Genome Technology Magazine and GenomeWeb News subscribers are already pre-registered to post comments to The Daily Scan. Just login and select a Username.
New to Genome Technology Online? Register here before posting.
A team of computational biologists and infectious disease scientists have developed methods to estimate the genetic diversity of virus populations within a single host. Publishing their results recently in PLoS Computational Biology, the researchers used computational analyses on pyrosequencing data from HIV patients with drug-resistant virus strains, and comparing these to 165 sequences of four independent HIV populations, were able to reconstruct the viral population. They hope to apply their methods to vaccine design and antiviral drug therapy.
At the Bayblab blog, they wonder just how much grant money is spent on applied research and how much on, well, overpriced equipment and missed targets. Canada's National Post printed a story about a scientist who was forced to re-pay grant money that he spent on personal gadgets. It begs the question, they write, "should we hold the researchers accountable for the money they use?" Though the rare (well, we hope so) person will abuse their grantor's generosity, in most cases conducting research is simply expensive. "I don't understand how an ice pack for a western apparatus can be 10 times more expensive than a regular one, or why a research fridge is four times the price of a regular fridge. It's certainly not for the reliability, from what I've seen of our fridges," the bloggers write.
Stephen Hawking is just one scientist backing the African Institute for Mathematical Sciences (Aims) project, founded four years ago in South Africa by Neil Turok, reports this Times Online article. Turok, who won a £50,000 TED prize earlier this year, started the project to help Africa develop its science base. It's also hoped to go a long way toward undoing negative stereotypes, perpetuated by comments like those rolling off James Watson's tongue. "The world of science needs Africa's brilliant talents and I look forward to meeting prospective young Einsteins from Africa," said Hawking at this week's launch ceremony.
Dartmouth's Gilbert Welch and UW's Wylie Burke teamed up to write an opinion piece in today's Newsday about the merits of consumer genomics. Though it sounds promising, they say the tests don't provide definitive information, especially about treatment. "We need more research, not pricey genomic scans. Until then, save your money, and spare your health," they write.
MIT's Technolgy Review reports on a prototype out of Harvard that places a microfluidic device on a piece of paper the size of a pinky fingernail. George Whitesides and his group designed this chip to use paper's innate capillary action to absorb the sample, instead of relying on pumps or other power sources. "The kinds of things we're developing here are intended to be useful for screening public health in the developing world," says Whitesides.
ScienceWoman is spending the day judging entries to the Intel International Science and Engineering Fair. On her blog, she posts some pictures of the entries from these young whippersnappers. One sophomore has a poster entitled, "Microfluidic image cytometry to detect PI3K pathway markers in brain cancer."
We don't know about you, but GTO is impressed — as sophomores, we couldn't even spell "microfluidic."
The New York Times reports on the genome sequence of the platypus -- which you probably already knew about, but we're partial to any publication that refers to the "freak-show charm" of one of the weirdest-looking critters on the planet (and we mean that in the nicest possible way). As NYT reports, the public responded to the announcement of the platypus genome last week "with considerably more enthusiasm than it had accorded similar bulletins about the sequencing of, say, the mustard plant, the mosquito or the wild chicken." Hey, don't feel bad, chicken -- maybe one day you, too, will acquire bizarre mammalian features.
Ricardo Vidal has a blog post at My Biotech Life about FoldIt, a project from David Baker's lab that puts protein folding into a gaming environment, challenging people to "solve puzzles for science." Ricardo writes that players try to "make the protein fold in the best way possible with points being given for stability through hydrogen bonding, compacting, hydrophobic and hydrophilic positioning of lateral protein chains, etc."
Well, there goes the time GTO was going to spend on Grand Theft Auto IV. So long, Niko Bellic, we've got proteins to fold.
Over at his blog, John Halamka weighs in from his experience with bosses good and bad to determine the most important factors in being great at managing people. He comes up with a list of 10, including "responds rapidly," "micromanages and macromanages," "provides resources," and "communicates consistently."
This newswire story reports that some watchdog groups are protesting recently published research demonstrating what may be the first time scientists genetically altered a human embryo. The scientist leading the study, Zev Rosenwaks at NewYork-Presbyterian/Weill Cornell Medical Center, says that the work centered around stem cells and that the embryo in question was chosen because it was abnormal and could never actually have developed into a viable baby.
Ewan Birney blogs about what he learned at Cold Spring Harbor's Biology of Genomes meeting last week. "As always, it was a great meeting," he writes. "Highlights for me was seeing the 1,000 genomes data starting to flow -- it is clear that the shift in technology is going to change the way we think about population genomics -- and for me, the best session was one on 'non-traditional models' -- Dogs, Horses and Cows, where the ability to do cost effective genotyping has completely revolutionised this field." He also includes more detailed looks at what his EBI teammates presented, such as Velvet and the Enredo-Pecan-Ortheus pipeline at Ensembl.
Over at bbgm, Deepak Singh blogs about the use of academic-developed software in industrial settings. He says the approach of licensing software from universities allows companies to "tap into the intellectual resources of some of the smartest academic researchers in the world." But because most of this software isn't given the kind of support and follow-on development of an industrial product, it can be tough to port these tools to large clusters, for instance, he writes. As industry scales up, Deepak wonders, will the use of academic software lessen? "I still feel that the underlying scientific research has to come from academia," he writes.
Get The Daily Scan e-mailed to you every weekday. Click here. RSS Feed for The Daily Scan. Request a FREE subscription to Genome Technology Magazine.
Genome Technology Podcasts NOW PLAYING:May 8 The Weekly Scan: genetic testing oversight, the diseasome, magnetic nanoparticles, creationism, and more.
Suggest an item worth reading: 
![Publishing Systems Powered by iProduction [ralph]](/images-genomeweb/small_iproduction_logo.gif "Publishing Systems Powered by iProduction [ ralph]"){kind=logo}