ENTRIES TAGGED "health care"
Fit2Cure taps the public's visual skills to match compounds to targets
In the inspiring tradition of Foldit, the game for determining protein shapes, Fit2Cure crowdsources the problem of finding drugs that can cure the many under-researched diseases of developing countries. Fit2Cure appeals to the player’s visual–even physical–sense of the world, and requires much less background knowledge than Foldit.
There about 7,000 rare diseases, fewer than 5% of which have cures. The number of people currently engaged in making drug discoveries is by no means adequate to study all these diseases. A recent gift to Harvard shows the importance that medical researchers attach to filling the gap. As an alternative approach, abstracting the drug discovery process into a game could empower thousands, if not millions, of people to contribute to this process and make discoveries in diseases that get little attention to scientists or pharmaceutical companies.
The biological concept behind Fit2Cure is that medicines have specific shapes that fit into the proteins of the victim’s biological structures like jig-saw puzzle pieces (but more rounded). Many cures require finding a drug that has the same jig-saw shape and can fit into the target protein molecule, thus preventing it from functioning normally.
How the field of genetics is using data within research and to evaluate researchers
Editor’s note: Earlier this week, Part 1 of this article described Sage Bionetworks, a recent Congress they held, and their way of promoting data sharing through a challenge.
Data sharing is not an unfamiliar practice in genetics. Plenty of cell lines and other data stores are publicly available from such places as the TCGA data set from the National Cancer Institute, Gene Expression Omnibus (GEO), and Array Expression (all of which can be accessed through Synapse). So to some extent the current revolution in sharing lies not in the data itself but in critical related areas.
First, many of the data sets are weakened by metadata problems. A Sage programmer told me that the famous TCGA set is enormous but poorly curated. For instance, different data sets in TCGA may refer to the same drug by different names, generic versus brand name. Provenance–a clear description of how the data was collected and prepared for use–is also weak in TCGA.
In contrast, GEO records tend to contain good provenance information (see an example), but only as free-form text, which presents the same barriers to searching and aggregation as free-form text in medical records. Synapse is developing a structured format for presenting provenance based on the W3C’s PROV standard. One researcher told me this was the most promising contribution of Synapse toward the shared used of genetic information.
Observations from Sage Congress and collaboration through its challenge
The glowing reports we read of biotech advances almost cause one’s brain to ache. They leave us thinking that medical researchers must command the latest in all technological tools. But the engines of genetic and pharmaceutical innovation are stuttering for lack of one key fuel: data. Here they are left with the equivalent of trying to build skyscrapers with lathes and screwdrivers.
Sage Congress, held this past week in San Francisco, investigated the multiple facets of data in these field: gene sequences, models for finding pathways, patient behavior and symptoms (known as phenotypic data), and code to process all these inputs. A survey of efforts by the organizers, Sage Bionetworks, and other innovations in genetic data handling can show how genetics resembles and differs from other disciplines.
An intense lesson in code sharing
At last year’s Congress, Sage announced a challenge, together with the DREAM project, intended to galvanize researchers in genetics while showing off the growing capabilities of Sage’s Synapse platform. Synapse ties together a number of data sets in genetics and provides tools for researchers to upload new data, while searching other researchers’ data sets. Its challenge highlighted the industry’s need for better data sharing, and some ways to get there.
Signs of the field's potential along with self-imposed limits
I spent most of the past week on my annual assessment of the progress that the field of health information technology is making toward culling the benefits offered by computers and Internet connectivity: instant access to data anywhere; a leveling of access for different patient populations and for health care providers big and small; the use of analytics to direct resources and attack problems better.
The big HIMSS conference in New Orleans, a crossroads for doctors, technologists, and policy-makers, provided a one-stop check-in. I already covered several aspects of the conference in two earlier postings, Singin’ the Blues: visions deferred at HIMSS health IT conference and Slow & Steady: looking toward a better health IT future at HIMSS. Here I’ll summarize a couple more trends in data exchange and basic functions of health IT systems.
Participatory medicine and hospital technologies take steps forward
After my funereal disparagement yesterday of the opening of the HIMSS health care conference in New Orleans, I decided to pick up the beat today and talk about some of the people and ideas I encountered with promise for the future.
Nobody Knows The Way I Feel This Morning: patient engagement and all that jazz
Yesterday I spoke of the gap between the reform-minded leaders of health care and the institutions that mostly take care of us. The latest battleground between these peaks of care is the movement variously called patient engagement, patient empowerment, and participatory medicine.
There’s nothing new about this concept. Desperate patients have been self-educating, negotiating with health care systems, and creating advocacy groups forever. On the self-help front, Prevention Magazine began (according to Wikipedia) in 1950. The Society for Participatory Medicine was founded in the mid 2000′s, around the time e-Patient Dave made the concept into a meme through his brave online sharing of his care.
HIMSS has thrown its support behind the Society for Participatory Medicine, which had a lunchtime meeting at the conference yesterday to discuss increasing membership and grass-roots promotional activities. (Folks, consider yourselves promoted.) HIMSS also invited teh popular author Eric Topol to deliver yesterday’s keynote. And the first statement offered by Topol was praise for Regina Holliday, a consumately self-educated patient advocate and creator of the famous artwork and painted jackets in the Walking Gallery. Read more…
The main concerns of health reformers don't rise to the top of health provider agendas
HIMSS, the leading health IT conference in the US, drew over 32,000 people to New Orleans this year (with another thousand or two expected to register by the end of the conference). High as this turn-out sounds, it represents a drop from last year, which exceeded 37,000.
Maybe HIMSS could do even better by adding a “Clueless” or “I don’t believe in health IT” track. Talking to the people who promote health IT issues to the doctors and their managers, I sense a gap–and to some extent, a spectrum of belief–in the recognition of the value of gathering and analyzing data about health care.
I do believe that American health care providers have evolved to accept computerization, if only in response to the HITECH act (passed with bipartisan Congressional support) and the law’s requirements for Meaningful Use of eleectronic records. Privately, many providers may still feel that electronic health records are a bad dream that will go away. This article presents a radically different view. I think electronic health records are a bad dream that will go on for many years to come. I’ll expand on this angle when blogging from HIMSS this year.
Critical data on hypoglycemia not collected before
In a mobile, texting, socially engaged society, one would expect medical researchers to move beyond clipboards and phone surveys to make the most of technology. Harvard Medical School and Boston Children’s Hospital are starting to do that with a series of studies they’ve done querying people with diabetes, a growing population with multiple, severe health needs. Elissa Weitzman, an assistant professor at HMS and Children’s Hospital, discusses a recent study that she and her team published, using a social network called TuDiabetes, the open source patient data repository Indivo (developed at HMS), and an app they developed called TuAnalyze.
Android TV systems provide low-cost interactive care
Video systems can streamline hospital care in all sorts of ways from displaying messages (“Quiet time is 1 to 2 PM today”) to taking patient surveys, showing patients their X-Rays, and helping patients view their records from their beds. But most of these systems lie outside the budgets of small and rural hospitals. Healthcare Information is halving the costs of the systems, largely by deploying Android in their sets, and is selling them to smaller healthcare institutions that could not afford them before. The use of Android also permits hospitals to choose among the hundreds of thousands of standard apps available in App Stores.
Sequence of screens showing path through a patient survey