MetaFilter posts tagged with bioinformatics and genomics

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.