# ENTRIES TAGGED "genomics"

## Four short links: 25 June 2010

### More NoSQL, Data Medicine, Startups to Government, and Cake-and-eat-it Open Source

1. Membasean open-source (Apache 2.0 license) distributed, key-value database management system optimized for storing data behind interactive web applications. These applications must service many concurrent users; creating, storing, retrieving, aggregating, manipulating and presenting data in real-time. Supporting these requirements, membase processes data operations with quasi-deterministic low latency and high sustained throughput. (via Hacker News)
2. Sergey’s Search (Wired) — Sergey Brin, one of the Google founders, learned he had a gene allele that gave him much higher odds of getting Parkinson’s. His response has been to help medical research, both with money and through 23andme. Langston decided to see whether the 23andMe Research Initiative might be able to shed some insight on the correlation, so he rang up 23andMe’s Eriksson, and asked him to run a search. In a few minutes, Eriksson was able to identify 350 people who had the mutation responsible for Gaucher’s. A few clicks more and he was able to calculate that they were five times more likely to have Parkinson’s disease, a result practically identical to the NEJM study. All told, it took about 20 minutes. “It would’ve taken years to learn that in traditional epidemiology,” Langston says. “Even though we’re in the Wright brothers early days with this stuff, to get a result so strongly and so quickly is remarkable.”
3. Startup.gov (YouTube) — Anil Dash talk at Personal Democracy Forum on applying insights from startups to government. I hope the more people say this, the greater the odds it’ll be acted on.
4. Open Core Software — Marten Mickos (ex-MySQL) talks up “open core” (open source base, proprietary extensions) as a way to resolve the conflict of “change the world with open source” and “make money”. Brian Aker disagrees: There has been no successful launch of an open core company that has reached any significant size, especially of the size that Marten hints at in the article. My take: there are three reasons for open source (freedoms, price, and development scale) and if you close the source to part of your product then the whole product loses those benefits. If you open source enough that the open source bit has massive momentum, then you probably don’t have enough left proprietary to gain huge financial benefit.

## Four short links: 14 May 2010

1. Genome Scan Gives Man Insight Into Future Health Risks the first completely mapped genome of a healthy person aimed at predicting future health risks. The scan was conducted by a team of Stanford researchers and cost about $50,000. The researchers say they can now predict [his] risk for dozens of diseases and how he might respond to a number of widely used medicines. Personalized medicine takes a step closer, and all powered by massive computational power. 2. Long Handle on Shorted Digital Object — digital object identifiers, and their relationship to shortener services like bit.ly (in which O’Reilly is an investor). The Handle System is relatively inexpensive, but the costs are now higher than the large scale URL shorteners. According to public tax returns, the DOI Foundation pays CNRI about$500,000 per year to run the DOI resolution system. That works out to about 0.7 cents per thousand resolutions. Compare this to Bit.ly, which has attracted $3.5 million of investment and has resolved about 20 billion shortened links- for a cost of about 0.2 cents per thousand. It remains to be seen whether bit.ly will find a sustainable business model; competing directly with DOI is not an impossibility. 3. We Are In The Information BusinessA well-architected news website leads to content that will keep on providing value, rather than leaving stories to wither away when their immediate news value has faded. Structured content is the stuff that makes a website malleable, rather than cementing you into certain ways of doing things. Structured content is like a big undo button that allows you to reverse decisions and change how your website looks and behaves. Since none of us can predict the future, the freedom to change course as often as we please and not having to worry about escalating legacy costs, well, that’s pretty close to heaven. 4. Sacramento Credit Union FAQThe answers to your Security Questions are case sensitive and cannot contain special characters like an apostrophe, or the words “insert,” “delete,” “drop,” “update,” “null,” or “select.” (via Simon Willison) Comments: 2 | ## Four short links: 29 March 2010 ### Distributed Comments, Graph Exploration, Body as UI, and Genomic Advertising 1. Salmon Protocol — protocol to unite comments and annotations with original web pages. A distributed solution to the problem that Disqus tackles in a centralised fashion. Important because we’ll all be historians of our earlier lives and dissipated prolific micro-content is a historian’s nightmare. 2. Gephi — open source (GPLv3) interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs. I believe tools for data exploration, versus static infographics, are the only way to develop a new sense for data. (via mattb on Delicious) 3. Skinput — a bio-acoustic sensor lets you use your skin to write, tap, drag, etc. See also BBC article. (via Mike Loukides) 4. First Synthetic Genome Secret Messages Decoded (Wired) — the first synthetic genome contained advertisements (“VENTNERINSTITVTE”, “CRAIGVENTNER”). I can’t figure out whether it’s a cheeky easter egg in the finest geek tradition, or whether it’s as if the Apollo 11 had “BUY COKE” on the side or Magellan’s yachts had sails emblazoned with “VENETIAN GLASS: BEST IN THE WORLD!”. (via christianbok on Twitter) Comments Off | ## Four short links: 20 November 2009 ### Social Network Search for Morons, Bulking Up Bio Data, Better E-Mail, Better Standards 1. 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) 2. 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) 3. 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. 4. Introducing the Open Web Foundation AgreementThe 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. Comment: 1 | ## 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

1. 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) 2. 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)
3. 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.
4. 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

1. 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)
2. We Are All African Now — a great article about our genetic history and the computational genomics that makes it possible. (via Tim Bray)
3. Standing Out In The Crowd — OSCON keynote by Kirrily Robert on women in open source. Excellent.
4. 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?

1. 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?
2. 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?
3. 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.
4. 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)