"bio" entries

Four short links: 6 September 2012

Four short links: 6 September 2012

Human Genome Doxed, Programmed by Movies, CritterDrones, and Responsive Websites

  1. ENCODE Project — International project (headed by Ewan Birney of BioPerl fame) doxes the human genome, bigtime. See the Nature piece, and Ed Yong’s explanation of the awesome for more. Not only did they release the data, but also the software, including a custom VM.
  2. 5 Ways You Don’t Realize Movies Are Controlling Your Brain — this! is! awesome!
  3. RC Grasshoppers — not a band name, an Israeli research project funded by the US Army, to remotely-control insects in flight. Instead of building a tiny plane whose dimensions would be measured in centimeters, the researchers are taking advantage of 300 million years of evolution.
  4. enquire.js — small Javascript library for building responsive websites. (via Darren Wood)
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Four short links: 9 August 2012

Four short links: 9 August 2012

Economics of Innovation, Bio Imagery, Open Source EEG for Smartphone, and Feynman Bio

  1. Doing Capitalism in the Innovation Economy (Amazon) — soon-to-be-released book by Bill Janeway, of Warburg-Pincus (and the O’Reilly board). People raved about his session at scifoo. I’m bummed I missed it, but I’ll console myself with his book.
  2. Cell Image Librarya freely accessible, easy-to-search, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. The purpose of this database is to advance research, education, and training, with the ultimate goal of improving human health. And an excellent source of desktop images.
  3. Smartphone EEG Scanner — unusually, there’s no Kickstarter project for an iPhone version. (Designs and software are open source)
  4. Feynman — excellent graphic novel bio of Feynman, covering the science as well as the personality. Easy to read and very enjoyable.
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Four short links: 8 August 2012

Four short links: 8 August 2012

Reading Minds, Satellites in the Cloud, Units for Risk, and Valuing Autism

  1. Reconstructing Visual Experiences (PDF) — early visual areas represent the information in movies. To demonstrate the power of our approach, we also constructed a Bayesian decoder by combining estimated encoding models with a sampled natural movie prior. The decoder provides remarkable reconstructions of the viewed movies. These results demonstrate that dynamic brain activity measured under naturalistic conditions can be decoded using current fMRI technology.
  2. Earth Engine — satellite imagery and API for coding against it, to do things like detecting deforestation, classifying land cover, estimating forest biomass and carbon, and mapping the world’s roadless areas.
  3. Microlives — 30m of your life expectancy. Here are some things that would, on average, cost a 30-year-old man 1 microlife: Smoking 2 cigarettes; Drinking 7 units of alcohol (eg 2 pints of strong beer); Each day of being 5 Kg overweight. A chest X-ray will set a middle-aged person back around 2 microlives, while a whole body CT-scan would weigh in at around 180 microlives.
  4. Autistics Need Opportunities More Than Treatment — Laurent gave a powerful talk at Sci Foo: if the autistic brain is better at pattern matching, find jobs where that’s useful. Like, say, science. The autistic woman who was delivering mail became a research assistant in his lab, now has papers galore to her name for original research.
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Four short links: 7 August 2012

Four short links: 7 August 2012

DIY Medical Devices, 3D Exoskeletal Arms, Scientific Data Depository, and Zombees

  1. Why Toys Make Good Medical Devices (YouTube) — Jose Gomez-Marquez profiled by CNN. His group at MIT is Little Devices.
  2. 3D Printed Exoskeletal Arms for Little Girlresearchers at a Delaware hospital 3D printed a durable custom device with the tiny, lightweight custom parts she needed. Good for iterations, replacements, and an astonishingly high number of “awww” moments in the video.
  3. Figshareallows researchers to publish all of their data in a citable, searchable and sharable manner. All data is persistently stored online under the most liberal Creative Commons licence, waiving copyright where possible. figshare was started by a frustrated Imperial College PhD student as a way to disseminate all research outputs and not just static images through traditional academic publishing. It is now supported by Digital Science, a Macmillan Publishers company.
  4. Zombeeshoney bees that have been parasitized by the Zombie Fly Apocephalus borealis. Fly-parasitized honey bees become “ZomBees” showing the “zombie-like behavior” of leaving their hives at night on “a flight of the living dead.” See also NPR interview.
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Four short links: 1 August 2012

Four short links: 1 August 2012

Chinese Hackers, Edible Sensors, Quantum Physics

  1. China Hackers Hit EU Point Man and DC (Bloomberg) — wow. The extent to which EU and US government and business computer systems have been penetrated is astonishing. Stolen information is flowing out of the networks of law firms, investment banks, oil companies, drug makers, and high technology manufacturers in such significant quantities that intelligence officials now say it could cause long-term harm to U.S. and European economies. (via Gady Epstein)
  2. Digestible Microchips (Nature) — The sand-particle sized sensor consists of a minute silicon chip containing trace amounts of magnesium and copper. When swallowed, it generates a slight voltage in response to digestive juices, which conveys a signal to the surface of a person’s skin where a patch then relays the information to a mobile phone belonging to a healthcare-provider. (via Sara Winge)
  3. Quantum Mechanics Make Simple(r) — clever way to avoid the brain pain of quantum mechanics and leap straight to the “oh!”. [N]ature is described not by probabilities (which are always nonnegative), but by numbers called amplitudes that can be positive, negative, or even complex. […] In the usual “hierarchy of sciences”—with biology at the top, then chemistry, then physics, then math—quantum mechanics sits at a level between math and physics that I don’t know a good name for. Basically, quantum mechanics is the operating system that other physical theories run on as application software (with the exception of general relativity, which hasn’t yet been successfully ported to this particular OS). (via Hacker News)
  4. Selectively De-Animating Video — SIGGRAPH talk showing how to keep some things still in a video. Check out the teaser video with samples: ZOMG. I note that Maneesh Agrawala was involved: I’m a fan of his from Line Drive maps and 3D exploded views, but his entire paper list is worth reading. Wow. (via Greg Borenstein)
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Four short links: 26 July 2012

Four short links: 26 July 2012

Drone Overload, Mac MySQL Tool, Better Cancer Diagnosis Through AI, and Inconstant Identifiers

  1. Drones Over Somalia are Hazard to Air Traffic (Washington Post) — In a recently completed report, U.N. officials describe several narrowly averted disasters in which drones crashed into a refu­gee camp, flew dangerously close to a fuel dump and almost collided with a large passenger plane over Mogadishu, the capital. (via Jason Leopold)
  2. Sequel Pro — free and open source Mac app for managing MySQL databases. It’s an update of CocoaMySQL.
  3. Neural Network Improves Accuracy of Least Invasive Breast Cancer Test — nice use of technology to make lives better, for which the creator won the Google Science Fair. Oh yeah, she’s 17. (via Miss Representation)
  4. Free Harder to Find on Amazon — so much for ASINs being permanent and unchangeable. Amazon “updated” the ASINs for a bunch of Project Gutenberg books, which means they’ve lost all the reviews, purchase history, incoming links, and other juice that would have put them at the top of searches for those titles. Incompetence, malice, greed, or a purely innocent mistake? (via Glyn Moody)
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Four short links: 25 July 2012

Four short links: 25 July 2012

No Augmenting Money, Cat CV, Quantified Mind, and Hackable Bio

  1. Bank of England Complains About AR Bank NotesAfter downloading the free Blippar app on iPhone or Android, customers were able to ‘blipp’ any ten-pound note in circulation by opening the app and holding their phone over the note. An animated Queen, and other members of the Royal Family, then appeared on the screen and voiced opinions on the latest football matters.
  2. Kittydar — open source computer vision library in Javascript for identifying cat faces. I am not making this up. (via Kyle McDonald
  3. Quantified Mind — battery of cognitive tests, so you can track performance over time and measure the effect of interventions (coffee, diet, exercise, whatever). (via Sara Winge)
  4. Jellyfish Made From Rat Cells (Nature) — an artificial jellyfish using silicone and muscle cells from a rat’s heart. The synthetic creature, dubbed a medusoid, looks like a flower with eight petals. When placed in an electric field, it pulses and swims exactly like its living counterpart. Very cool, but the bit that caught my eye was: the team built the medusoid as a way of understanding the “fundamental laws of muscular pumps”. It is an engineer’s approach to basic science: prove that you have identified the right principles by building something with them.
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Four short links: 23 July 2012

Four short links: 23 July 2012

Drone Show, Ads, GitHub's Importance, and Crowdfunding Science

  1. Unmanned Systems North America 2012 — huge tradeshow for drones. (via Directions Magazine)
  2. On Thneeds and the Death of Display Ads (John Battelle) — the video interstitial. Once anathema to nearly every publisher on the planet, this full page unit is now standard on the New York Times, Wired, Forbes, and countless other publishing sites. And while audiences may balk at seeing a full-page video ad after clicking from a search engine or other referring agent, the fact is, skipping the ad is about as hard as turning the page in a magazine. And in magazines, full page ads work for marketers. If you’d raised a kid on AdBlocker, and then at age 15 she saw the ad-filled Internet for the first time, she’d think her browser had been taken over by malware. (via Tim Bray)
  3. The Most Important Social Network: GitHubI suspect that GitHub’s servers now contain the world’s largest corpus of commentary around intellectual production.
  4. Crowdfunded Genomics — a girl with a never-before-seen developmental disorder had her exome (the useful bits of DNA) sequenced, and a never-before-seen DNA mutation found. The money for it was raised by crowdfunding. (via Ed Yong)
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Four short links: 16 July 2012

Four short links: 16 July 2012

Open Access, Emergency Social Media, A/B Testing Traps, and Post-Moore Sequencing Costs

  1. Britain To Provide Free Access to Scientific Publications (Guardian) — the Finch report is being implemented! British universities now pay around £200m a year in subscription fees to journal publishers, but under the new scheme, authors will pay “article processing charges” (APCs) to have their papers peer reviewed, edited and made freely available online. The typical APC is around £2,000 per article.
  2. Social Media in an Emergency: A Best Practice Guide — from the Wellington City Council in New Zealand, who have been learning from Christchurch earthquakes and Tauranga’s oil spill.
  3. Trustworthy Online Controlled Experiments: Five Puzzling Outcomes Explained (PDF) — Microsoft Research dug into A/B tests done on Bing and reveal some subtle truths. The statistical theory of controlled experiments is well understood, but the devil is in the details and the difference between theory and practice is greater in practice than in theory […] Generating numbers is easy; generating numbers you should trust is hard! (via Greg Linden)
  4. Data Sequencing Costs (National Human Genome Research Institute) — Cost-per-megabase and cost-per-genome are dropping faster than Moore’s Law now they’ve introduced “second generation techniques” for sequencing, aka “high-throughput sequencing” or a parallelization of the process. (via JP Rangaswami)
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Four short links: 9 July 2012

Four short links: 9 July 2012

Personalized Medicine, Reporting on Execution, Software-Defined Radio, and Beyond Hadoop

  1. Personalized Leukemia Treatment (NY Times) — sequenced the tumor’s DNA, found the misbehaving gene, realized there was an existing experimental treatment to tackle that gene, and it worked. Reminds me of My Daughter’s DNA, which had its origin in the poignant story of Hugh Reinhoff sequencing his daughter’s DNA to diagnose her condition. It’s all about medical professionals now, but that’s no different from the Internet starting with geeks and moving out to the masses.
  2. Bullseye HD — web app which allows you to make the most of the time you spend with your team, by focusing your attention on the projects and actions that are off-track or not getting enough focus, rather than wasting precious time on status updates. (via Rowan Simpson)
  3. Per Vices — selling software-defined radio boards (for Linux only at the moment). (via Ars Technica)
  4. Post-Hadoop (GigaOm) — Google have moved beyond the basic software that Hadoop was copying. Lots of interesting points in this article, including one fundamental reality – MapReduce (and thereby Hadoop) is purpose-built for organized data processing (jobs). It is baked from the core for workflows, not ad hoc exploration.
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