper” means “anonymously criticizing a research article considered for publication in a scientific journal”. (For those of you familiar with the process, you can jump to the text after the first figure.) Here’s how science […]

Not “Ancient”. Still Cool.

 This commentary appeared in Nature  recently. Title:  Ancient Fungi Found in Deep Sea Mud. Quote: Researchers have found evidence of fungi thriving far below the floor of the Pacific Ocean, in nutrient-starved sediments more than 100 million years old….To follow up on earlier reports of deep-sea fungi, Reese and her colleagues studied sediments pulled up from […]

Nobel Prize Quips at PDBe

I received this email today from Gary Battle at PDBe . Very cool:   Nobel Prize Quips: Explore the structure of B2AR bound to its G-protein. Today, Nobel Laureates Robert J. Lefkowitz and Brian K. Kobilka take center stage in Stockholm where they will receive their Nobel Prize Medals for their studies of G-protein–coupled receptors […]

DIGging into Images and Genomes

Our lab has a new project and website up. The project is BioDIG: Biological Database of Images and Genomes.  BioDIG lets you combine image data and genome data of, well, just about anything which you can make images and have a genome, or partial genomic information. You can upload your image, annotate (tag) parts of […]

Equal pay for equal primates

See what happens when a Capuchin monkey receives unequal pay: The article in Nature (2004): Monkeys reject unequal pay Sarah F. Brosnan & Frans B. M. de Waal

Our Home’s Wild Life

  Today Nitzan & I were citizen-scientists, sampling several locations in our home for microbial sequencing. We did this as part of Your Wild Life, a project hosted at North Carolina State University’s Biology Department. The Wild Life of Our Homes looks to sequence household microbial communities in a large number of homes. From their […]

Open Access Explained. Well.

Today is the last day of Open Access Week, where all things Open Access are heralded. William Gunn gave a great talk here at MU on how open access is changing scholarship. (And a big thank you to our librarians Jen Waller & Kevin Messner for hosting William!)  I have posted about Open Access before, […]

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 […]

Grants are the scientist’s homework

I can’t believe I did not realize this before. Thanks to Mickey Kosloff for enlightening me by posting this on his Facebook.   Of course grants are like homework. You don’t want to do them; anything is better, really; multiple excuses why not to do them right now; anything has more priority, suddenly. BUT if […]

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 […]