linkstream2 microblog

Nice overview of the programs

http://commonfund.nih.gov/initiativeslist

High-throughput functional testing of ENCODE segmentation
predictionsGenome Res. October 2014 24: 1595-1602; Published in Advance July 17, 2014,

that can be used for training predicted enhancers

http://genome.cshlp.org/content/24/10/1595.full.pdf

http://www.nature.com/nature/journal/v514/n7520/full/514032a.html?WT.ec_id=NATURE-20141002

NATURE | BOOKS AND ARTS
Computing history: Geeks, Inc.
Jennifer Light
Nature 514, 32–33 (02 October 2014) doi:10.1038/514032a

Jennifer Light enjoys a chronicle of the collaborations that conjured the digital realm.

The Innovators: How a Group of Inventors, Hackers, Geniuses, and Geeks Created the Digital Revolution
Walter Isaacson Simon & Schuster: 2014.ISBN: 9781471138799

Why So Few Blockbuster #Drugs Invented Today? (Eroom’s law) http://www.nytimes.com/2014/11/16/magazine/why-are-there-so-few-new-drugs-invented-today.html Short answer: use of genomics v traditional pharmacology

QT:{{"
“If you read them now, the claims made for genomics in the 1990s sound
a bit like predictions made in the 1950s for flying cars and
anti-gravity devices,” Jack Scannell, an industry analyst, told me.
But rather than speeding drug development, genomics may have slowed it
down. So far it has produced fewer returns on greater investments.
Scannell and Brian Warrington, who worked for 40 years inventing drugs
for pharmaceutical companies, published a grim paper in 2012 that
showed the plummeting efficiency of the pharmaceutical industry. They
found that for every billion dollars spent on research and development
since 1950, the number of new drugs approved has fallen by half
roughly every nine years, meaning a total decline by a factor of 80.
They called this Eroom’s Law, because it resembled an inversion of
Moore’s Law (the observation, first made by the Intel co-founder
Gorden E. Moore in 1965, that the number of transistors in an
integrated circuit doubles approximately about every two years).

That’s not to say that target-based drug discovery, informed by
genomics, hasn’t had its share of spectacular successes. Gleevec, used
since 2001 to treat chronic myelogenous leukemia (C.M.L.) and a
variety of other cancers, is often pointed to as one of the great
gene-to-medicine success stories. Its design followed logically from
the identification of an abnormal protein caused by a genetic glitch
found in almost every cancer cell of patients with C.M.L.

Many of the drugs developed through target-based discovery, however,
work for only single-mutation diseases affecting a tiny number of
people. Seventy percent of new drugs approved by the F.D.A. last year
were so-called specialty drugs used by no more than 1 percent of the
population. The drug Kalydeco, for instance, was approved in 2012 for
people with a particular genetic mutation that causes cystic fibrosis.
But only about 1,200 people in the United States have the mutation it
corrects.
"}}

https://itunes.apple.com/us/app/classic-pong/id698209222?mt=8

http://appadvice.com/appguides/show/space-war

the spirit of Bushnell

QT:{{”
If you want to play the original, look no further than the Atari Classic app. The graphics, sound, and retro experience are all here. Currently the control mechanism is not the most intuitive thing, but if you can get good at the controls this is a fantastic notable option. The app is free to download and included one game, Mission Control. You’ll need to purchase each of the other titles after that. The other games, such as Space War, will be $.99 apiece; though of course there are package deals you can purchase if you’re a die-hard retro Atari fan.
“}}

http://phys.org/news/2014-11-mammals-genomes-aid-human-clinical.html

Interesting interactive map, showing a heatmap of $/SF & numb. of stories

http://www.city-data.com/ny-properties/assessments/Manhattan/B/Broad-Street-1.html

http://www.vanityfair.com/politics/2014/10/secret-service-jfk-assassination

What the shape of our cities says about the way we live
http://www.salon.com/2014/11/16/what_the_shape_of_our_cities_says_about_the_way_that_we_live Longer commutes from more distended layout (via night lights)

Nighttime light shows more distended layout gives longer commutes & a lower standard of living… but this only applies to walking-only cities

QT:{{”

What she found is that “compactness” — in her paper, the nearer, basically, that a city’s shape is to a circle — is a kind of urban amenity, like a subway line or a movie theater, that people will pay for. All else being equal, India’s compact cities have lower wages, higher rents and shorter commutes. “One standard deviation
deterioration in city shape, corresponding to a 720 meter increase in the average within-city round-trip,” Harari writes, “entails a welfare loss equivalent to a 5 percent decrease in income.”

An instructive comparison is between Kolkota (Calcutta) and Bengaluru (Bangalore). Among the country’s largest cities, these are on opposite ends of Harari’s measurement system: giraffe-like Kolkota has the “worst” geometry, squat Bengaluru the “best.” According to Harari, “if Kolkota had the same compact shape that Bengaluru has, the average trip to the center would be shorter by 4.5 kilometers and the average trip within the city would be shorter by 6.2 km.”

Just a couple of miles difference, right? But the average commute speed in India is 12 km per hour, and is forecast to fall to 9 km per hour within the decade. For the average person, on an average potential trip, compactness could save an hour a day.

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