MetaFilter posts tagged with bioinformatics

Bring me more genomes

catlet — Sat, 26 Jan 2013 07:10:30 -0800

"If the history of public health has until now been embodied by the map—as in British physician John Snow’s famous map, which allowed him to curb the London cholera outbreak of 1854 and to found, in doing so, the modern field of epidemiology—Snitkin was embarking on a new kind of epidemiology: one founded on the phylogenetic tree." Writing for Wired, Carl Zimmer describes how Evan Snitkin and Julie Segre used genome sequencing to halt a bacterial outbreak at the National Institute of Health's Clinical Center. (via The Feature)

"The data that we actually used."

lizarrd — Sat, 08 Dec 2012 20:24:47 -0800

Rosalind.info is a website with bioinformatics problems inspired by Project Euler (previously, previouslier.) From the about page: "We hope that Rosalind will inspire a new generation of bioinformatics students by attracting biologists who want to develop vital programming skills at their own pace in a unique environment as well as programmers who have never been exposed to some of the stimulating computational problems generated by molecular biology." It is named after Rosalind Franklin because of her work on X-ray crystallography with Raymond Gosling that helped the Watson and Crick discover the DNA double helix. "Rosalind is a joint project between the University of California at San Diego and Saint Petersburg Academic University along with the Russian Academy of Sciences." Once you have downloaded a dataset you have five minutes to upload your solution. This forces your solutions to be efficient as well as not be random chance. Y combinator had a post about it recently as well.

ENCODE: the Encyclopedia of DNA Elements

Westringia F. — Thu, 06 Sep 2012 07:52:35 -0800

In 2001, we learned the sequence of our genome; now, we have amassed a vast amount of knowledge about what those sequences actually do. Yesterday, the data from the ENCODE project went live. ENCODE, the Encyclopedia of DNA Elements, is a project to identify and annotate all functional elements of the human genome, including transcription, transcription factor association, chromatin structure, and histone modification. It is a major achievement that was announced in a fanfare of publications. An elegant and accessible description of the project was posted by science writer Ed Yong on his Discover blog Not Exactly Rocket Science. The data is publicly explorable through a very nice interface, including an iPad app and a virtual machine. ENCODE constitutes a vast amount of data that will have a significant impact on research in genetics, bioinformatics, and medicine. Ewan Birney, the lead data analysis coordinator, discusses in Nature how the vast amount of data was wrangled, and has posted additional thoughts on his blog.

Buzzing about network graphs

Blazecock Pileon — Sun, 04 Dec 2011 02:07:51 -0800

A hive plot (slides) is a beautiful and compelling way to visualize multiple, complex networks, without resorting to "hairball" graphs that are often difficult to qualitatively compare and contrast. Hive plots were conceived by Martin Krzywinski, the primary author of the Circos software package, used to represent genomic and other data that render well in circular form. To make your own hive plots, take a look at Krzywinski's linnet library, or if you like R, there's HiveR.

master of information

kliuless — Sat, 09 Apr 2011 11:00:18 -0800

The New Biology - Eric Schadt's quest to upend molecular biology and open source it. (via)

I'm sure this'll end well....

zarq — Mon, 22 Feb 2010 09:48:15 -0800

We may soon be able to clone Neanderthals. But should we? An essay from Archaeology Magazine examines the ethical, scientific and legal ramifications. (Via Heather Pringle's Time Machine blog, where essay author Zach Zorich posted a reply and elicited a response.) Background: Last year, a team of researchers led by geneticist Svante Pääbo at the Max Planck Institute announced that they had completed a draft sequence of the Neanderthal genome. The project was begun in 2006. William Saletan covered some of the same ground in Slate in 2008, as did Reason.com last year: One science fiction trope says that it is impossible for two intelligent species to evolve simultaneously on the same planet since one would inevitably out-compete the other. This may have happened on our planet. Neanderthals disappeared around the same time that modern humans began to move into their territory. New research suggests that our ancestors killed them off. Perhaps we should use modern science to resurrect Neanderthals in order to right an ancestral wrong.

"No crime is so great as daring to excel." -- Winston Churchill

orthogonality — Wed, 04 Mar 2009 02:00:29 -0800

A little detective work traced the problem to default date format conversions and floating-point format conversions in the very useful Excel program package. The date conversions affect at least 30 gene names; the floating-point conversions affect at least 2,000 if Riken identifiers are included. These conversions are irreversible; the original gene names cannot be recovered.

Yet another reason not to use Excel as your "database".

Your body as data

Tlogmer — Wed, 23 Mar 2005 12:02:42 -0800

2 GB of data per second, piggybacking on your skin's electrical field. You == organic lan for small electronic devices. And it's a little more secure than bluetooth. via kottke, like everything else.