Byte Size Biology will be hosting the first edition of the bioinformatics blog carnival. All you bioinformatics bloggers, submit your entries by Mar 9, 2010 23:59:03 EST. Note the 3 second extension I have already given. There will be no more deadline extensions, I’ve been generous enough as it is. The carnival will be posted […]
As part of the process of manufacturing a new car, the designers will take the blueprints to the factory floor. There they will set up an experimental assembly line, tinkering with the manufacturing process of the prototype until it is ready for mass-production. Can we do the same with the machinery of life — the assembly […]
Seriously, this is what I first thought when I saw the cover of this week’s Nature, and the associated drawings in the press. The dude’s haircut seems like it was even bad in the ’80s… 2080 BCE that is, which is when his body is dated. Approximately. A large group of researchers were involved in […]
If the title of this post makes you cringe, then you belong to a minority of people who realize why the phrase “highly evolved” is so wrong. Unfortunately, “highly evolved” (as an absolute term) and “more evolved” (as a comparative term) seem to be used all-too frequently. They are uttered not only by non-scientists and […]
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 […]
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 […]
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 […]
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, […]
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 […]
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 […]
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 […]
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. […]
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 […]
Speaking of sampling bacteria, this ties in well with the previous post about GEBA. And by “well” I mean “in an alternate-universe/ altered-consciousness manner”. The voices in the song are sampled from this KFC employee training tape. The video won a prize in machinima.com. So if you like World of Warcraft, bacteria, KFC, sampled music, […]
After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of […]
