Tag Archives: qsaccess

Runkeeper & Research: The Keeping Pace Study

Yesterday evening I laced up my running shoes, connected my bluetooth headphones, turned on my Spotify playlist, and most importantly, hit “Go Running” on my Runkeeper app. About an hour later and I had run 6 miles at a decent pace of around 8 minutes per mile. And I knew this thanks to Runkeeper.

Founded in 2008, Runkeeper is designed to assist individuals who want to track their activities with GPS precision, whether that is walking, running, hiking, or cycling. If you’re moving outdoors, Runkeeper and similar apps, such as Strava or MapMyRun, use your smartphone’s GPS to pinpoint exactly where you are and how fast you’re moving. With all that data, you can train for your next marathon, discover new routes, and now, thanks to efforts by New York University researchers, take part in advancing public health research.

“We know from the existing literature that spatial characteristics like walkable neighborhoods and green spaces encourage exercise, but a lot of the details are still unknown.”

 

Last week, Dr. Rumi Chunara and her colleagues launched the Keeping Pace study. Over the next few months they hope to enroll participants who are willing to share their geo-located exercise data from Runkeeper. Because Runkeeper keeps a log of not only what you did, but where you did it, researchers hope to use the large amount of aggregated data to better understand physical activity patterns in communities around the United States.

“Typically, this type of research takes a long time and includes long, ardorous surveys or giving out GPS devices to participants,” said Dr. Chunara. “But with this type of data from apps people already use, we will be able to understand how the environment and exercise are related over more rapid and longer time periods.” With this data being contributed, the research team hope to understand differences in exercise choice between commuting and recreational activities, variation in activities among neighborhoods, and where people spend their time while being active.

Participants who enroll in Keeping Pace will be asked to complete a short demographic survey and then connect their Runkeeper account so researchers can access the type of activities they do and the GPS-based map associated with the activity. The Runkeeper data connection is being handled by a unique research platform, Open Humans.

A few years ago, Dr. Rumi Chunara was at a meeting hosted by the US Department of Health and Human Services. She was there to present and speak with colleagues about the growing importance of citizen science and crowdsourced data. There she met Jason Bobe, Executive Director of PersonalGenomes.org. They got to talking about some of their common insterests in open data, research, and new models for research participation. Later, when Dr. Chunara was designing GoViral, a project to examine how to leverage crowdsourced flu symptom information and diagnostics to predict illness risk, she ran into some issues with hosting and handling the amount of data participants were contributing. “It was obvious we needed some sort of platform to handle data,” said Dr. Chunara. She got back in touch with Jason, who helped her think about the issues and how to solve them.

This year, when it came to build out the infrastructure for the Keeping Pace study, Dr. Chunara decided to get back in touch with Jason and his colleagues, who were now developing OpenHumans.org. As we’ve written before, Open Humans represents a new way of thinking regarding researcher studies, participants, and the data being transferred between the two. The two teams, Open Humans and Dr. Chunara’s lab at NYU, worked together to develop an easy method for individuals to simultaneously allow researchers access to their Runkeeper data, and also maintain control over where and how that data flowed. Specifically, each individual who chooses to participate in the Keeping Pace study will be asked to create an Open Humans account, connect their Runkeeper account, and then authorize the Keeping Pace study to access their data. It sounds like a lot of work, but thanks to the designers and the use of Runkeeper’s API, it takes no more than five minutes to complete.

But why go through that trouble at all? Why not just have participants export their Runkeeper data and send it to the researchers? Why didn’t Dr Chunara and her colleagues build that data connection themselves?

Thanks to the proliferation of sensors, wearables, and smartphones, the ability to generate data about our lives is rapidly expanding. Pair that data with new efforts like the Precision Medicine Initiative and it’s easy to see the potential for researchers to understand our lives and our health in new and interesting ways. But what about the people who create that data? People, like myself, who strap on their phones when they go out for a run or log onto a website to report their flu symptoms. What do they have a right to in regards to their data? This is the question many researchers and scientific institutions are grappling with. But some have already taken a stand.

 

“What data are collected and how varies across research studies, but the question remains, ‘Who owns it?’ If someone is spending time generating then they should have control over it.”

 

Dr. Chunara and her colleagues chose to work with Open Humans because they shared the same perspective — participants should be in control of their data. “Open Humans has created an infrastructure that makes it easy to share and learn while respecting the participant and their data. That’s a noble motive, and it’s important,” said Dr. Chunara. Today, Keeping Pace is the first study to use Open Humans for data access and management for a research study. If successful, researchers may not only learn about exercise and the environment, but also about how studies that place an emphasis on participants’ data access and control may engage the public in new ways.

Keeping Pace is currently enrolling participants. If you’re a Runkeeper user and want to contribute your data to research, please visit the study website to learn more.


Keeping Pace was funded as part of the Agile Projects grants by the Health Data Exploration Network. If you’re a researcher, company, or individual interested in personal health data, sign up to become a network member. Membership is free.


Quantified Self Labs is dedicated to sharing stories and insights about the role of data access for personal and public health. We invite you to share your data access stories and this article. Then follow along on quantifiedself.com and @quantifiedself.

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Our Data, Our Health: Thoughts on using mHealth for the Precision Medicine Cohort

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On January 30th, President Obama announced the funding of a possibly groundbreaking research program — The Precision Medicine Initiative (PMI).

Launched with a $215 million investment in the President’s 2016 Budget, the Precision Medicine Initiative will pioneer a new model of patient-powered research that promises to accelerate biomedical discoveries and provide clinicians with new tools, knowledge, and therapies to select which treatments will work best for which patients.

Since the announcement the National Institutes of Health (NIH) have been hard at work convening a working group to build a foundation of rules, standards, and principles upon which they hope will generate meaningful outcomes: improving the health for all Americans by moving towards a more nuanced and individual view of health and wellness. As part of this project, the largest portiont of funding is being dedicated to the “development of a voluntary national research cohort of a million or more volunteers to propel our understanding of health and disease and set the foundation for a new way of doing research through engaged participants and open, responsible data sharing.”

As part of engaging this cohort the NIH is considering the role of patient generated data from mobile phones and sensors. Of course this is where we at Quantified Self Labs become intrigued. We have a long history of supporting individual’s ingenuity, insight, and expertise when it comes to personal data they collect on their own. Since 2008, we’ve been bringing together people to share their stories of self-tracking using a variety of different methods, some of which are no doubt being examined by researchers and NIH leadership for use in the proposed Precision Medicine Cohort.

We are excited to hear that the NIH is taking the time to listen to the American public through the use of online feedback forms. They are currently seeking comments on the use of mHealth for the Precision Medicine Cohort. Specifically, they want to know how people think that data generated by current and future biometric and physiologic sensors (such as heart rate and physical activity tracking devices) could be useful. Furthermore, the NIH isinterested in reactions to using smartphones to collect data on volunteer participants in the cohort. In the short description of the feedback request they highlight five key considerations:

1. Willingness of participants to carry their smartphone and wear wireless sensor devices sufficiently throughout the day so researchers can assess their health and activities.

2. Willingness of participants without smartphones to upgrade to a smartphone at no expense.

3. How often people would be willing to let researchers collect data through devices without being an inconvenience.

4. The kind of information participants might like to receive back from researchers, and how often.

5. Other ways to conveniently collect information from participants apart from smart phones or wearable devices.

We spent a little time browsing through the current crop of comments, which didn’t take long as there are only 52 at the time of this writing, to understand how people are thinking about mHealth, their data, and what it means to contribute personal data for public health research.

Privacy & Confidentiality

A common theme was a concern over what type of privacy protections would be implemented to protect volunteers who contribute their data. Comments ranged from outright fear of the government “tapping into personal computers, phones or other devices for collecting health information” to thoughts on access, control and protection of data contributed as part of this project.

As long as citizens can remain in control of the collection, flow and use of their data — and the government can guarantee anonymity, much benefit can be had from this. If it is going to be a government initiative, then standardized collection methodologies and protections will be required and the data should not “also” be collected for commercial usage. Clarity surrounding use models, sharing permissions and general privacy and security are a must.

I would also like to make sure that it is clear who ‘owns’ the data. Many times health professionals collect data about patients and then use it–often without letting the person know the data is aggregated and studied.

Diversity and Representativeness

As with any research study, there is a call to make sure that the sample being studied is representative of the population. This is especially important given the expressed interest in using different types of technology to track, measure, and engage with research participants. Those who have offered feedback have clearly picked up on the need to make sure that even those who are not current users of wearable sensors and/or smartphones are considered.

This will leave out the severely ill and disabled who are bedridden, unable to move, and definitely unable to manage a smart phone (as well as anyone whose illness causes cognitive challenges). Yet these are the patients who really need to be studied. So while it’s not a bad idea, please factor in selection bias and please, please, accommodate the most ill if you decide to implement this.

Interestingly, there are a few comments on how dependence on a smartphone may limit the diversity of the cohort.

Smartphones, etc. will limit the diversity of the sample. For example, large areas of Appalachia will be excluded. Internet access is limited in rural areas; even if available, the technology is not adequate to support many applications.

While the diversity of the sample is something that must be considered, I’m left wondering about the true impact of using smartphones for data collection as recent data from Pew suggests that nearly two-thirds of Americans own a smartphone. It appears that economic diversity may be the limiting factor when it comes to using smartphones as part of the cohort. Clearly there is a gap in smartphone ownership across income and education levels, but also when we consider geographic location.

However, one of the considerations clearly states that an “upgrade to a smartphone at no expense” may be part of this research initiative. What is the true cost of this free upgrade? It appears to be unknown, but it’s going to be important to think about the recurring costs of data plans associated with these devices, especially when data transfer is part of participating in the research.

The issue probably depends on the participant and what is being provided. I’m assuming providing the smartphone would include providing the data plan, which can be expensive.

Barriers to Using mHealth

While using wearable sensors, apps, and smartphones to collect personal health data is growing trend, there are still concerns regarding how long individuals will actively use the tools. While the Fitbits of the world are selling millions of devices, we don’t really know how long people are willing to use them, and if they’re willing to contribute that data to research (although preliminary studies are promising).

There is concern that adding devices, measurement, and data collection to the everyday lives of individuals may present a burden and that the data will suffer from inconsistent engagement. The “life gets in the way” of participating in research is a common, and justified, refrain.

In our experience, conducting a number of trials using devices, many people do not carry or use devices for very long that do not fit into their existing habits. People may use new devices provided by researchers for short periods of time, if provided research support, monitoring, and prompting, but for large scale trials and longer assessment periods, adherence will fall off considerably.

Benefits of mHealth

It’s not all doom and gloom and negativity though, there is an overwhelmingly positive outlook on the use of wearables and mobile-based data collection for informing personal and public health. From researchers to individuals already using these devices to understand their own health, the current comments are full of support for exploring new technologies, sensing capabilities, and personal data collection methods to deliver personal precision medicine.

Integration of data from personal sensors and mobile devices has the potential to change the role of the patient in their health and care, to improve the accuracy and value of behavioral data in healthcare, and to provide unparalleled insights into the how and why of behavior change in health.

I am 60 but use a Withing Blood Pressure Cuff, Basis Peak and Alive EKG. I am a cancer survivor of Hodgkin’s Lymphoma and Breast Cancer. Due to my treatment I am left with complications that need to be monitored. I feel more secure using these devices. Knowledge is power.

Our Feedback

In the name of transparency, below you’ll find the full text of our comments submitted to the NIH.

The world is changing, more information is flowing across what were once impassable borders. That information is changing the way we see the world, and how we understand ourselves. Health and healthcare is a big part of this evolution in information flows. At Quantified Self, we’ve seen hundreds of examples from individuals around the world who have used personal data collected through a variety of means to impact and understand their health. It’s with these examples in mind that I’d like to share my thoughts on using mHealth for the Precision Medicine Cohort.

The considerations mentioned above are clear, but vague enough to make the only appropriate answer, “it depends.”

Will participants carry their smartphones and wear sensors? It depends. It depends on how participants are recruited and what they are being asked to contribute to. Do they have a say in what questions are being asked? Is constant data collection a requirement for participation, or can participants engage inconistently, contributing data sparsely? What activities would researchers want to understand? Some individuals may be perfectly okay with contributing physical activity data, but not geolocation data supplied by a smartphone GPS.

Will participants be willing to upgrade to a smartphone? It depends. Will they also be compensated for an increase in costs associated with data plans so that their smartphone can send data to a researcher? Will they be able to use their smartphone for personal use, downloading apps and services freely? Is the smartphone upgrade dependent on participation in research for a given amount of time, and if so, how long? Is this form of compensation coercive for those who have never been able to afford a smartphone? Including a socially and economically diverse population in the cohort while not introducing increased costs and burden will be important to consider.

Will participants allow researchers to collect data, and how often? It depends. Will participants play an active role in the data collection, or will it be passively collected through sensors and background data transfer? Will participants be engaged in the full research process, helping develop the questions, data collection methods, and even the analysis? Will participants be able to choose the frequency of data transfer that makes sense to them and their lifestyle? It’s possible to envision participants contributing infrquently over a long timescale. Will these type of contributions help push precision medicine forward?

What kind of information would participants like to receive, and how often? It depends. Are participants able to access and control the data they create? Do they get to choose what researchers or studies are able to use their data? Will they receive the same information and data that researchers have access to? All participants may not actually want their data, but I believe that the research community has an ethical obligation to be open, honest, and transparent when it comes to what we collect. This includes giving data back to participants, especially with regards to health data. Participants should also receive timely access to any and all research findings. Published work that results from Cohort data should be published in open access and freely available outlets (and open data sets should be published simultaneously).

What other ways might their be to collect information from participants? It depends. What type of information is important to researchers? Many different research groups, and even commercial entities, have discovered the power of using text messaging for data collection. Text messaging should be examined as a possible large-scale and low-cost (financial and time) method for understanding many different aspects of personal health.

Smartphones, wearable devices, and personal data applications and services represent an unprecedented look into our daily lives. The Precision Medicine Initiative should continue to explore how best to incorporate the public in the process of crafting the protocols and methods. The public will be the participants, and we should remember that this research is being conducting with them, not on them. A spirit of openness and transparency should guide this important work.

The public comment period for input on using mHealth for the Precision Medicine Cohort closes on Friday, July 24. We invite you to add your thoughts and ideas.

 

This post is part of our Access Matters publication. We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on @quantifiedself.

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Announcing the QS Access Program

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Self-knowledge through numbers. Personal meaning from personal data. These are the guiding principles of the work we do here at Quantified Self Labs. Through our editorial work, our events, and our support of a worldwide network of meetups we are focused on shaping the culture of personal data and it’s impact on our lives. We realized some time ago that impact is determined not only by data analysis skills, scientific training, or even the use of new tools and technologies (although all of these play an important role). Rather, impact is directly related to our ability to access the data we’re creating and collecting during the course of our lives.

We’re happy to announce our new QS Access Program with support from the Robert Wood Johnson Foundation. We’re working together to bring issues, ideas, and insights related to personal data access for personal and public health to the forefront of this evolving conversation. We hope you join us.

You can read the full release here. Below are two quotes from the release that embody our current and future work.

“The Robert Wood Johnson Foundation is working with many partners to build a Culture of Health in the U.S., and in that culture of health, people are attuned to the factors that influence their health and the health of their communities,” said Stephen Downs, Chief Information and Technology Officer at the Robert Wood Johnson Foundation. “The explosion of data on day-to-day life creates tremendous potential for new insights about health at both the personal and population levels. To realize this potential, people need access to their data — so they can use services that surface the connections between symptoms, behaviors and community environments and so they can choose to contribute their data to important research efforts.”

“We believe that when individuals, families, and communities are able to ask their own questions of their own data, everybody benefits,” said Gary Wolf, Director of QS Labs. “We look forward to doing our part to build a culture of health with the support of the Robert Wood Johnson Foundation, and we invite anybody who has an access story to tell to get in touch.”

If you’d like to learn more or get involved. Please contact:
Ernesto Ramirez
Program Director
Quantified Self Labs
ernesto@quantifiedself.com

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Better by Default: An Access Conversation with John Wilbanks

Photo by Joi Ito

Photo by Joi Ito

John Wilbanks is the Chief Commons Officer for Sage Bionetworks. You may not recognize John’s name or the name of his organization, but after today, you may want to commit it to memory. On March 9, 2014 Tim Cook introduced us to the idea of ResearchKit and then turned it over to Jeff Williams who described the new initiative and the five applications that were launched in collaboration with leading academic labs, advocacy groups, and research organizations. Sage Bionetworks is responsible for two of those apps, and John is responsible for leading design and development of many of the novel research tools and methods used by Sage. The following is an edited transcript of a conversation we had with John after the announcement.


Parkinson mPower App

This is Big

Think about what we’re doing in the context of it being open source. ResearchKit is going to be great for the QS community. They are perfectly suited to take advantage of ResearchKit. Let’s look at the five apps that were released today. They cover complex, but ubiquitious diseases. Plus the diseases are a great fit for the technology and sensor capabilities. But what is going to be amazing is when ResearchKit is released as open source. Anyone will have the ability to reskin these existing five apps to make novel research tools. Our Parkinson’s app might become a Huntington’s app. Our breast cancer app measures cognition really well, maybe it gets reskinned into a focused cognition tool. The app that focuses on diabetes could become a diet research app.

Large research institutions are going to jump all over this, but I’m more excited about the idea that small groups of people who have a bit of technical skill can work together to reskin the apps and turn them into longitudinal studies of 20 or 50 people. There may be five of those small groups, maybe 100. We can then work to stich those groups together and learn even more.

So the rare and chronic disease folks and the tech and QS community are involved. Now we come to everyone else. Everyone who isn’t suffering or presenting with a medical issue. We have to figure out ways to get them to participate.

We have a long tradition of creating incentives to participate. There is no reason we can’t create novel incentive methods to bring people into research. Maybe you receive a federal income tax credit. Maybe you’re allowed to enroll in long term care insurance at a reduced rate. There are a lot of ways to bring people in and that’s not touching the innate altruism of people and their curiosity. We’re already seeing this with the Precision Medicine Initiative. People want to take part, they want to engage.

Once we start getting that engagement, and we begin to see a diverse ecology of applications built on top of ResearchKit, then we’ll start to see success. It may take a bit of time. It won’t happen with this iteration. Maybe not even the second, but when we get enough devices, apps, participants, and improved interoperability between them all we’ll start to see the power of network effects.

You have to remember, there are no “killer apps” without network effects. Email wasn’t a big deal in the late 80′s because you couldn’t reach anyone outside your system. But then the web came, we connected the dots, the nodes, and then there it was, the power of the newtork.

I see QS and our current state of devices, apps, and tools being very similar to all those nerds typing away in the 80′s. They were okay with what they had because they could work with it. Then the net came and you have more control and more interefaces. That leads to the killer apps. That’s why we’re building this, for the third or fourth wave.


Share the Journey app

Everything we’re doing, the whole stack working together, is new. Consenting participants using well-designed and open-source Participant-Centered Consent toolkits. Giving participants direct access to their data. Securely hosting automatically de-identified data in the cloud using our Bridge Server. None of these have been done before at the same time.

We’re a non-profit, so we can be this icebreaker. We can take these risks and experiment and iterate and learn. No one asks us how we’re going to make money. We have a different bottom line — what is best for everyone involved? That outlook gives us the freedom to do this work.

I’m honored to have the opportunity to create a product that pushed my beliefs: participants-centric principles. If you’re a participant, then you decide. You’re in control. You can do cool stuff with the data. You can stop answering questions whenever you want. You can delete the app. We live in a world in which the politics of technology are dicteated by code and they often don’t share those ideas. To get this opportunity is amazing.

These moments don’t happen often. This is IBM going open source in the late 90s. It’s that big. I wasn’t sure I was going to be a piece of something that big. We’re trying to change culture.

In 1998 Lawrence Lessig proposed the pathetic dot theory in his book, Code and Other Laws of CyberspaceHe theorized that four forces control what we do: Law, Architecture, Social Norms, and the Market. He went futher and differentiated west coast law, which was quickly becoming dominated by software code and east coast law, what we normally think of when we think of laws.

I think up until now we’ve failed to properly take up that lever, to use software code, west coast law, to express something better. People often forget that building software means expressing an opinion. We created our apps, our tools, our systems to reflect our opinion, that participants should be at the center of research. And then we’re giving it away. That’s our position, and it’s better by default.

But, we’ve just started. The fun now is that we get to test it. I’ve always said that we can’t screw it up any worse than it already is. This isn’t the end. It’s not finished. We’re going to keep changing and learning.


John can be found online at del-fi.org and @wilbanks.

We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on quantifiedself.com@quantifiedself and our Access Matters Medium publication.

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Quantified Self and Apple’s ResearchKit

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Apple’s announcement of ResearchKit is strong evidence that Quantified Self practices are emerging as a major influence on medical research and other forms of knowledge making.

Apple talked about how their new effort focused on opening up health research is designed to combat five main current issues:

  • Limited Participation
  • Small sample sizes limit our understanding of diseases
  • Reliance on subjective data
  • Infrequent data provide only snapshots through time
  • One-way communication from researcher to participant (and only at the end of the study, if at all)

Furthermore, the design of ResearchKit allows the  participant to decide how data is shared. Apple will not see the data. Participants are allowed to be involved in the data collection in real-time, using the data they’re collecting to understand and inform their own health improvement plans.

In light of today’s announcement we wanted to highlight some of our favorite and most powerful examples of taking the research process into one’s own hands, making their own knowledge through thoughtful data collection and reflection. We invite you watch what’s possible now, and imagine with us what could be accomplished tomorrow.

Mark Drangsholt: Deciphering My Brain Fog

Lindsay Meyer on Tracking Hearing Loss

Thomas Christiansen on Learning from 60,000 Observations

Nan Shellabarger: 26 Years of Weight Tracking

Rob Rothfarb on Tracking My Blood

Last year we gather a fantastic group of researchers, toolmakers, and science leadership at the 2014 Quantified Self Public Health Symposium to discuss how personal data can impact personal and public health. That meeting culminated in a great report that touches on many of the aspects discussed today regarding ResearchKit. We invite you to download, read, and share that report. For a more nuanced look into how ResearchKit may impact the research community, we’re highlighting four great talks from the the meeting.

Susannah Fox shares research from the Pew Internet and Life Project and describes the challenges ahead for promoting self-tracking.

Margaret McKenna explores the issues, challenges, and ideas large scale self-tracking applications have in mind when they consider working with the research community.

Jason Bobe talks about the lessons learned from involving research participants in the data ownership and discovery process.

Doug Kanter describes what he’s learned from tracking and visualizing his diabetes data.

If you’re interested in how ResearchKit will be affecting self-tracking, personal data, and access to information, research and knowledge making, then stay tuned to our Access Channel here on QuantifiedSelf.com and on Medium.

We are sure to have many great talks and sessions that focus on ResearchKit at our QS15 Conference and Actrivate Exposition. We invite you to join us.


We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on quantifiedself.com and @quantifiedself.

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What is in My Gut?

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This past fall we learned about a unique study, conducted at Stanford University, designed to contribute to the understanding of the human microbiome. This study also has a component not common to academic research — data is being returned to the participants. Intrigued, I contacted the principle investigator, Les Dethlefson, to learn more.

Ernesto: Tell me about the Dynamics of Human Microbiota study.

les_dethlefsen_at_the_benchLes Dethlefsen: Since I joined the Relman Lab at Stanford, I’ve been looking at the human gut microbiota, focusing on what affects it and how it changes over time. In our study, we are looking at three different perturbations, deliberate changes to the gut ecology, to see how the microbiota population is affected.

We are very interested in the patterns that emerge. In people who have very stable gut microbiota, does their microbiota remain that way when they undergo diet shifts, a colon cleanout, or an antibiotic? Or maybe people who have a stable gut microbiota most of the time are the ones who are most affected by something unusual such as taking antibiotics. We just don’t know enough to understand these patterns right now. So, we’re really looking for basic ecological information.

Ernesto: If you look at the popular press, it seems the microbiome is the new golden child of biological life sciences. We’re even seeing companies in Silicon Valley get involved with this kind of work.

Les: It is broader than that. It really is a worldwide interest on the parts of both the scientific community and the public. And unfortunately, we are probably going to see some overhype, just as we did with the Human Genome Project. But I do believe this is a very important area. I think there will be a lot of payoffs and health impacts from this research, although it’s not going to be everything.

The shift that, I think, would be good for us to make intellectually is to get rid of the “us vs. them” thinking, because we are symbiotic organisms.

We have evolved with a native gut microbiota, and native microbiota is pretty much everywhere. We have evolved together, so it’s fallacious — an artifact of our past ignorance — that we don’t think of our microbes as part of our physiology.

Ernesto: It seems like exploring the deep sea, an unknown world that we’re just starting to peek into.

Les: It’s along those lines. You’re not wrong about that. But unlike, let’s say, the deep waters surrounding an undersea hydrothermal vent, we already know a lot about human physiology. There are a lot of molecular details and genetic pathways that we already have worked out. The context is somewhat understood.

And now, we have a reasonable start on the initial research: What microbes are present, and where? What’s the range of what we think is the normal distribution? We certainly don’t know enough, because we only know about people in the developed world. However, this may not represent all of human diversity or a very natural state of the gut microbiota.

Candida albicans

Candida albicans

Ernesto: Let’s get back to your study. You are asking participants to send microbiome data in the form of fecal matter and urine to your lab. What are you doing with those samples?

Les: We ask participants to provide both stool and urine samples. With the stool sample, we apply four different methodologies to turn it into data. One is the very common 16S ribosomal RNA (16S rRNA) gene sequencing approach. It’s relatively standard and inexpensive. It acts like an ID card for microbial taxa — telling us approximately what strains are present and in what relative abundance. We have a lot of data like that already for comparison.

sequencerThe second approach we will be applying is metagenomic sequencing, wherein we will be sequencing a random selection of all the genomes of the microbial types that are present. We can’t take this to completion, even with the dropping cost of sequencing, especially because there are some very, very rare microbes that we barely even have the chance to see at all. But we can get a pretty good swathe of genetic sequence data from all the microbes.

The third approach is even more ambitious. It’s called metatranscriptomics. Genes can be carried by any critter, you and I included, but not expressed. Knowing which genes are turned on, and to what extent they’re turned on is a better measure of the biological activity that is actually happening. The metagenome is a measure of potential activities, what the bugs can do. The metatranscriptome shows what the microbes are actually doing. Metatranscriptomics is even more challenging than metagenomics partly because of the nature of messenger RNA (mRNA). It’s a highly unstable molecule. There are technical challenges, but we’re ambitious enough to try to collect information on gene expression.

The fourth approach is not based on gene sequences, but on chemical composition. Metabolomics is the name given to a number of these approaches that are not directed to a specific chemical. These are techniques that try to measure a broad swathe of chemicals present in the environment and their relative abundance. This is a technology that we, in the Relman Lab, know very little about. We’re collaborating with the Nicholson Lab in Imperial College in London, and they will be doing the metabolomic analyses on the stool samples. That may be even closer to where the rubber meets the road — knowing not just the gene expression but also the resulting chemical changes that are happening in the environment.

MicrobeHeatMapMetabolomics takes us to the other type of sample we’re collecting: the urine samples. We aren’t doing this because we have an interest in the urinary microbiome itself, but because, as the Nicholson Lab suggested, the urine provides a more complete, integrated picture of the co-metabolism between the human host and most of the gut microbiota. So while metabolomics for the stool samples would primarily measure the gut microbial activity and what they contribute to the host’s physiology, the urine provides a more integrated picture about how the host metabolism works in concert with the gut microbiota.

Ernesto: If a participant is going to be contributing all of that data, will they have access to it?

Les: As someone with similar interests, I certainly knew that a huge motivation for people to join the study would be the access to their own data. We offer monetary compensation, but for the amount of time that will be spent in contributing samples, it is probably trivial. We knew we would attract the curious, scientifically inclined, and practising scientists. Of course, they would want to see their data.

The Institutional Review Board (IRB) was quite open to us sharing information with the participants about their own microbiota. It probably helped that there’s publicity  about ways people can get this information. There is the American Gut project, offering an assessment of your microbiota for a donation, and uBiome, a private company offering the same kind of service.

I, or another staff member of the study, are going to share this microbiota data with each participant in a conference call. So in effect, I’m going to be a microbiota counselor. It’s nowhere near as high-stakes as sharing genome information. We don’t know enough to say, for example, that this microbiome is definitively healthy, or that it’s unhealthy, or what the exact risks of diseases are due to this particular composition. So we will be putting this information in context, and we will be available as interpreters of the scientific literature. We may be able to say that there is a statistical association between a particular microbial group that someone may have in their gut and some health-related outcome.

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Microbiome sequence data

Ernesto: Will participants be getting a copy of their data as well?

Les: Yes, we will provide that. I have an open source mentality. Added to that is the fact that there are many practicing scientists signing up for the study and saying they want data, not just a PDF summary. I am happy to provide the data in as raw a format as people want. They can get the raw sequence information, a low-level summary (which is the result of the first pass of data processing), or the final summary. I have permission and full intention to share all the data derived from a person’s samples with that person.

Ernesto: Do you think we will see this happening more in the future?

Les: I think we will probably see more of it in the future. We’re moving in the direction of access to information. The open source movement has reached the health and medical realm from its origins in tech and computing. I think the participatory nature of access to data and scientific information is a good thing. It has started, and I don’t see any way of reversing the trend. I would hope that it becomes the norm that there is some appropriate level of sharing, that research participants have access to their data if they wish, and in a way that lets them interpret that data appropriately.

I believe that people have a right to that level of knowledge about their bodies, and if we, scientists, are generating that knowledge, there’s no reason not to share it with the individuals.


The Dynamics of Human Microbiota study is currenlty recruiting participants. If you’re interested in learning more about the ecosystem within read more about the study and check to see if you’re eligible to participate here.

We invite you to share your data access stories, and this article with the #qsaccess hashtag and follow along on quantifiedself.com and @quantifiedself.

 

 

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Do It Yourself Diabetes

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Dana Lewis and Scott Leibrand are the creators of the amazing “Do-It-Yourself-Pancreas-System,” also known by #DIYPS. We had a few question for them.

Ernesto: Why build your own pancreas?

IMG_3561Dana: I’ve had Type 1 diabetes for about 12 years. I use an insulin pump and a continuous glucose monitor (CGM), but the devices are separate. They don’t talk to each other. I have to look at the data from the CGM and then make decisions about my insulin. I have to make about 300 decisions per day on average. It’s really fatiguing. So we created some algorithms that took my blood glucose data, the amount of insulin that I’ve given myself, and the amount of carbohydrates that I’ve decided that I’ve eaten, and ran them over and over again to give me a prediction of what my blood sugar was going to be and whether I need to take any action. Instead of having to constantly do the math myself, our system will push an alert to my phone or watch.

Ernesto: Does it dose you automatically?

Dana: Originally no, but more recently we’ve built a full closed loop version of #DIYPS, that is essentially an artificial pancreas, that talks to my pump and adjusts to give me a little more or a little less insulin.

Ernesto: Who writes the code?

Scott: I’m doing all the coding. I’m sure Dana could, but she has a lot going on and designs the algorithms. My title is Chief Spaghetti-Coder. This is the bleeding edge. It doesn’t need to be elegant code.

Ernesto: What have you learned from building your own pancreas?

Dana: The beauty of a CGM is that it gives you a data point every five minutes. Over the past year I’ve produced more than 130,000 data points of blood sugar levels alone. That gives me an incredible picture of what’s happening. With a traditional meter, it’s rare to find somebody who tests up to even 10 times a day. And the standard use for an insulin pump is very much “set it and forget it.” The #DIYPS allows me to customize without having to constantly adjust my insulin pump manually, and that frees me up to live my life, work, and do whatever it is that I want to do.

A visualization of Dana’s Data over the first year of the #DIYPS system.

A visualization of Dana’s Data over the first year of the #DIYPS system.

Ernesto: How did this project start?

Dana: We first started building the system just to make the alarms on the device louder, to wake me up because I would sleep through them. The device manufacturers didn’t seem to have a solution. Then we started looking at getting the data onto a computer so Scott would be able to view it. At the time, we had recently started dating, and he lives 20 miles away. I wanted him to be able to see what my blood glucose level was, so if it was low, he could text me; and if I didn’t respond, he could call 911. But we didn’t have a way to get the data off of the device.

Scott: The key moment was when we saw a tweet from John Costik, who was working on the Nightscout Project. Nightscout is open source code that helps people transmit their CGM data to other devices. I tweeted John right away: “Hey it would be awesome if we could get access to this code.” That’s really where it started. And along the way the whole process has been extremely public. We’ve been tweeting, blogging, and making everything we’ve been doing completely visible.

Ernesto: I’ve seen you tweet using the hashtag #wearenotwaiting. What does that mean?

Dana: #WeAreNotWaiting is a hashtag that was coined at a conference hosted by an online diabetes advocacy and information sharing community called DiabetesMine.com. For me it means that we’re not waiting for traditional device manufacturers to come out with the product. In three to ten years there’ll be devices like our artificial pancreas systems out in the market, being sold by companies approved by the FDA. I need to be alive when that system gets out in the market in, perhaps, five years.

I need to be alive when a cure becomes available.

Scott: Right about the time that we started working on #DIYPS, the Nightscout Project started to grow really quickly. There are now over 10,000 people in the CGM in the Cloud group. Over 2,000 people are using Nightscout to view their own or their loved ones’ blood sugar levels remotely on phones, watches, and other devices. This is real stuff that’s making a real difference in the world. And that’s only going to accelerate as more people do more interesting things like this closed loop that we’ve just done.

Ernesto: You’ve written about “data as free speech.” What do you mean? How can data be speech?

Dana: People often don’t understand why its legal for us to ‘hack’ a CGM and an insulin pump. (Note that hacking isn’t a negative thing; we’re just sharing the data across devices!) They assume that because all my DIY gadgets are not FDA-approved to use them the way I’m using them is somehow against the rules. But I can treat my own body, my own diabetes, the way I want to. And if I share my data, that’s obviously a kind of speech. But if we decide to share our code? I think the FDA sees this as a gray area. We very much want to continue our conversations with regulators.

Ernesto: Where do you see your project going?

Dana: I feel that every time I answer this question my answer changes, because my understanding of its potential is constantly changing. I never would have thought that any of what we’ve done was possible. Right now one of our goals is to make sure that the knowledge we gained about diabetes through our work with #DIYPS is adopted by clinicians, and that patients have access to this new information for treating diabetes. We’re also taking #DIYPS to a new level with #OpenAPS, an open and transparent effort to make safe and effective basic Artificial Pancreas System (APS) technology widely available to more quickly improve and save as many lives as possible and reduce the burden of Type 1 diabetes.

Dana with the #OpenAPS system.

Dana with the #OpenAPS system.

Scott: A few of months ago, at a conference convened by the advocacy group DiabetesMine, we got up and talked about our project, and I said: “I’m putting a stake in the ground that we’re going to make a closed loop artificial pancreas by August 1st, which is the date we’re getting married.” Everybody applauded and thought that was awesome. Then we went home. And we had it done in two weeks.

Dana: For anybody who wants to get involved in this, we would love to talk to you. There are so many people with diabetes and there is so much data that drives the management of this disease.

But there’s not a lot of awareness of how many diseases, including diabetes, could have their care revolutionized just by having better access to data.

That’s the thread of Quantified Self that I’m most interested in. The diabetes community happens to be one of the first to take advantage of what’s possible.

Dana tweeted her blood glucose data during this interview.

We invite you to share your data access stories, and this Access Conversation with the #qsaccess hashtag and follow along here in our Access Channel quantifiedself.com and @quantifiedself.

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QS Access: Personal Data Freedom

We are happy to welcome this guest post by Madeleine Ball. Madeleine is the Senior Research Scientist at PersonalGenomes.org, co-founder of the upcoming Open Humans project, and the Director of Research at the Harvard Personal Genome Project. She can be found online @madprime.

MBallThe digital trails we create are becoming thick and personal. Increasingly, people choose to collect meaningful data about themselves. Activity tracking to understand health and fitness. Genetic testing to understand ancestry and inheritance. Incidental data also expands: smartphones quietly observe our location through the day. Who gets to see our data? Can we see our own data? Beyond “privacy policy” documents, people are starting to call for something stronger: for personal data ownership.

Unpacking “data ownership”

It’s worth unpacking this phrase. What do we mean by “data ownership”? If we want to see changes, we need to start with a little more clarity.

Legally, data is not property. There is no copyright ownership of facts, as they are not “creative work”: the United States Supreme Court famously established this in the landmark case Feist vs. Rural. They are not patents, there is no invention. They are not trademarks. There is no “intellectual property” framework for data.

 Yes, data is controlled: through security measures, access control, and data use agreements that legally restrict its usage. But it’s not owned. So let’s set aside the word “ownership” and talk about what we really want.

Control over what others do

One thing we might want is: “to control what others do with our data”. Whom they share it with, what they use it for. Practically this can be difficult to enforce, but the legal instruments exist.

 If a company is generating data about you, then the “control” you have is spelled out in their contractual agreement with you. Check the policies: “Privacy policy” or “Data use policy” documents are a standard feature.

 Think about what you really want. Are you opposed to commercial use of your data? Look for words like “sell”, “lease”, and “commercial”. Are you concerned about privacy? Look for words like “share”, “third-parties”, and “aggregate” – and if individual data is shared, find out what that data is.

Companies won’t change if nobody is paying attention and nobody knows what they want. We can encourage change by getting specific, and by paying more attention to current policies. Raise awareness, criticize the bad actors, and praise the good ones.

Personal data access and freedom

The flip side of “data control” is our own rights: what can we do with our own data? We want access to our personal data, and the right to use it.

 This idea is newer, and it has a lot of potential. This was what Tim Berners-Lee called for, when he called for data ownership last fall.

“That data that [firms] have about you isn’t valuable to them as it is to you.”

I think it’s worth listening, when the inventor of the world wide web thinks we should have a right to our data.

So let’s spell it out. Let’s turn this into a list of freedoms we demand. We should be inspired by the free software and free culture movements, which advocate for other acts of sharing with users and consumers. In particular, inspired by Richard Stallman’s “Four Freedoms” for free software, I have a suggested list.

Three Freedoms of Personal Data Rights

Raw data access – Access to digital files in standard, non-proprietary file formats.

Without raw data, we are captive to the “interface” to data that a data holder provides. Raw data is the “source code” underlying this experience. Access to raw data is fundamental to giving us the freedom to use our data in other ways.

Freedom to share - No restriction on how we share our data with others.

Typically, when data holders provide access to data, their data use agreements limit how this data may be shared. These agreements are vital to protecting user privacy rights when third parties have access, but we have the right make our own sharing decisions about our own data.

Unrestricted use – Freedom to modify and use our data for any purpose.

 Data use agreements can also impose other limitations on what individuals can do with data. Any restriction imposed on our use of our data impinges on our personal data rights. Freedom for personal data means having the right to do anything we wish with data that came from us.

In the short term, access to raw data can seem obscure and irrelevant: most users cannot explore this data. But like the source code to software, access to this data has great potential: a few will be able to use it, and they can share their methods and software to create new tools.

Raw data access is also an opportunity for us to share for the greater good, on our own terms. We could share this data with research studies, to advance knowledge and technology. We could share data with developers, to develop software around it. We could share it with educators, with artists, with citizen scientists. We could even cut the red tape: dedicate our data public domain and make it a public good.

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My Device, My Body, My Data

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In 2007, after collapsing while rushing to board a train, Hugo Campos was diagnosed with hypertrophic cardiomyopathy, and an ICD (implantable cardioverter defibrillator) was implanted in his chest to track and regulate his heart rhythm. To his great surprise, he discovered that it was very difficult to gain access to the data being generated inside his own body. Today we’re inaugurating what we hope will be a regular series of “QS Conversations” about data access with an interview with Hugo about his long battle for the right to see what’s happening inside himself.

Ernesto: Why does access to your ICD data seem so important to you?

campos_hugo_medx2014 copyHugo: I have a computer with firmware, processor and memory regulating my every heartbeat, wired into my heart, and buried inside my body. I can’t even see it. A corporation in the cloud, located out of state, has a wireless, transparent access to a device that’s implanted in my body, but the only control I have is to unplug the remote monitoring unit in my house to prevent them from getting the data. This creates a very unsettling feeling of not having autonomy. I’m paying thirty thousand dollars for a device, having it implanted inside my body, and then being locked out of it.

Ernesto: Was there something that happened that set you on this path?

Hugo: Yes. For a long time I’d been on my spouse’s health care plan, but when he decided to freelance and quit his job, I couldn’t get health insurance. This was before the Patient Protection and Affordable Care Act. Kaiser denied me because I had a heart condition. Anthem Blue Cross denied me as well. Now put yourself in my shoes. Here I am, being denied access to the device because the system “knows better” and I could harm myself, but now they can’t give me service at all.

Ernesto: You can only get access to your ICD through the medical system, but the medical system won’t take you because you have an ICD?

IMG_1542 copyHugo: Right, so I had to figure out a way to protect myself. I looked at it as kind of an extension of my Second Amendment rights. I’m not particularly pro-gun, but I look at it as the ability to defend myself. If the system was really unavailable, I have to at least be able to interrogate my ICD. So, I went on eBay and bought a pacemaker programmer that gave me full, unrestricted access to my implanted device. I can change its programming, shut it off, deliver therapy, and do as I wish. In fact, it’s the same machine that clinics use. I also went to Greenville, South Carolina, and took a class on how to program ICDs and pacemakers. I thought, “Okay, I may not become a cardiac electrophysiologist by any stretch of imagination, but”–to use the firearm metaphor again–”at least I have a basic understanding of gun safety so I don’t shoot myself.”

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QS Access: Backing up HealthKit Data

As you may know, we’re very interested in how HealthKit is shaping and extending the reach of personal self-tracking data. Last week, during Apple’s quarterly earnings call, Tim Cook mentioned that “There’s also been incredible interest in HealthKit, with over 600 developers now integrating it into their apps.” (emphasis mine).

This morning, we were alerted by Sam Rijver and Daniel Yates that special attention to how you backup up your phone is required in order to backup and have access to your HealthKit data:

 

For those of you that are unfamiliar with backup options for your iOS device. Here’s a quick gif to walk you through the process of encrypting your iOS backup so that you can restore your HealthKit data if anything happens to your device:


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