- On Being a Senior Engineer (Etsy) — Mature engineers know that no matter how complete, elegant, or superior their designs are, it won’t matter if no one wants to work alongside them because they are assholes.
- Control Theory (Coursera) — Learn about how to make mobile robots move in effective, safe, predictable, and collaborative ways using modern control theory. (via DIY Drones)
- US Moves Towards Open Access (WaPo) — Congress passed a budget that will make about half of taxpayer-funded research available to the public.
- NHS Patient Data Available for Companies to Buy (The Guardian) — Once live, organisations such as university research departments – but also insurers and drug companies – will be able to apply to the new Health and Social Care Information Centre (HSCIC) to gain access to the database, called care.data. If an application is approved then firms will have to pay to extract this information, which will be scrubbed of some personal identifiers but not enough to make the information completely anonymous – a process known as “pseudonymisation”. Recipe for disaster as it has been repeatedly shown that it’s easy to identify individuals, given enough scrubbed data. Can’t see why the NHS just doesn’t make it an app in Facebook. “Nat’s Prostate status: it’s complicated.”
Four short links: 21 January 2014
Mature Engineering, Control Theory, Open Access USA, and UK Health Data Too-Open?
Four short links: 28 October 2013
The Internot of Things, Explainy Learning, Medical Microcontroller Board, and Coder Sutra
- A Cyber Attack Against Israel Shut Down a Road — The hackers targeted the Tunnels’ camera system which put the roadway into an immediate lockdown mode, shutting it down for twenty minutes. The next day the attackers managed to break in for even longer during the heavy morning rush hour, shutting the entire system for eight hours. Because all that is digital melts into code, and code is an unsolved problem.
- Random Decision Forests (PDF) — “Due to the nature of the algorithm, most Random Decision Forest implementations provide an extraordinary amount of information about the final state of the classifier and how it derived from the training data.” (via Greg Borenstein)
- BITalino — 149 Euro microcontroller board full of physiological sensors: muscles, skin conductivity, light, acceleration, and heartbeat. A platform for healthcare hardware hacking?
- How to Be a Programmer — a braindump from a guru.
Denny Ausiello discusses phenotypes, pathways, and stratification
A video interview with Colin Hill
Last month, Strata Rx Program Chair Colin Hill, of GNS Healthcare, sat down with Dr. Dennis Ausiello, Jackson Professor of Clinical Medicine at the Harvard Medical School, Co-Director at CATCH, Pfizer Board of Directors Member, and Former Chief of Medicine at the Massachusetts General Hospital (MGH), for a fireside chat at a private reception hosted by GNS. Their insightful conversation covered a range of topics that all touched on or intersected with the need to create smaller and more precise cohorts, as well as the need to focus on phenotypic data as much as we do on genotypic data.
The full video appears below.
Doctors vs Data
There is a storm brewing in Healthcare. Doctors have been in charge of healthcare for a long time, and have become comfortable, sometimes even arrogant, with their authority and power. But dumb data beats smart doctors every time. Forward thinking doctors are embracing data, with surprising grace and humility. Others are having much more trouble adjusting.
Doctors, historically, have been the “end of the discussion” on clinical matters. Doctors make the diagnosis, they make the calls in the surgery suite, they get to decide if someone is suffering enough to justify pain medications, they frequently decide whether someone is mentally incompetent or merely eccentric. Our society places a lot of trust in doctors, because they have the training needed to make really hard choices.
Doctors, as a group, have been in charge of how healthcare operates for centuries. In times past, the only way to determine whether a doctor was doing a good job was to become a doctor yourself, and then perform case reviews. Even in court, if you wanted to refute a doctor, you needed another doctor.
Genomics and the Role of Big Data in Personalizing the Healthcare Experience
Increasingly available data spurs organizations to make analysis easier
This article was written with Ellen M. Martin and Tobi Skotnes. Dr. Feldman will deliver a webinar on this topic on September 18 and will speak about it at the Strata Rx conference.
Genomics is making headlines in both academia and the celebrity world. With intense media coverage of Angelina Jolie’s recent double mastectomy after genetic tests revealed that she was predisposed to breast cancer, genetic testing and genomics have been propelled to the front of many more minds.
In this new data field, companies are approaching the collection, analysis, and turning of data into usable information from a variety of angles.
A Day at the 2013 Genomes, Environments and Traits Conference
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.
A bit about Strata Rx: our goals, our content, and you
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.
Making government health data personal again
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?”
Four short links: 11 February 2013
Virtual Fences, State Fonts, Simple Prompts, and MIT Health Hackery
- 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.