- Spokeo — abysmal indictment of society, first prize in mankind’s race to the bottom. Uncover personal photos, videos, and secrets … GUARANTEED! Spokeo deep searches within 48 major social networks to find truly mouth-watering news about friends and coworkers. PS, anybody who gives their gmail username and password to a site that specializes in dishing dirt can only be described as a fucking idiot. (via Jim Stogdill, who was equally disappointed in our species)
- Biologists rally to sequence ‘neglected’ microbes (Nature) — The Genomic Encyclopedia of Bacteria and Archaea is project to sequence genomes from more branches of the evolutionary tree of life. Eisen’s team selected and sequenced more than 100 ‘neglected’ species that lacked close relatives among the 1,000 genomes already in GenBank. The researchers reported earlier this year at the JGI’s Fourth Annual User Meeting that even mapping the first 56 of these microbes’ genomes increased the rate of discovery of new gene and protein families with new biological properties. It also improved the researchers’ ability to predict the role of genes with unknown functions in already sequenced organisms. (via Jonathan Eisen)
- Mail Learning: The What and the How (Simon Cozens) — a few things that a really good mail analysis tool needs to do. I hope that my mail client and server does these out of the box in the next five years.
- Introducing the Open Web Foundation Agreement — The Open Web Foundation Agreement itself establishes the copyright and patent rights for a specification, ensuring that downstream consumers may freely implement and reuse the licensed specification without seeking further permission. In addition to the agreement itself, we also created an easy-to-read “Deed” that provides a high level overview of the agreement. Applying the open source approach to better standards.
ENTRIES TAGGED "genomics"
Four short links: 20 November 2009
Social Network Search for Morons, Bulking Up Bio Data, Better E-Mail, Better Standards
Four short links: 10 November 2009
DIY Diagnostic Chips, Genetics on $5k a Genome, Cellphones as Diagnostic Microscopes, AR-Equipped Mechanics Do It Heads-Up
- A children’s toy inspires a cheap, easy production method for high-tech diagnostic chips — microfluidic chips (with tiny liquid-filled channels) can cost $100k and more. Michelle Khine used the Shrinky Dinks childrens’ toy to make her own. “I thought if I could print out the [designs] at a certain resolution and then make them shrink, I could make channels the right size for microfluidics,” she says. (via BoingBoing)
- Complete Genomics publishes in Science on low-cost sequencing of 3 human genomes (press release) — The consumables cost for these three genomes sequenced on the proof-of-principle genomic DNA nanoarrays ranged from $8,005 for 87x coverage to $1,726 for 45x coverage for the samples described in this report. Drive that cost down! There’s a gold rush in biological discovery at the moment as we pick the low-hanging fruit of gross correlations between genome and physiome, but the science to reveal the workings of cause and effect is still in its infancy. We’re in the position of the 18th century natural philosophers who were playing with static electricity, oxygen, anaesthetics, and so on but who lacked today’s deeper insights into physical and chemical structure that explain the effects they were able to obtain. More data at this stage means more low-hanging fruit can be plucked, but the real power comes when we understand “how” and not just “what”. (via BoingBoing)
- Far From a Lab? Turn a Cellphone into a Microscope (NY Times) — for some tests, you can use a camphone instead of a microscope. In one prototype, a slide holding a finger prick of blood can be inserted over the phone’s camera sensor. The sensor detects the slide’s contents and sends the information wirelessly to a hospital or regional health center. For instance, the phones can detect the asymmetric shape of diseased blood cells or other abnormal cells, or note an increase of white blood cells, a sign of infection, he said.
- Augmented reality helps Marine mechanics carry out repair work (MIT TR) — A user wears a head-worn display, and the AR system provides assistance by showing 3-D arrows that point to a relevant component, text instructions, floating labels and warnings, and animated, 3-D models of the appropriate tools. An Android-powered G1 smart phone attached to the mechanic’s wrist provides touchscreen controls for cueing up the next sequence of instructions. [...] The mechanics using the AR system located and started repair tasks 56 percent faster, on average, than when wearing the untracked headset, and 47 percent faster than when using just a stationary computer screen.
Four short links: 29 July 2009
- Bioweathermap — crowdsourcing the gathering of environmental samples for DNA sequencing to study the changing distribution of microbial life. Another George Church project. (via timoreilly at Twitter)
- We Are All African Now — a great article about our genetic history and the computational genomics that makes it possible. (via Tim Bray)
- Standing Out In The Crowd — OSCON keynote by Kirrily Robert on women in open source. Excellent.
- Energy Harvesting Powers Printed LED — an interesting combination of two emerging technologies. Like an RFID, the circuit has a current induced by the presence of a changing RF field. The EL display and the RFID circuit are printed in organic compounds, whereas the power control is built with traditional circuit fabrication techniques. (via Freaklabs)
Sequencing a Genome a Week
Radar Talks to OSCON Speaker David Dooling
The Human Genome Project took X years to fully sequence a single human's genetic information. At Washington University's Genome Center, they can now do one in a week. But when you're generating that much data, just keeping track of it can become a major challenge in itself. David Dooling is in charge of managing the massive output of the Center's herd of gene sequencing machines, and making it available to researchers inside the Center and around the world. He'll be speaking at OSCON, O'Reilly's Open Source Conference, on how he uses open source tools to keep things under control, and he agreed to give us an overview of how the field of genomics is evolving.
Four short links: 9 Jan 2009
Four questions, one per link: what next, can it solve a big problem, what’s the final boss for Python programming, and why on earth would anyone want yogurt that glows in the dark?
- End Times – gloomy piece on the future of journalism, to be added to the large pile of other gloomy pieces on the future of journalism (e.g., Bad News, Good News). The critical problem is still how to pay for journalism if the new media revenues are significant lower than old, and if the new media economics decree that journalism is dead then who fills the social good role that journalism’s death will leave?
- Ward Cunningham’s Visible Workings – an intriguing glimpse, from March last year, into the way Ward lays out web interactions. Nice system for laying out these interactions, but it’s also fascinating for how it makes transparent what will happen as a result of the data you submit. How scalable is this? Could it tackle privacy?
- Project Euler – fun programming exercises that require more than math to finish. We learn by doing, not by reading, so interesting exercises are part and parcel of training. It’s interesting to see educators are moving from being authors to being game designers, providing a series of staged challenges that make us stronger by defeating them. I’m presently dieing in as many ways as I can while learning iterators and generators in Python, as a way of ensuring I have Python’s “game physics” sussed.
- Rise of the Garage Genome Hackers – more on hobbyist molecular biology. It mentions DIYBio, the Cambridge biohacker collective that I first heard about at BioBarCamp. (via Glynn Moody)
Challenges for the New Genomics
New guest blogger Matt Wood heads up the Production Software team at the Wellcome Trust Sanger Institute, where he builds tools and processes to manage tens of terabytes of data per day in support of genomic research. Matt will be exploring the intersection of data, computer technology, and science on Radar. The original Human Genome Project was completed in 2003,…
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