ENTRIES TAGGED "genetics"

Technology that gets under your skin

Embeddables won't just be a revolution in functionality, but will dramatically alter how people fit into society.

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Editor’s note: we’re running a series of five excerpts from our forthcoming book Designing for Emerging Technologies, a compilation of works by industry experts in areas of user experience design related to genomics, robotics, the Internet of Things, and the Industrial Internet of Things.

In this excerpt, author Andy Goodman, group director at Fjord Madrid, looks beyond wearable computing to a deeper, more personal emerging computing technology: embeddables. Goodman says that beyond wearables and implants lies a future symbiosis of human and machine that will transform not only the delivery of information and services, but human nature as well.


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Author Andy Goodman, group director at Fjord Madrid.

Wearables are yesterday’s news; tomorrow’s news will be all about embeddables, tiny computing devices implanted inside your body that monitor your health, improve your functioning, and connect you to the digital world.

There is currently a lot of buzz in technology and design circles about wearables, living services, the Internet of Things, and smart materials. As designers working in these realms, we’ve begun to think about even more transformative things, envisioning a future where evolved technology is embedded inside our digestive tracts, sense organs, blood vessels, and even our cells. Everyday objects will become responsive and predictive, connecting us to the data sphere and reducing the distance between our skin and the surfaces of the made world. What we see further out, beyond the realm of wearables and implants, is the future symbiosis of the human body and the machine. Read more…

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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.
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Podcast: George Church on genomics

"Like a spaceship that was parked in our back yard"

A few weeks ago some of my colleagues and I recorded a conversation with George Church, a Harvard University geneticist and one of the founders of modern genomics. In the resulting podcast, you’ll hear Church offer his thoughts on the coming transformation of medicine, whether genes should be patentable, and whether the public is prepared to deal with genetic data.

Here’s how Church characterizes the state of genomics:

It’s kind of like ’93 on the Web. In fact, in a certain sense, it’s more sophisticated than electronics because we have inherited three billion years of amazing technology that was just like a spaceship that was parked in our back yard and we’re just reverse-engineering and probably not fully utilizing even the stuff that we’ve discovered so far.

A few other helpful links:

On this podcast from O’Reilly Media: Tim O’Reilly, Roger Magoulas, Jim Stogdill, Mike Loukides, and Jon Bruner. Subscribe to the O’Reilly Radar podcast through iTunes or SoundCloud, or directly through our podcast’s RSS feed.

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A very serious game that can cure the orphan diseases

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.

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Data sharing drives diagnoses and cures, if we can get there (part 2)

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.

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Data sharing drives diagnoses and cures, if we can get there (part 1)

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.

Read more…

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Discovering genetic associations using large data

David Heckerman's research uses big datasets to tackle essential health questions.

David Heckerman from Microsoft Research presents a summary of his work in the session “Discovering Genetic Associations on Large Data.” This was part of the Strata Rx Online Conference: Personalized Medicine, a preview of O’Reilly’s conference Strata Rx, highlighting the use of data in medical research and delivery.

Heckerman’s research attempts to answer essential questions such as “What is your propensity for getting a particular disease?” and “How are you likely to react to a particular drug?”

Key points from Heckerman’s presentation include: Read more…

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Health records support genetics research at Children's Hospital of Philadelphia

Michael Italia on making use of data collected in health care settings.

Michael Italia from Children's Hospital of Philadelphia discusses the tools and methods his team uses to manage health care data.

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Health records support genetics research at Children’s Hospital of Philadelphia

Michael Italia on making use of data collected in health care settings.

Michael Italia from Children's Hospital of Philadelphia discusses the tools and methods his team uses to manage health care data.

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Recombinant Research: Breaking open rewards and incentives

Can open data dominate biological science as open source has in software?

To move from a hothouse environment of experimentation to the mainstream of one of the world's most lucrative and tradition-bound industries, Sage Bionetworks must aim for its nucleus: rewards and incentives. Comparisons to open source software and a summary of tasks for Sage Congress.

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