James Turner

James Turner, contributing editor for oreilly.com, is a freelance journalist who has written for publications as diverse as the Christian Science Monitor, Processor, Linuxworld Magazine, Developer.com and WIRED Magazine. In addition to his shorter writing, he has also written two books on Java Web Development (MySQL & JSP Web Applications" and "Struts: Kick Start"). He is the former Senior Editor of LinuxWorld Magazine and Senior Contributing Editor for Linux Today. He has also spent more than 25 years as a software engineer and system administrator, and currently works as a Senior Software Engineer for a company in the Boston area. His past employers have included the MIT Artificial Intelligence Laboratory, Xerox AI Systems, Solbourne Computer, Interleaf, the Christian Science Monitor and contracting positions at BBN and Fidelity Investments. He is a committer on the Apache Jakarta Struts project and served as the Struts 1.1B3 release manager. He lives in a 200 year old Colonial farmhouse in Derry, NH along with his wife and son. He is an open water diver and instrument-rated private pilot, as well as an avid science fiction fan.

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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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.

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Improving healthcare in Zambia with CouchDB

Improving healthcare in Zambia with CouchDB

CouchDB proves a good fit for a project with technical limits.

A new project in Zambia is trying to integrate supervisors, clinics, and community healthcare workers into a system that can improve patient service and provide more data. In this interview, Cory Zue explains how CouchDB is playing a role.

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Hadoop: What it is, how it works, and what it can do

Hadoop: What it is, how it works, and what it can do

Cloudera CEO Mike Olson on Hadoop's architecture and its data applications.

Hadoop gets a lot of buzz in database circles, but some folks are still hazy about what it is and how it works. In this interview, Cloudera CEO and Strata speaker Mike Olson discusses Hadoop's background and its current utility.

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Joe Stump on data, APIs, and why location is up for grabs

Joe Stump on data, APIs, and why location is up for grabs

The SimpleGEO CTO and former Digg architect discusses NoSQL and location's future

I recently had a long conversation with Joe Stump, CTO of SimpleGeo, about location, geodata, and the NoSQL movement. Stump, who was formerly lead architect at Digg, had a lot to say. Here’s the highlights, you can find the full interview elsewhere on Radar.

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ETech Preview: Science Commons Wants Data to Be Free

ETech Preview: Science Commons Wants Data to Be Free

John Wilbanks has a passion for lowering the barrier between scientists who want to share information. A graduate of Tulane University, Mr. Wilbanks started his career working as a legislative aide, before moving on to pursue work in bioinformatics, which included the founding of Incellico, a company which built semantic graph networks for use in pharmaceutical research and development. Mr. Wilbanks now serves as the Vice President of Science at Creative Commons, and runs the Science Commons project. He will be speaking at The O'Reilly Emerging Technology Conference in March, on the challenges and accomplishments of Science Commons, and he's joining us today to talk a bit about it.

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