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Short bioinformatic hacks: reading between the genes

In celebration of the biohackathon happening now in Tokyo, I am putting up a script that is oddly missing from many bioinformatic packages: extracting intergenic regions. This one was written together with my student, Ian. As for the biohackathon itself, I’m not there, but I am following the tweets and  Brad Chapman’s excellent posts: Day […]

Leonardo da Vinci’s Resume

Marketing yourself is a process you go through many times. The job hunt comes to mind — but not only. Academia is rife with self-marketing: grant applications, promotion & tenure reports, attracting students to your courses and to your lab,  competing for conference lecture slots, giving a lecture. But not only academia, and not only […]

All theories proven with one graph

Boys and girls, it can be done. Published in the Journal of Irreproducible Results (Where else?)

JSUR? Yes, sir. (Updated 2-FEB-2010)

The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’, but ‘That’s funny…’ -Isaac Asimov Thanks to Ruchira Datta for pointing out this one. Science is many things to many people, but any lab-rat will tell you that research is mainly long stretches of frustration, interspersed with flashes […]

BsB in high school science… nice

A  small spike on my blog traffic yesterday led me to look for the source via Google Analytics. (If you are a blogger, you should really use this tool, lots of useful traffic information.) Seems like most of the traffic came from the page of a high school science teacher at Badin High School in […]

The polypharmacome

Pharmaceutical companies are always on the lookout for secondary drug targets. After all, if you invest billions developing a single drug, you would be more than happy to sell it as a treatment for two, three, or more different ailments. Sildenafil citrate was developed to treat angina and hypertension, but during phase I clinical trials, […]

Poll: favorite kingdom?

Seems like I had a couple of taxonomic posts recently.  So BsB would like to know what is your favorite Kingdom of life. I used the 6 kingdom system just to make things slightly more interesting. Vote in the pollbox on the righthand sidebar. You only have yourself to blame if your favorite kingdom is […]

Social networking for taxonomists

Despite our best attempts to remove species from the face of the Earth, there is still quite a bit of life out there and it is still quite diverse. Also, there are still quite a few people who want to document, describe and make the rest of us aware of the magnitude and diversity of […]

Fold.it: wasting time in a good cause

I just spent the better part of a Saturday playing with Foldit. Foldit is an ongoing experiment in finding protein structures by harnessing the power of the mob – or gamers, as is the case here. The player is presented with a backbone & sidechain configuration, with the secondary structures mostly pre-determined. The problem is […]

The Science(?) in Avatar

Saw Avatar with OhOne last weekend. Awesome cinematography, cool effects, great work. A few random observations, with no particular theme in mind. Note that James Cameron says that “Avatar [is not] science fiction, it is an action/adventure/science fantasy film”. So, I might just being too sciency here. 1. All of Pandora’s animals are hexapods, except […]

w00t! Post selected for Open Laboratory 2009

My post The Incredible Shrinking Genome was selected for publication in Open Laboratory 2009. The Open Laboratory books are anthologies of 52 posts from various science blogs selected annually by a panel of judges . This year the judges waded through 470 740 nominations (thanks for catching this Bora), so it is great to be […]

Happy Birthday Elvis

Celebrate with a peanut butter and banana sandwich, while listening to The King.

Newton’s birthday and crop diversity

Today is the 366th birthday of Sir Isaac Newton. Formulator of the three laws of motion, the theory of gravity, inventor of the first reflecting telescope, theory of color, calculus (with due credit to Gottfried Leibniz), the generalized binomial theorem, and president of the Royal Society. All which ties in directly to retail, and biodiversity. […]

Real programmers use…

A nice take on the vi / emacs wars Also, real programmers browse the web using the vimperator.

Going to GOA, pt. 2: children of a lesser GO

The source file associated with this post can be downloaded here. The last time I talked about how to read a GOA gene_associations file into a Python dictionary data structure.  Our goal was to find all genes that are annotated as hydrolases in the GOA gene_associations file. The tricky part is, most enzymes are not […]