Monthly Archives: August 2016

Study Update: Keeping Pace

One of our goals at Open Humans is to provide updates on participating studies.

Keeping Pace examines how exercise patterns correlate to the environment. Dr. Rumi Chunara spoke in depth about the study at this year’s Health Data Exploration Network Meeting:

  • Watch her talk on YouTube to learn:

    • Why the ‘built environment’ matters

    • Implications of using personally-generated data for research

    • Specific exercise trends observed so far

Dr. Chunara and her team have proven the efficacy of their data by garnering results consistent with findings from social media research:

  • People are most active on the weekends.

  • People are least active on Fridays.

  • The most popular weekday for exercise is Tuesday. (Feel free to speculate on why this is!)

They use data from the free Runkeeper app* to find out:

  1. Where are people most active?

  2. How does this compare to others who live nearby?

  3. What activities do people choose for recreation?

  4. What activities do people choose for transportation?

*They’re looking into expanding to other sources. Stay tuned!

According to the CDC, 71% of adults in the United States are overweight and 35% are obese. Although diet is a significant factor, there are environmental influences as well. Keeping Pace aspires to help inform urban planning and transportation policy changes that could improve public health.

So keep exercising…
And let your workout data be a resource for the greater good! 


Spotlight on a Participant: James Turner

James Turner is one of our most ‘connected’ members, creator of two Open Humans activities, and an endlessly interesting guy.
james_turner_nyscf (1)
Donating tissue for stem cell creation at the New York Stem Cell Foundation

Hope: What is most fulfilling to you about being a member of open-access data studies?

James: Getting to meet and, in a few cases, form friendships with the researchers involved. When I was a teenager, I was seriously considering going into genetics before I got bit by the computer bug. Through the PGP and Open Humans, I feel like I’ve gotten a chance to reconnect with that early interest. Because the researchers and participants have a much more collaborative attitude than the typical research project, you really feel like you’re a part of the science, not just another anonymized identifier in a database.

Hope: You created the ‘Open Humans HealthKit Integration’ as well as the ‘Cross-Genome Error Check’ activity on our site. We’ve already written a blogpost about the ‘HealthKit Integration’. Can you talk a little about the ‘Cross-Genome Error Check’ activity?

James: The tool, which is still in it’s very early days, allows someone with more than one variant file (such as a PGP WGS or 23andMe data) to compare the files for discrepancies (i.e., calls that aren’t in agreement between the files.) It’s a work in progress, and anyone who participates should expect to get incrementally more interesting reports over time, as I improve the tool. I’m still learning all the nuances of the VCF format, so take the early results with a grain of salt. We’re seeing some early interesting data, mainly around homozygous vs heterozygous calls, although there have been a few calls that just seem to be consistently wrong.

One caveat: If you don’t have at least two independent genetic datasets uploaded to OH, don’t bother signing up, I won’t be able to return anything useful for you.

Hope: What health-tracking technology do you wish existed?

James: Oh my, such a list I’d have. A really reliable sleep monitoring technology that wasn’t intrusive. A non-invasive continuous blood glucose monitoring device (Apple Watch 3.0?) But probably the biggest one would be to be able to get really accurate nutritional information about anything I was able to put into my mouth, be it purchased, cooked or ordered.

Hope: You learned about Open Humans through the Personal Genome Project. How did you find out about the PGP and what made you join?

James: I’ve always been a big science geek, all the way since I was a kid. I’ve been lucky enough to be able to pursue this interest by being a freelance journalist as a side career, and as part of that, I have to keep up on sci-tech news on a regular basis. I don’t remember exactly what article I was reading that lead by to the PGP, but I had always been fascinated by genetics, and the idea of being able to get my own genome for free was immediately appealing to me.

Hope: Had you ever shared your health data before?

James: I had participated in a couple of clinical trials due to health issues, but they had been more “participate in this trial to get early access to some medical goodie” types of things. I hadn’t publicly shared any of my health or genomic data. I had been a 23andMe customer, and participated in the surveys on the site they were using to do GWAS.

Hope: What type of research are you most interested in?

James: Boy, that’s a hard question. I think that learning more about how all of the disparate ‘nomes (microbiome, genome, epigenome, connectome, proteome, immunome) work together and interact with each other to make us who we are, and how they fail, is going to end up being the holy grail of the 21st century. The idea that understanding the genome would give us the entire picture has proven to be naive, and the next decades are going to have as much to do with understanding how all the systems play together as how any one gene or group of genes function in isolation.

Hope: Have you changed any of your habits because of the knowledge you’ve gained from the studies and projects you’ve joined?

James: Not really. There’s not a lot of actionable information in my data. I did find out why I’ve always had an issue with alcohol making me ill, it turns out I have a rare nonsense mutation in one copy of my alcohol dehydrogenase enzyme (that’s the enzyme that is responsible for metabolizing booze…) But, since I was a very occasional drinker anyway (because it tended to make me feel ill), it didn’t really change my lifestyle. The same mutation has been associated with an increased risk of Parkinson’s, however, so that’s definitely something I’m going to keep an eye out for as I get older.

Hope: Do any of your friends and family share your curiosity for health data tracking? Do you ever try to make converts to your way of thinking about health?

James: My son (who is a biochem major at UNH) is also a member of the PGP and Open Humans, and we chat a lot about biotech and biology in general. My wife is much more skeptical of the idea, mainly because of privacy concerns and the potential for her data to be used for things she would object to. I definitely try to spread the word about PGP and OH to people who I think would be interested, or who seem to have health issues that I suspect would be valuable to add to the public dataset.

Hope: What is your impression of Open Humans so far?

James: It’s obviously early days. I’m seeing a lot of the back-end technical side, working with Madeleine and Beau as one of their beta-test guinea pigs for the new data APIs they’re developing for third parties to work with OH. The big challenge, as with the PGP, is going to be to get enough people contributing enough useful data to make it more than just a boutique dataset. Right now, there seems to be a lot of duplicative effort between projects such as OH, Genes for Good, the 1,000 Genome Project, and the new federal programs starting to ramp up. Everyone is trying to skin the same open consent cat, but my concern is that we’re going to end up with a lot of isolated data sets rather than one big one that lets researchers really leverage the power of tools like GWAS. Hopefully, OH will be able to act as a common hub to get all of them sharing their data together.

The other big challenge is how to represent all the diverse types of data that are coming in ways that are going to be useful to researchers. If I want to be able to easily say “give me the allele frequency of variant X for everyone who has ever had a systolic blood pressure reading about 150”, there’s no good way to do it right now. It’s JSON files and text files and VAR files, etc, etc. It’s going to be a lot of manual groveling (or clever scripting) for anyone trying to mine that kind of data. But this is a problem bigger than OH.

Hope: On your Member page, you mention that you run a charity. What does it do?

James: I’m the President and Chairman of the Board of the Brony Thank You Fund, a 501(c)3 public charity that fundraises from fans of the new My Little Pony animated series. We print a yearly calendar and do other fundraising activities, supporting a variety of causes. We’ve raised close to $200,000 in the past four years, and notably endowed an animation scholarship at the California Institute of the Arts. Currently, we’re supporting the Dana Farber Cancer Institute.

Also, have some pony genomics.

Applejack: Now how in thunderation is one of them twins a Pegasus and the other one a unicorn?

Mr. Cake: Easy. My great-great-great-great grandfather was a unicorn, and Cup Cake’s great aunt’s second cousin twice removed was a Pegasus. That makes sense, right?

— Season 2, “Baby Cakes”

Hope: You’re also a certified open water diver and private pilot. Is that because walking around at sea level gets boring?

James: I’d really like to be out exploring space, but given the relatively low chances that’s going to happen in my lifetime, flying or diving are about the closest I’m going to get to exploring a strange new world. Flying has always been a passion of mine, and getting to earn my license has let me have some spectacular experiences, including circling Niagara Falls at 2,000’ and flying over downtown Boston below roof-level (pre-9/11). Unfortunately, the combination of putting a kid through college, the post-9/11 security environment for civil aviation, and the difficulty of keeping up my medical certificate had resulted in me having to walk away from piloting, at least in the short run.

I learned to dive because my girlfriend (now wife) had won a trip for two to Australia, and there was no way I was going to go to the other side of the world and not dive the Great Barrier Reef. I’m glad I did, because the reefs around the world are disappearing rapidly due to climate change, so it may have very much been an example of seeing them while they were still there. I went diving with my family down in St. Martin about 10 years ago, but haven’t had a chance to since.

Hope: What’s your favorite sci-fi story about health and/or medicine?

James: The book that turned me on to biology and genetics was The Andromeda Strain by Michael Crichton. I read it when I was 8, and it had a tremendous impact on my life. I’m much less of a fan of Crichton’s later works, as he got increasingly political and tin-foil-hatty, but the book (and the outstanding Robert Wise movie adaptation) still are among my favorites.

Hope: Finally, would you be willing to chat with other OH members on our forum if they have follow-up questions?

James: Absolutely, I’m pathologically extroverted and would love to chat with anyone who has questions or just want to shoot the breeze about geeky stuff.

Join ‘Circles’ and help study a uniquely human trait!

Circles in Human Biology studies a “sensitive” topic: The human areola!

All mammals have nipples, but only humans have areolas. Areolas are the pigmented circular markings that surround our nipples. How did we get these markings? Why are some areolas large and others small? Can we find the genes that build these circles and discover why we have them?

Anyone – of any gender! – can join. The study is especially interested in participants who have had genetic sequencing.


Participation is easy:

  • Sign up on Open Humans
  • Complete an online survey
  • Use simple measurement tools to share data about your own body
  • Share photos of your areolas with the researchers (helpful but not required)

Almost 400 people have signed up and shared their data so far!

By analyzing participant-reported data, the ‘Circles’ team has already learned that areolas are much more diverse than previously thought. They’ve also discovered that the diameter of a person’s areolas is unrelated to the number of areolar glands they have. In fact, people can have anywhere from 0 to more than 30 of these little bumps. Scientists believe these bumps help protect nipples during nursing and provide an olfactory cue to help newborn infants nurse, but research has yet to confirm this.

Learning about diversity in areola morphology could not only help scientists understand breast health, it could teach us about human genetic diversity in general.

To read a New York Times article about this study, click here.

We vary in all kinds of traits, from physical traits like height and hair color to sensory traits like taste or odor perception. These differences impact our lives in big ways, from what foods we eat to what medicines work for us to how we feed our babies. We are just starting to understand how these traits are built genetically and why they vary. These discoveries are going to give us fascinating new insights into the way our genomes build our bodies and influence our lives.

– Abby Wark, Project Director of ‘Circles’

Join ‘Circles in Human Biology’ today!

Citizen Science for iPhone or Fitbit Users!

Open Humans enables participatory research. Blurring the line between scientist and research participant is part of our mission – because we know that data sharers can become data explorers and tool builders, too!

Our two new activities are prime examples:

  • Open Humans HealthKit Integration
    You can install this member-created app to add ‘Health’ data from your iPhone to Open Humans.
  • Open Pokemon GO GO GO!
    Whether or not you’ve played the game, you can share HealthKit or Fitbit data to create a shared data set that we can explore together!

Read on to learn more…

Open Humans HealthKit Integration
Pasted image at 2016_07_07 02_55 PM_picmonkeyed

Did you know iPhones store health data? You might have data you didn’t know about! Since 2014, iPhones have been tracking your activity (e.g. steps) data through the ‘Health’ app. They can also log lots of health data – from blood glucose to weight!

This data is private on your iPhone, but you can decide to share it. James Turner, one of our most engaged and “connected” participants, has applied his iOS developer skills to create the Open Humans HealthKit Integration app to allow you to export HealthKit data to Open Humans!

In the past few months, Open Humans has expanded our features to allow projects to add data to member accounts. We hope researchers use this to return data, but we’re thrilled to see it used by a community member to create a new, valuable data source!

There’s a ton of health and fitness data being captured by iOS users now, and the HealthKit Export app is an attempt to make that data accessible to researchers in a standardized format. 

– James Turner, app creator and Open Humans member


Open Pokemon GO GO GO

This non-study project allows you to contribute to an open data set of physical activity levels for summer 2016. The inspiration for this project was the Pokemon GO craze, but anyone with an iPhone or Fitbit can participate.

This is mostly a personal project. Pokemon GO has been such a phenomenon, and I wanted to create something fun in response! Sharing data like this can create invaluable resources for students and citizen scientists to explore. I also wanted to provide an open source demo for how to make projects on Open Humans – it’s easier than you think! I’ll be writing up an explanation on how it was set it up, and open sourcing the code used. 

– Madeleine Ball, project creator and Open Humans platform co-founder

Contribute to science.
Join studies, connect and share data today.