"genomics" entries

Genomics and Privacy at the Crossroads

Would you let people know about your dandruff problem if it might mean a cure for Lupus?

Two weeks ago, I had the privilege to attend the 2013 Genomes, Environments and Traits conference in Boston, as a participant of Harvard Medical School’s Personal Genome Project. Several hundreds of us attended the conference, eager to learn what new breakthroughs might be in the works using the data and samples we have contributed, and to network with the researchers and each other.

The Personal Genome Project (PGP) is a very different type of beast from the traditional research study model, in several ways. To begin with, it is a Open Consent study, which means that all the data that participants donate is available for research by anyone without further consent by the subject. In other words, having initially consented to participate in the PGP, anyone can download my genome sequence, look at my phenotypic traits (my physical characteristics and medical history), or even order some of my blood from a cell line that has been established at the Coriell biobank, and they do not need to gain specific consent from me to do so. By contrast, in most research studies, data and samples can only be collected for one specific study, and no other purposes. This is all in an effort to protect the privacy of the participants, as was famously violated in the establishment of the HeLa cell line.

The other big difference is that in most studies, the participants rarely receive any information back from the researchers. For example, if the researcher does a brain MRI to gather data about the structure of a part of your brain, and sees a huge tumor, they are under no obligation to inform you about it, or even to give you a copy of the scan. This is because researchers are not certified as clinical laboratories, and thus are not authorized to report medical findings. This makes sense, to a certain extent, with traditional medical tests, as the research version may not be calibrated to detect the same things, and the researcher is not qualified to interpret the results for medical purposes.

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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: 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: 7 June 2012

Four short links: 7 June 2012

Ubicomp Middleware, Big Dairy Data, Privacy, and Timelines

  1. Electric Imp — yet another group working on the necessary middleware for ubiquitous networked devices.
  2. How Big Data Transformed the Dairy Industry (The Atlantic) — cutting-edge genomics company Illumina has precisely one applied market: animal science. They make a chip that measures 50,000 markers on the cow genome for attributes that control the economically important functions of those animals.
  3. The Curious Case of Internet Privacy (Cory Doctorow) — I’m with Cory on the perniciousness of privacy-digesting deals between free sites and users, but I’m increasingly becoming convinced that privacy is built into business models and not technology.
  4. Chronoline (Github) — Javascript to make a horizontal timeline out of a list of events.
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Four short links: 28 July 2011

Four short links: 28 July 2011

Personal Genomics, NodeJS FTP, Bad Workshops, and Piggy Eclipse

  1. 23andMe Disproves Its Own Business Model — a hostile article talking about how there’s little predictive power in genetics for diabetes and Parkinson’s so what’s the point of buying a 23andMe subscription? The wider issue is that, as we’ve known for a while, mapping out your genome only helps with a few clearcut conditions. For most medical things that we care about, environment is critical too–but that doesn’t mean that personalized genomics won’t help us better target therapies.
  2. jsftp — lightweight implementation of FTP client protocol for NodeJS. (via Sergi Mansilla)
  3. Really Bad Workshops — PDF eBook with rock-solid advice for everyone who runs a workshop.
  4. PigEditor (GitHub) — Eclipse plugin for those working with Pig and Hadoop. (via Josh Patterson)
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Four short links: 28 June 2010

Four short links: 28 June 2010

Reflective Spaces, Slow Media, Chinese Genomics, and a Code Blog

  1. They Don’t Complain and They Die Quietly (Derek Powazek) — In this hyper-modern age of real-time always-on location-based info-overload, perhaps a moment of true peace and quiet is the greatest gift one can receive.
  2. The Slow Media ManifestoSlow Media inspire, continuously affect the users’ thoughts and actions and are still perceptible years later. Steven Levy ran a Slow Media session at Foo. (via Bruce Sterling)
  3. The Dragon’s DNA (The Economist) — Beijing Genomics Institute putting more DNA-sequencing capacity into the top floor of a refurbished printing works than is available in the whole USA.
  4. Scribd Coding Blog — very interesting blog about the technology behind and inside Scribd. They process over 150M polygons a day, building web fonts from the fonts in PDF files, and tell you why it’s not straightforward. I wish there were more of these genuinely interesting technology blogs from companies that do interesting things.
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Four short links: 25 June 2010

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.
Comments: 6
Four short links: 14 May 2010

Four short links: 14 May 2010

Personalised Healthcare, Academic Link Shorteners, Journalism Futures, Security

  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

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)
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