Open Humans is now a community of 3,000 members…And counting!
As a token of our gratitude for your participation, we’d like to send you an Open Humans sticker. You can put it on your laptop, phone, luggage — wherever you want (but preferably somewhere that others will see it and know you’re cool).
Please note: This promotion is valid through March 2017 only.
THEN, NOW & NEXT
When we launched in March 2015, we envisioned a platform where participants could ‘open-source’ their body for science. We’ve evolved into a community of researchers, citizen scientists, and individuals whose embrace of open values has indeed enabled new types of scientific study and innovation:
Alex Biel and Eric Hekler, PhD used James Turner’s app as a data source and created a Pokemon Go study pilot to gain a better understanding of how games might influence physical activity
Open Humans and developers from the Nightscout Project (type 1 diabetes + open source) created a tool to upload data to the Open Humans platform so it can be easily shared with researchers
Dana Lewis is using the Open Humans platform to collect data from DIY artificial pancreas users and facilitate research in partnership with the DIY “closed loop” community
…And there’s more! We invite you to check out all of our activities here.
We remain fully committed to sharing data that is centered on our greatest resource: YOU. Open Humans’ future is bright, and our current research pipeline includes diverse projects being developed by academic and citizen scientists who study genomics, toxins, viruses, and more.
Together, we will transform the status quo in humans subjects research!
Keeping Pace uses personal sensor data for its research. Along with data from the free Runkeeper app, it is now accepting data from the free Moves app
Movesis an activity diary that passively tracks your movement and calories burned. Unlike other movement trackers, once installed on your smartphone, it runs all the time so you never have to remember to turn it on or off.
Open Humans is excited to announce our newest activity: Seeq, a phone app and sequencing study that helps people learn about their ancestry and microbiome. Seeq participants can now add and share their data in Open Humans!
Last week, I spoke to Joe Pickrell, PhD, geneticist at the New York Genome Center and co-founder of Seeq, about this venture, the future of genomics and microbiome research, and more.
Hope: What makes Seeq a unique way for people to learn about themselves?
Joe: I think of genome sequencing as this amazingly powerful microscope that we’re just figuring out how to use. We’re one of the only places where people can actually turn this microscope on themselves.
Right now, we give people a look back at their past with their ancestry, and at their current environmental surroundings with their microbiome.
But we also give people their own data, and the data itself contain much more information than that–in principle, there’s information on mutations that have arisen recently in your blood (DNA from saliva is mostly from white blood cells), traits you may pass on to your children, and more.
We’re constantly looking for ways to give participants more back, and we hope people will come up with things we haven’t even thought of ourselves.
Hope:Why did you want to partner with Open Humans?
Overall, I think there’s potential to completely change the way genomics research is done, using the Internet and cheap sequencing to empower different communities–disease communities, social networks, and so on–to collectively decide they would like to pool their data to solve major scientific problems.
Building up the infrastructure to make this work is seriously non-trivial, and it’s going to take a lot of experimentation with different models to get it right.
Open Humans is a neat model, and it seems like there’s a great community of people who share this type of vision. So it’s exciting to get a chance to be a part of it, and hopefully we can provide some data and tools that are useful.
Hope:What are you trying to learn from the genetic data Seeq collects?
Joe: We are collecting questionnaire information to go along with the genetic data, and have a whole bunch of analyses going on.
A couple questions I’m particularly interested in now are: are the microbes in your mouth associated with psychological phenotypes like your personality? And: how do genetic and environmental factors interact to influence human lifespan?
Hope: What is Seeq’s relationship with the New York Genome Center?
Joe:This project is run out of my lab, which is part of the New York Genome Center.
Hope:How do most of your participants find out about Seeq?
Joe:There’s a social aspect to Seeq–if you add someone as a friend, you can compare your ancestry and microbiomes, and see what the ancestry of your (hypothetical) child is likely to be. So the majority of people get to Seeq through social connections to existing users–initially this was just people that the three of us know (Seeq is run by myself, Tomaz Berisa, and Kaja Wasik), but now this has expanded considerably as we’ve gotten into the thousands of users.
Hope:Do you have a favorite story that you can share about someone who has been sequenced by Seeq?
Joe: In our microbiome reports, we also report other things (mostly food) that we see DNA from in your mouth.
We’ve had a few people contact us a bit confused, wondering why “dog” showed up in their list of results. To be clear, we don’t think people are unknowingly eating dog! In most cases, these are people that live with dogs, so it’s probable that dog hair or something is in their mouth sometimes. In a couple of cases though, we’re not totally sure what’s going on.
Hope:What made you want to study genetics?
Joe:I’ve always been intrigued by what makes people see the world differently–sometimes literally, in the sense of how colorblind people see colors in a different way, and sometimes more figuratively, in the sense of how people with different personalities respond differently to stress.
We know that some of this variation is due to genetics, and genetics is currently tractable–that is, we now have the tools to tell people they see colors differently (maybe people don’t realize this until they’re relatively old) or respond to foods differently, and the tools to discover part of the reason people vary in their personalities.
So it’s a really exciting time, and frankly I just stumbled into it because I thought the topic was cool. I’ve been lucky in that it was the right time to do it.
Hope:What genetic, microbiome, or genomic discovery has surprised you the most?
Joe: Probably the most surprises in genomics recently have come from studies of ancient DNA. We now know that, for example, people in Europe today are descended from a mix of populations that existed a few thousand years ago–some related to European hunter-gatherers, some related to Middle Eastern farmers, and some related to population who were living in Siberia (see e.g. http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html).
The standard view in population genetics was basically that Europeans today are descended from the people who were there 10,000 years ago, so it was really surprising to me to see that the populations we call “European” in some genetic sense didn’t exist until recently.
Hope:What questions do you expect genomics and microbiome research to be able to answer in the next decade?
Joe: On the genomics side, it’s going to be possible to tell you what makes you and your family unique–we’re going to find the rare genetic variants that cause your family members to have early-onset heart disease, or why you and your dad happily sleep only four hours a night, or (on a more trivial note) why you and your mom burp when you yawn (no joke! https://www.reddit.com/r/NoStupidQuestions/comments/2lgjht/i_always_burpmake_a_burp_like_sound_when_i_yawn/). This is because the technology needed for this (genome sequencing) is only now cheap enough to get to the sample sizes necessary for these types of study.
On the microbiome side, in ten years I’d hope we’ll figure out what the hell it means. There’s a lot of hype about microbiome research, but there’s a fundamental problem in that the microbiome is like any other epidemiological variable–it changes in response to your environment in a way the genome doesn’t. So when you see a study that says “Presence of microbe X is associated with obesity”, it’s hard to know if the microbe causes obesity, obese people are a better host for the microbe, or whether it’s just that obese people tend to have a diet that’s favorable to the microbe. These sorts of issues are really hard to tease apart, but I do think it’s a tractable problem.
Hope:How do you foresee engaged, data-sharing participants will impact research?
Joe: I think this has the potential to completely change the way research in some fields is conducted. Specifically, the power to decide which research questions are “important” lies with the people who collect and fund data collection, and this is a fairly small number of people.
Once everyone has access to their own data, there’s the potential for a huge influx of new ideas and approaches and really exciting things can happen. But this is not a foregone conclusion, people have been saying this for years and it hasn’t really happened yet. There’s a lot of work that needs to be done on building infrastructure, making participation fun, and more. We hope to play a role in this, and it’s why I’ve been a member of Open Humans as well.
Hope:Do you do any regular health tracking?
Joe: I don’t.
Hope:Have you changed any of your lifestyle or dietary habits due to the information you’ve received from sequencing or health tracking?
Hope:What health-tracking technology do you wish existed?
Joe: One thing that would be really useful is a real-time measurement of your immune system–maybe a wearable that monitored expression levels of some important immune genes. Then if you saw some particular marker spiking, you might be able to say “Uh oh, that guy who sneezed on me in the subway had a bacterial infection, time to start a course of antibiotics”, or “Something I just ate seems to be triggering an autoimmune reaction, maybe I should talk to my doctor”, or things like that. Obviously it’s currently impossible to make these measurement non-invasively, but in the long term who knows.
To read Joe’s interview with Madeleine Ball, cofounder of Open Humans, CLICK HERE to go to Seeq’s blog.
Special bonus for Open Humans – they are opening their holiday special a week early for members! Use discount code shared in our newsletter
Offer valid until Saturday January 7 or while supplies last
NOTE: There is an additional $99 fee to receive your Variant Call Format (VCF) file. (You’ll need to contact email@example.com.) VCF raw data is needed for third-party interpretation and/or sharing on Open Humans.
Alex Biel is pursuing graduate education in Obesity Prevention and Management at Arizona State University. As part of his master’s thesis in Eric Hekler’s Designing Health Lab, he created ‘Pokemon Go: A Socio-Technical Exploratory Study’. The aim of this pilot study was to gain a better understanding of how games might influence physical activity.
Hope:What do you think are the most glaring mistakes that society makes regarding obesity prevention and management?
Alex: Our entire environment is pretty great at making us fail to be active. I also think the media does a crappy job of showing what’s realistic. That can be discouraging — it was for me. But we have enough information now on the consequences our built environment have, so we should rethink how we’re doing things. It’s time for us as a society to pivot and come up with healthier strategies. The obesity epidemic didn’t happen because of personal failures.
Hope:Why did you want to study people playing Pokemon Go?
Alex: I wanted to look at whether Pokemon Go impacts physical activity. Since Pokemon Go inadvertently prompted people to walk more, it provided a unique opportunity for research to understand how this game, and other games more generally, can be used for fostering physical activity. Also, it’s considered one of the top games ever in terms of initial downloads.
Hope:What was most challenging about the Pokemon study? What was most interesting?
Alex: I heard from others in the lab that recruitment is difficult. I didn’t really understand this until I worked on finding people myself. My recruitment strategy wasn’t as fluid as I would have liked. I just walked up to 500-600 random students on the ASU campus and asked them if they play Pokemon Go.
I got ethics board approval on October 1st and the first run of the study was done in less than a month. That’s an incredibly quick turnaround that was made possible partially because of all of the great infrastructure that Open Humans provides. It allowed me to learn some interesting points, such as what seems to be driving gameplay, relatively quickly.
Hope: Is this the first research study that you designed? If not, what else have you worked on?
Alex: This was my first study. Thankfully, Open Humans made it a lot easier than I expected to get started. It gave me the information about steps, which was my main outcome variable,become easily available via their connection with Health Kit.
Hope:Can you describe what gamification is and how it relates to your research?
Alex: Gamification is using game thinking and game mechanics to solve problems and engage users. In this study, my goal was to explore if PokeMon Go appears to influence steps taken per day (spoiler alert, so far it looks like a small trend, but nothing significant based on our current sample) and then to look at the game mechanics of PokeMon Go.
Going forward, I’d like to explore how to create a more efficient recruitment process. I’d also like to add more validated measures to the protocol. A couple of the questions I’d wanted to ask were excluded because they were too open-ended and there were no definitive way to analyze them.
Hope: You’re currently writing your thesis. How do you see yourself using your degree in the future?
Alex: If all goes according to plan, I will be continuing my education at ASU in Dr. Hekler’s lab. I am hoping to use my degree to specialize in designing programs catered to healthy living and healthy food choices. Dr. Hekler has a couple awesome studies that are currently being reviewed, so I am hoping to dive into one of those just as soon as they get approved. *fingers crossed*
Hope:Besides being a graduate student, you’re also a certified personal trainer. What piece of advice have you repeated most often when working with clients?
Alex: One of my old professors said, “Eat less, move more.” I really think that’s the best advice. I’m a huge advocate for developing a healthy lifestyle. I lost 60 pounds by trial and error. When you put immediate gratification aside, anything is possible. It’s hard to change, but doable — especially if you have the right motivation. Find something that gets you psyched and channel that to find better ways to cope. I think a lot of people who claim to be healthy don’t have very healthy coping behaviors.
Hope: Do you do any personal health-tracking on a regular basis? If so, what have you found most helpful about the data you’ve collected?
Alex: Not really. I’ve used them in the past. Theoretically, health trackers are awesome. But I think they’re a way better tool to get people started on a healthier lifestyle than they are to get people to sustain that lifestyle. They’re more like a wake up call. The first time you use one, you think, “That’s all I’m moving?!” People are bad at guessing how much they move. Using a tracker makes you more realistic about your own behaviors, but it’s not necessarily going to get you to change your habits. For instance, I know I don’t walk a lot – I don’t need a tracker to tell me that. So I try to make up for that by standing and stretching as much as possible. I believe that if you’re not getting one thing, then try to balance it out by doing something else.
Hope:What health-tracking technology do you wish existed?
Alex: There’s only so much you can do with the information given to you by the current trackers. Say I’ve walked 7,000 steps today. I don’t know how that’s impacting me. It would be cool to have a one-stop shop that tracks food quantities, health behaviors, and physical activities. I’m optimistic that this will happen one day, but right now you have to be really dedicated to make use of trackers. Plus, most devices and techniques are not that accurate. Even the calories on the back of a box of food are only as accurate as the FDA requires.
Hope: According to your LinkedIn profile, your interests are fitness, coffee, reading, learning, and writing. Is coffee the fuel that sustains your other interests?
Alex: Pretty much.. A nice cup of coffee is my reward for doing the things that I should be doing.
Want to join Alex’s study?
You can join on Open Humans! The Designing Health Lab might have funding for another round. If it does, Alex will get in touch with you.
Check out this inspiring video featuring Open Humans participant Liz Salmi and participant/board member Steven Keating.
Search & filter members.
Looking for someone’s profile? Want to see who else has joined an activity? We’ve upgraded the Member List! You can now search for other participants by name or username. You can also use a drop-down to filter the list according to activity, study, or data source.
Want to join a study? Add a data source? Manage related data? Find new ways to share? We’ve pulled all these features together with pages for each activity.
Here are some activity pages you might want to check out…
Open Humans HealthKit Integration
Got an iPhone? This project and open source app, created by James Turner, enables you to add your iPhone’s Health data to Open Humans.
Are you a 23andMe customer? You can add this data to Open Humans. Already added your data? Visit this page to see your files, and find projects you can share it with!
Got nipples? (Probably!) Join this study to help Abby Wark at Harvard Medical School learn more about the areola – an understudied & uniquely human anatomy feature.
Activity pages are also easy URLs to send to friends. Feel free to share!
A new name for our nonprofit.
Our nonprofit has a new name: the Open Humans Foundation.
Open Humans is a project of a 501(c)(3) charitable organization. Since its founding in 2008, this organization’s name has been “PersonalGenomes.org”. We’ve now got a new name, but our mission remains the same: to make a wide spectrum of data about humans accessible to increase biological literacy and improve human health.
Liz Salmi is a “healthcare communications nerd, patient advocate, brain cancer blogger, neuro-geek and all around OK gal.” She has had two brain surgeries, 24 months of chemotherapy, and says it is her duty and honor to tell her story. We spoke a few weeks ago.
Hope: How did you find out about Open Humans and what made you join?
Liz: I first heard of Open Humans from Steven Keating. I’d been following his story for a couple years since we’re both living with a brain tumor. We met when we were asked to participate in “The Open Patient,” a documentary about applying the “open source” philosophy in health care. He was asked to be featured in the documentary because he has open sourced a lot of his health data, and I was asked to do so because I’ve been open sourcing my healthcare story through my blog. I joined Open Humans because I wanted to share some of my health data, too.
Hope: What is most fulfilling to you about sharing your data?
Liz: There’s sharing data and then there’s sharing information about an experience. What I find fulfilling about sharing my story is that I’m able to connect with others who are going through a similar experience. So many of the people who read my blog write to me, and I get to learn their stories as well. Fewer than 2% of cancers are brain cancers, which means there aren’t many people living with it. Also, the prognosis for most brain cancers is not very good. But someone diagnosed today could stumble across my blog and learn what it’s like to live with this! That’s why I’ve decided to continue it and write about the survivor stage. I still get brain scans every 6 months, and I take medicine for the side effects of my tumor, such as epileptic seizures. I talk about all of this on my blog. Even if the tumor grows, I will continue to share my story.
I’m getting more into the idea of sharing my health data. I believe this data could be a valuable resource not just now, but also in the future. I sometimes wonder if I’d be this open if I felt stigmatized because of my disease, but I have never felt discriminated against because of it. I know people who have rare diseases who haven’t been as fortunate in this regard. It’s a very personal choice to share health information. What is right for me isn’t necessarily right for everyone.
Hope: Before you started your blog, had you ever shared health data — for example, by participating in traditional research studies?
Liz: I’d never shared health data before my diagnosis because I’d never been in a position to. I wasn’t on a university campus where students were being recruited for studies, so I never felt I had access to any sort of research. However, one of the places I went for a second opinion on my diagnosis was the University of California, San Francisco, a teaching hospital. They asked me to join a study, and said I’d get $20 for it. I said, “Sign me up!” A year later, they contacted me to see how I was doing, and by that time I was already blogging about my experience. I’m one of those people who likes filling out forms and surveys, so at some point I realized I didn’t need any sort of financial incentive to share my data. I felt I had valuable information, and it was fulfilling to know that researchers were looking at it and some good could come out of it.
Hope:You said that it was a huge decision to change the setting on your blog from private to public. Was the decision to publicly share some of your health data on Open Humans similarly momentous, or a no-brainer?
Liz: It was a no-brainer! Even though I had my blog and various other opportunities to be “out” as someone living with brain cancer, I didn’t have a platform to share my health data. When I learned about Open Humans, I knew it was the just the kind of platform I was looking for.
I’ve learned that there are a lot of people who want to contribute data, but who don’t fit into existing studies. It would be great if Open Humans could become a repository for their data, so researchers could access it now or in the future.
Hope:Tom Delbanco, MD and co-founder of OpenNotes, said in the excellent Open Patient video, “If you’re healthy, you worry about privacy. If you’re sick, or if you’re in the emergency room, you could give a damn about privacy. You just want everyone to have access to everything right away so you can be helped.” Do you think the needle is moving at all on this? Do you get a sense that people you meet – either online or off – generally share a commitment to data sharing?
Liz: I was diagnosed with my brain tumor in 2008, and my instinct was to blog about it because I couldn’t find a lot of the sort of information I wanted online. But my boyfriend (now husband), friends, and health care advocates cautioned me against this. They were concerned that I’d regret it because my feelings about my privacy could change over time. But pretty soon they thought it was really cool how I was reaching people!
I’m a member of a generation that has grown up sharing stuff on the Internet, so – for better or worse – we’re used to sharing what older generations consider too personal to talk about publicly. Sharing is ingrained in us. We’re not judging each other. I know people from certain cultural or religious backgrounds still believe that talking about disease is somehow inviting ill will, but most of us just don’t think it’s a big deal.
Hope:You mentioned in your TEDx talk that friends of yours crowdfunded for your medical bills and that your blog is an effort to redefine the support group. Obviously, you’re also sharing your data online on our site. Do you feel you’ve experienced any drawbacks from this 21-century model for healthcare, or has it all been positive?
Liz: Everything has been really positive. Web communication used to be the wild, wild west, but it’s not anymore. It can be very rewarding.
Hope: What are the biggest misconceptions about people living with rare or serious diseases?
Liz: It depends on the disease. I know people with diseases you’ve never heard of. They often feel left out and as if they have no support. I’ve mostly met them over Twitter — through #RareDisease and #BTSM, which stands for Brain Tumor Social Media. I can relate to what they’re going through because there are about 120 types of brain tumors, but we’re still the black sheep of the cancer world. As with rare diseases, there’s not a lot of money flowing in for treatment.
I’ve become a vocal patient advocate partly because I know what it’s like to not be able to find an appropriate support group. Different diseases require different types of support. For instance, people with brain tumors have neurological issues. People with other cancers can’t relate to this, so a generic cancer support group isn’t right for us. Larger cities have more options, but not everyone lives in large cities.
As a side note, there are a lot of things laypeople can do to impact healthcare — like lobbying for more funding. I’ve done this at the federal level, but calling your local district office can make a difference, too.
Hope: Last question. What health-tracking technology do you wish existed?
Liz: I wish there were more ways to share health data and more partnerships between researchers. Also, that more data sites had an app version and that some health tracking apps already in existence were more user friendly!
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:
Where are people most active?
How does this compare to others who live nearby?
What activities do people choose for recreation?
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!
James Turner is one of our most ‘connected’ members, creator of two Open Humans activities, and an endlessly interesting guy.
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.
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.