- How Virtual Fences Will Transform Rural America (The Atlantic) — When it comes to managing animals, every conventional fence that I have ever built has been in the wrong place the next year.
- Stately — a font of states which mesh together, so you can style individual states in CSS. Clever! (via Andy Baio)
- Code Triage — mails you a todo from your favourite Github projects. Interesting to see (a) what happens once there’s an easy way to access things like issues across multiple projects; and (b) what a lightweight hack it is for increasing participation. What small things could you send out each day, something different to each person, that’d help you make progress? Hm.
- MIT’s Health and Wellness Hack Day — 80 participants, two weeks. Good writeup in Fast Company. The focus here is on producing commercially viable products.
In which the question of whether research subjects have any rights to their data is pondered.
The GET (Genomes, Environments and Traits) conference is a confluence of parties interested in the advances being made in human genomes, the measurement of how the environment impacts individuals, and how the two come together to produce traits. Sponsored by the organizers of the Personal Genome Project (PGP) at Harvard, it is a two-day event whose topics range from the appropriate amount of access that patients should have to their genetics data to the ways that Hollywood can be convinced to portray genomics more accurately.
It also is a yearly meeting place for the participants in the Personal Genome Project (one of whom is your humble narrator), people who have agreed to participate in an “open consent” research model. Among other things, this means that PGP participants agree to let their cell lines be used for any purposes (research or commercial). They also acknowledge ahead of time that because their genomes and phenotypic traits are being released publicly, there is a high likelihood that interested parties may be able to identify them from their data. The long term goal of the PGP is to enroll 100,000 participants and perform whole genome sequencing of their DNA, they currently have nearly 2,300 enrolled participants and have sequenced around 165 genomes.
How our vision for this important conference is shaping the program we hope to present, and how you can get involved
After a strong inaugural event in October 2012, Strata Rx is heading into its second year. My fellow chair, Colin Hill, and I have spent a lot of time thinking about and discussing what we’d like to see on the program this year, and I thought I’d share some of those thoughts for anyone considering submitting a proposal or attending the event. (The Call for Proposals is currently open until April 10.)
One of the most interesting challenges in creating a program about data science in healthcare has been deciding what to leave out. Topics like genomics and cancer research are so vast and complex that they can and do have entire conferences about just them. While we won’t reject a talk for centering on a topic like this, it has to be relevant to one of our larger goals, as well.
What we hope to accomplish with Strata Rx
So what are those larger goals? Well, here are a few of the key ones.
Promote dialog across silos
Right now, there are already a lot of niche conferences for specific groups in healthcare. There are events for specific areas of research, such as oncology and genomics, as previously mentioned. There are also events for specific kinds of people, like pharmaceutical reps, or insurance providers. Those conferences that do cut across the industry are only for one level of people, such as Chief Officers.
We want Strata Rx to convene a broad swath of people with an interest and a stake in the healthcare system: researchers, funders, providers, application developers, patient advocates, board members, insurers, IT staff, legislators, and everyone in between. By starting conversations among these different specialists, and by combining their relative expertise, we believe we can build a stronger community that is better able to solve problems.
We aim to be fire-starters, igniting connections and conversations.
An interview with Fred Smith of the CDC on their open content APIs.
Health care data liquidity (the ability of data to move freely and securely through the system) is an increasingly crucial topic in the era of big data. Most conversations about data liquidity focus on patient data, but other kinds of information need to be able to move freely and securely, too. Enter several government initiatives, including efforts at agencies within the Department of Health and Human Services (HHS) to make their content more easily available.
Fred Smith is team lead for the Interactive Media Technology Team in the Division of News and Electronic Media in the Office of the Associate Director for Communication for the U.S. Centers for Disease Control and Prevention (CDC) in Atlanta. We recently spoke by phone to discuss ways in which the CDC is working to make their information more “liquid”: easier to access, easier to repurpose, and easier to combine with other data sources.
Which data is available from the CDC APIs?
Fred Smith: In essence, what we’re doing is taking our unstructured web content and turning it into a structured database, so we can call an API into it for reuse. It’s making our content available for our partners to build into their websites or applications or whatever they’re building.
Todd Park likes to talk about “liberating data” — well, this is liberating content. What is a more high-value dataset than our own public health messaging? It incorporates not only HTML-based text, but also we’re building this to include multimedia — whether it’s podcasts, images, web badges, or other content — and have all that content be aware of other content based on category or taxonomy. So it will be easy to query, for example: “What content does the CDC have on smoking prevention?”
Virtual Fences, State Fonts, Simple Prompts, and MIT Health Hackery
Five ways we can improve the information we collect to help us solve hard problems in health care.
I was honored to chair O’Reilly’s inaugural edition of Strata Rx, our conference on data science in health care, this past October along with Colin Hill. As we’re beginning to plan this year’s event, I find myself thinking a lot about a theme that emerged from some of the keynotes last fall: in order to solve the problems we’re facing in health care — to lower costs and provide more personal, targeted treatments to patients — we don’t just need more data; we need better data.
Much has been made about the era of big data we find ourselves in. But though the data we collect is straining the limits of our tools and models, we’re still not making the kind of headway we hoped for in areas like health care. So big data isn’t enough. We need better data.
What does it mean to have better data in health care? Here are some things on my list; perhaps you can think of others. Read more…
From sensor journalism to lean government to preemptive health care, 2013 will be interesting.
2012 was a remarkable year for technology, government and society. In my 2012 year in review, I looked back at 10 trends that mattered. Below, I look ahead to the big ideas and technologies that will change the world, again. Read more…
3D Printed Drones, When Pacemakers Attack, N-Gram Updated, and Deanonymizing Datasets
- Home-made 3D-Printed Drones — if only they used computer-vision to sequence DNA, they’d be the perfect storm of O’Reilly memes :-)
- Hacking Pacemakers For Death — IOActive researcher Barnaby Jack has reverse-engineered a pacemaker transmitter to make it possible to deliver deadly electric shocks to pacemakers within 30 feet and rewrite their firmware.
- Google N-Gram Viewer Updated — now with more books, better OCR, parts of speech, and complex queries. e.g., the declining ratio of sex to drugs. Awesome work by Friend of O’Reilly, Jon Orwant.
- Deanonymizing Mobility Traces: Using Social Networks as a Side-Channel — a set of location traces can be deanonymized given an easily obtained social network graph. [...] Our experiments [on standard datasets] show that 80% of users are identiﬁed precisely, while only 8% are identiﬁed incorrectly, with the remainder mapped to a small set of users. (via Network World)
Voice your support for a proposed federal rule that expands patients' access to test results.
I’m convinced that there’s a wave of innovation coming in healthcare, driven by new kinds of data, new ways of extracting meaning from that data, and new business models that data can enable. That’s one of the reasons why we launched our StrataRx Conference, which focuses on the importance of data science to the future of health care.
Unfortunately, much of the data that will enable an entrepreneurial explosion is still locked up — in paper records, in proprietary data formats, and by well-intentioned but conflicting privacy regulations.
We’re making progress towards open data in healthcare, but there are still so many obstacles! Ann Waldo recently introduced me to one of these.
A 2009 law modernized patient access rights by allowing individuals to get copies of their medical records in electronic format. Unfortunately, however, these patients’ access rights surprisingly do not include lab test results – one of the types of medical records that people are most likely to find urgent and useful. Due to the interaction of HIPAA (the Federal medical privacy law), CLIA (a Federal laboratory regulatory law), and state laws, patients can only get direct access to their their test results from labs in a handful of states.
A recent New York Times story highlighted just how much pain and suffering can be caused by this inability to get access to your own lab results.
In 2011, the Department of Health and Human Services put forward a proposed Rule that would give patients the right to get their test results directly from laboratories. This Rule is still waiting to be finalized. In hopes of breaking the logjam, O’Reilly Media and a variety of other players have written a consensus letter that voices our whole-hearted support for that proposed Rule and encourages the Federal government to finalize it promptly.
We’d love to invite you to join us in signing this letter.
Patients’ rights should include direct access to their lab results, just like all their other medical records!
We're working with GE to explore the coming internet of very big things.
Consumer networks have revolutionized the way companies understand and reach their customers, making possible intricate measurement and accurate prediction at every step of every transaction. The same revolution is underway in our infrastructure, where new generations of sensor-laden power plants, cars and medical devices will generate vast quantities of data that could bring about improvements in quality, reliability and cost. Big machines will enter the modern era of big data, where they’ll be subject to constant analysis and optimization.
We’ve teamed up with General Electric to explore the industrial Internet and convene a series of conversations that we hope will accelerate its development. GE’s strong presence in many industries has given it a great deal of insight into the ways that industrial data might be gathered, distributed and linked together.
Linking together big smart devices into a true industrial Internet presents enormous challenges: standards need to be developed with the full engagement of the technology industry. Software innovators will need to develop tools that can handle vast quantities of sensor data under tight security constraints, sharing information that can improve the performance of systems that have many operators — without leaking anything important to malicious groups.
Launching the industrial Internet will require big investment on the part of those who will operate each of its nodes, so in addition to looking at the concept’s technical aspects we’ll also explore its promise as a business revolution in ways that are both practical and already in use (like remote operation of mining equipment) and promising but largely conceptual (like mobile health and big data in diagnostics).
GE won’t be the only voice in this conversation: other companies have developed their own visions for the industrial Internet and we’ll be exploring those as well, looking for commonalities and engaging as many voices as we can from our neutral place in the technology industry.
The promise of the industrial Internet is that it will bring intelligence to industries that are hugely capital-intensive and create broad value that all of the industrial Internet’s participants will share. We’ll look for stories that illustrate that future.
Chinese Hackers, Edible Sensors, Quantum Physics
- 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)
- 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)
- 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)
- 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)