An interview with project grant awardee Benjamin Carr


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Today we’re interviewing Benjamin Carr. He is not only a long-term member of the Open Humans community, but also the recipient of two(!) of our Project Grants.

His two – closely related – projects are the integration of both Google Fit and Microsoft Healthvault into the Open Humans Network.

Benjamin, please give our blog readers a quick introduction about who you are!

I originally became aware of the Personal Genome Project, way way back at its dawn in 2005 while I was working at Woods Hole Oceanographic Institution in Physical Oceanography. The idea to a young scientist that PGP was basically providing seed money to make human DNA sequencing affordable was amazing, and I was quick to sign up, and encourage my whole family to join as well. For those that don’t know, becoming a PGP volunteer was a multi-year process requiring a multitude of questionnaires. I didn’t receive my tubes to spit into until 2012! I attended a couple of the GET conferences in Cambridge, MA when I was across the river working on my PhD in Biology at Boston University. My science and technology passions found an excellent intersection with Open Humans.

You have been a part of the Open Humans community for a long time. How did you initially come to Open Humans?

I’m not sure of the exact date, but it was shortly after launch in 2015 that I joined Open Humans. Most likely due to an email blast from Madeleine Ball to the PGP group. I quickly linked up as much data as I had available at the time, and made things like Wildlife of Our Homes public. Furthermore, I am one of just 26 People to admit that we owned a “Jawbone Fitness tracker,” an early step counter and Fitbit competitor.

Between trying to spur communications on the forum and Slack channel, submitting issues and pull requests for the website itself and individual projects, I’ve banged my head against most things Open Humans, save the legal bits.  

You volunteer for Open Humans, what are your responsibilities and how did you end up in that role?

Like all of us I volunteer data. But I also help to edit mailings and postings that go out in email blasts and on the blog. I report issues on Github and Slack. I try to help new users and developers when I can and do  a bit of coding for different parts of the system myself, and keeping an eye out for bugs and vulnerabilities. I also started managing the Facebook Page in March.

Open Humans is looking for more than just data, programmers, and scientists, the idea is to make lots of information “open”. Having had some experience and the resources to manage a social media system and strategy my offer to try to make the Facebook Community more vibrant was welcomed with open arms. Hopefully you’ve noticed the steady stream of what I hope are interesting links and stories on our Facebook Page.

If you have any ideas for content or want to host something like a Reddit AMA on our Facebook drop me a line! I am always looking for new exciting things to share. Being a scientist myself, I am actually running a Facebook experiment. I started posting over the weekend, and Sunday posts seem like a winner for interaction with our Facebook fans! I’m also trying to see if changing the timing of the posts inspires more people to like, share or comment. We’ll see!

Open Humans could always use help making things more accessible. We try our best to make each piece understandable to a wide audience, but just having volunteers review the documentation and explanations of projects and goals would be welcomed!.

You did not only get one Open Humans project grant, but two. What are these two projects you have planned?

The first as you mentioned is to incorporate Google Fit data into the Open Humans platform. Google Fit ships with every Android phone that uses the Google Apps, which means as of this interview there are more than 2.6 Billion active Android phones. While Fit natively tracks things like steps and stairs, there is an entire ecosystem of products that plug into it, like Running, Biking, and even Push Up Apps! As well as many devices from glucose meters for diabetics to blood pressure cuffs, and even CPAP machines for people with sleep apnea! The second project has some overlap with the devices supported, but MS HealthVault is really a repository for millions of people to keep track of medical records, MRI images, XRays, Prescriptions, and even directly link Electronic Health Records!

Your two projects sound a bit related. How did you get the idea for them? Are you using these services yourself?

The two are related, honestly the Google Fit seemed like a logical integration I just hadn’t had time to work on it, the Healthvault occurred to be during a discussion with you on Slack about openSNP and pulling that data into Open Humans. By my using the APIs (Application programming interfaces) provided by Google and Microsoft I can allow participants to share data collected in these two “silos” with the Open Humans community and researchers. By adding these two integrations I hope to increase the appeal for researchers to look at and use the Open Humans datasets, as we have years, and in some cases in MS HealthVault, decades of data that can be accessed along with genetic sequences from those that have provided it it from services using microarrays or chips like 23andMe and Ancestry, or full genome sequences!

When I’m done with the grant work, the code should be self updating, or offer the ability for users to request data be pulled in at the push of a button. I do use both MS HealthVault and Google Fit, both directly and with attached devices and services. I started using MS HealthVault when Google Health closed, and I migrated all of the data I had put into Google Health for PGP from Google to the Microsoft platform. I’m also a long time Google Phone user, these two facts makes coding for both APIs easier as I have a ton of data in each of the respective warehouses.

Is there anything important that we didn’t cover so far that you’d like to add?

I have seen how genomics can play a huge part in one’s life. I am very open with my doctors about being lucky enough to have a sequenced genome. By being able to do a little bit of my own research and ‘checking my genome for Z’ based on doctor’s suggestions, symptoms that previously eluded diagnosis started to line up. I also lost my first wife to Ovarian Cancer that was accelerated – if not actually caused – by a family history of Prostate Cancer, something we wouldn’t know until after she had passed.

On the lighter side I’m an avid photographer, and when I was doing my PhD work in Boston went to the woods nearly every weekend, to clear my head, rejuvenate my soul, throw a tennis ball for my labrador retriever, and rack up a very high shutter count on my old DSLR. I took this picture of the first of three upcoming “Supermoons” a couple weekends ago.

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I am also an environmentalist. My background spans fisheries and oceanography, but also the hereditary traits passed on from mother to offspring of Walleye fish, the biocomplexity and interconnectedness of the Great Lakes.I was one of the four man crew who did the 9/11 impact assessment of the Hudson River Estuary from the George Washington Bridge to the Battery! I’ve been Chief Scientist on multiple cruises including working from small boats to large 115 ft, 200 ton vessels! Even though my first cruise in 1999 was one of the worst weather-wise (it was so bad the glass in the windows shattered), I still have an undying love for the oceans, being on the water or just being near it.

Meet the first recipients of the Open Humans Project Grants

Open Humans is a collaborative endeavour that would be impossible without the individual support of each and every user. The whole idea behind Open Humans relies on a healthy ecosystem that flourishes with each contribution made by individuals. Our project grants are thus designed to support individual ideas that have the potential to help grow the whole Open Humans ecosystem. For example, such projects can provide new ways of analyzing and visualizing existing data sources. Or they can connect new data sources that were so far not represented in Open Humans. This open-endedness has inspired many of you. Since the initial announcement of the project grants in July 2017 we got many great submissions. And as the grants are on a rolling schedule there is no deadline to apply: You can go ahead right now!

After carefully going through the applications we got so far we are happy to now announce the first three projects. Each of them will be funded with $5,000 to support them in realizing their vision for how Open Humans should grow.

MyFitnessPal Miner

Millions of users all over the globe already use MyFitnessPal. This thriving community makes MyFitnessPal (MFP) one of the most successful apps to track both your calorie intake and your exercise. Anh Nguyet Vu’s goal is to bring this community to Open Humans. Her MyFitnessPal Miner will not only enable the import of public MFP data into Open Humans, but also generate insightful visualizations out of the MFP data. Long-term goals for the MFP Miner are the inclusion of genetic data from 23andMe and the inclusion of private data.

You can find an early prototype of the MyFitnessPal Miner on Anh Nguyet’s website, Bring Your Own Biology.

Open Humans Google Fit Integration

Google Fit allows Android users to merge activity data from different sensors, devices and apps into a single data stream. In that sense it is Google’s health-tracking answer to Apple’s HealthKit. But while Open Humans could already import data from HealthKit, there was so far no easy way to do the same for Google Fit data. Thanks to Benjamin Carr this is about to change. His Open Humans Google Fit Integration will allow both services to communicate to each other. With over 80% of all smartphones running Android this will allow a large community to put their data into Open Humans!

You can find Benjamin on Twitter and his first stab at the Google Fit Integration can already be found on GitHub.

Microsoft Healthvault Integration

Microsoft as a third big player, alongside Google and Apple, when it comes to health-related data about individuals. Microsoft’s Healthvault is a web-based personal health record that has been around for around 10 years by now. It not only takes in data from personal fitness devices, but Healthvault can also aggregate medical records and prescription fillings. This makes it go a step further than HealthKit and Google Fit and offers great potential for a connection with Open Humans. Luckily API-programming nerd Benjamin Carr – yes, the same who will work on the Google Fit Integration – did have some more time on his hands. This is why he proposed a second project that will bring together Microsoft Healthvault and Open Humans.

Find Benjamin’s current progress on this on GitHub!

What’s next?

In the next weeks we will release some short interviews our grantees so that we all can get to know them (and their projects) better. Did seeing these projects inspire you to run your own? Apply with your own project idea right now!

What is Open Humans to me?

I’m Steph, I’ve just started as a software developer at Open Humans, and in this post I want to describe what the organisation means to me.

 

I feel like the value of Open Humans can be split into three main categories, perhaps of increasing fuzziness in terms of concrete assets, but also, in my opinion, of increasing importance and rarity. Open Humans is a technological platform; it’s a vibrant community; and it’s a paradigm shift.

 

At its very core, Open Humans is a technological platform. People are increasingly finding themselves in possession of their own personal data. Whether this be from fitness tracking devices; commercial genome sequencing services; or internet search history, we are, somewhat inadvertently, gathering more and more data about ourselves.

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Fig1: people are gathering data about themselves

 

The Open Humans platform allows members to upload and store these data privately, to choose whether to share some publicly, and to use their data to contribute to research projects and learn more about themselves.

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Fig2: people can upload their data easily using data tools

 

For researchers and citizen scientists, the platform enables painless and efficient data collection from engaged research participants. It is a seamless pipeline for human subjects research, which puts the individual participants in charge of how their data is used, avoiding a one-size-fits-all ethics approach which is common in traditional research protocols.

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Fig3: data can be used to further human subjects research

 

Open Humans is defined by its vibrant community. In recent years there has been a sharp rise in production and use of personal tracking systems: wearable devices; smart scales; lifestyle logging apps (including diet, exercise, and sleep); and commercial genetic and ancestry tools. People are intrigued by their own data. For this reason, there is no single user profile: we are researchers; patients; data scientists; citizen scientists; any and all people who want to learn more about themselves. The Open Humans community have written 19 data transfer tools enabling data from external projects to be added to Open Humans by users at the touch of a button. They have contributed 9 projects to the site, where research can be done on participants’ shared data. And they have continued to be enthusiastic, motivated, and truly engaged in the work of the organisation.

 

Open Humans is a paradigm shift: a totally new way to do humans subjects research. For me this is the most exciting way to look at Open Humans. Personal data can be sensitive: sharing can cause embarrassment, expose health concerns leading to discrimination, or lead to identity theft. Historically in the medical world, this has been handled by keeping health and human subjects research data anonymous. However as data becomes richer and more descriptive (for example, a genome, or internet search history), it is becoming easier to identify the original subject. So now we have more data than ever, and keeping it private when using it in research is becoming harder than ever.

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Fig4: the traditional human subjects research pipeline: data is handed over to scientists and generally not returned, subjects do not learn about the results and don’t get a say in how they are shared

 

Open Humans turns the traditional research pipeline on its head. It puts individual subjects at the centre of the sharing process, and in full control of how their own data is used in research. People are unique, and each will have their own reasons for wanting to keep some data private. These diverse sharing preferences call for a new system for human subjects research, that focuses on the subjects themselves, and meets their own personal privacy requirements.

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Fig5: the Open Humans research pipeline: participants have autonomy over their data and can choose which studies they share their data with

 

Giving research subjects the autonomy they deserve and at the same time increasing the efficiency of the research pipeline seems like a great idea, but the project is ambitious. Large scale open projects do have the ability to change the world (think Wikipedia), but changing the status quo in a system that has been around for a long time will always come with a lot of friction. However the vast amount of data being generated these days means that we are in new territory. This is a great time for change. Making sure that people are empowered to make their own decisions about how their data is used is an important endeavor. Working closely with our community, we hope to reach a critical mass of membership such that personal data sharing in this way becomes the standard approach. I am excited and optimistic about how Open Humans can revolutionise human subjects research, and I’m very grateful to be a part of this exciting movement.

Keeping Pace: You can advance health research with your smartphone!

Want to help advance Dr. Chunara’s study to the next phase? Anyone with a smartphone can help! Install apps to add Moves data, Runkeeper data (if you record your exercise), or HealthKit data (if you have an iPhone). The study invites Fitbit data too! You can donate any of these – or all of them – to the Keeping Pace study on Open Humans.

Click to donate data to Keeping Pace!

Keeping Pace is currently participating in the Healthy Behavior Data Challenge which is jointly run by the Centers for Disease Control and Prevention and the Department of Health and Human Services. This challenge is looking for ideas on how novel data sources and methods can support public health surveillance for healthy behaviors.

Keeping Pace was amongst the winners of Phase I of the challenge – in part thanks to 167 Open Humans members who already donated their activity data! For Phase II the goal is to further implement their proposed prototype. For this, Keeping Pace is looking for more participants.

Visit Keeping Pace!

About the projectKeeping Pace was one of the first studies to join Open Humans, back in July 2015! It is a study led by Dr. Rumi Chunara, an assistant professor at New York University. Her research interests are at the intersection of computer science and public health and make a great match to Open Humans! With Keeping Pace she aims to gain new insights into how seasons and the local environment influence our movement patterns.

Why Open Humans is an essential part of my work to change the future of healthcare research

Madeleine: I’m excited to share a Q&A with an innovator – Dana Lewis!

Dana was recently awarded a grant to further her work in patient-driven research, and she’s been using Open Humans in an exciting way. You can follow her on Twitter at @DanaMLewis.


So, what do you like about Open Humans?

Health data is important to individuals, including myself, and I think it’s important that we as a society find ways to allow individuals to be able to chose when and how we share our data. Open Humans makes that very easy, and I love being able to work with the Open Humans team to create tools like the Nightscout Data Transfer uploader tool that further anonymizes data  uploads. As an individual, this makes it easy to upload my own diabetes data (continuous glucose monitoring data, insulin dosing data, food info, and other data) and share it with projects that I trust. As a researcher, and as a partner to other researchers, it makes it easy to build Data Commons projects on Open Humans to leverage data from the DIY artificial pancreas community to further healthcare research overall.

Wait, “artificial pancreas”? What’s that?

I helped build a DIY “artificial pancreas” that is really an “automated insulin delivery system”. That means a small computer & radio device that can get data from an insulin pump & continuous glucose monitor, process the data and decide what needs to be done, and send commands to adjust the insulin dosing that the insulin pump is doing. Read, write, read, rinse, repeat!

I got into this because, as a patient, I rely on my medical equipment. I want my equipment to be better, for me and everyone else. Medical equipment often isn’t perfect. “One size fits all” really doesn’t fit all. In 2013, I built a smarter alarm system for my continuous glucose monitor to make louder alarms. In 2014, with the partnership of others like Ben West who is also a passionate advocate for understanding medical devices, I “closed the loop” and built a hybrid closed loop artificial pancreas system for myself. In early 2015, we open sourced it, launching the OpenAPS movement to make this kind of technology more broadly accessible to those who wanted it.

You must be the only one who’s doing something like this.

Actually, no. There are more than 400+ people worldwide using various types of DIY closed loop systems – and that’s a low estimate! It’s neat to live during a time when off the shelf hardware, existing medical devices, and open source software can be paired to improve our lives. There’s also half a dozen (or more) other DIY solutions in the diabetes community, and likely other examples (think 3D-printing prosthetics, etc.) in other types of communities, too. And there should be even more than there are – which is what I’m hoping to work on.


So what exactly is your project that’s being funded?

I created the OpenAPS Data Commons to address a few issues. First, to stop researchers from emailing and asking me for my individual data. I by no means represent all other DIY closed loopers or people with diabetes! Second, the Data Commons approach allows people to donate their data anonymously to research; since it’s anonymized, it is often IRB-exempt. It also makes this data available to people (patient researchers) who aren’t affiliated with an organization and don’t need IRB approval or anything fancy, and just need data to test new algorithm features or investigate theories.

But, not everyone implicitly knows how to do research. Many people learn research skills, but not everyone has the wherewithal and time to do so. Or maybe they don’t want to become a data science expert! For a variety of reasons, that’s why we decided to create an on-call data science and research team, that can provide support around forming research questions and working through the process of scientific discovery, as well as provide data science resources to expedite the research process. This portion of the project does focus on the diabetes community, since we have multiple Data Commons and communities of people donating data for research, as well as dozens of citizen scientists and researchers already in action (with more interested in getting involved).

What else does Open Humans have to do with it?

Since I’ve been administering the Nightscout and OpenAPS Data Commons, I’ve spent a lot of time on the Open Humans site as both a “participant” of research donating my data, as well as a “researcher” who is pulling down and using data for research (and working to get it to other researchers). I’ve been able to work closely with Madeleine and suggest the addition of a few features to make it easier to use for research and downloading large data sets from projects. I’ve also been documenting some tools I’ve created (like a complex json to csv converter; scripts to pull data from multiple OH download files and into a single file for analysis; plus writing up more details about how to work with data files coming from Nightscout into OH), also with the goal of facilitating more researchers to be able to dive in and do research without needing specific tool or technical experience.

It’s also great to work with a platform like Open Humans that allows us to share data or use data for multiple projects simultaneously. There’s no burdensome data collection or study procedures for individuals to be able to contribute to numerous research projects where their data is useful. People consent to share their data with the commons, fill out an optional survey (which will save them from having to repeat basic demographic-type information that every research project is interested in), and are done!

Are you *only* working with the diabetes community?

Not at all. The first part of our project does focus on learning best practices and lessons learned from the DIY diabetes communities, but with an eye toward creating open source toolkit and materials that will be of use to many other patient health communities. My goal is to help as many other patient health communities spark similar #WeAreNotWaiting projects in the areas that are of most use to them, based on their needs.

How can I find out more about this work?

Make sure to read our project announcement blog post if you haven’t already – it’s got some calls to action for people with diabetes; people interested in leading projects in other health communities; as well as other researchers interested in collaborating! Also, follow me on Twitter, for more posts about this work in progress!

Joining Open Humans

Note: Cross-posted from my original post at http://ruleofthirds.de/joining-open-humans/

I am more than delighted to announce that I will join Open Humans. Supported by a fellowship I will assume the role of Director of Research in November. Open Humans as a platform connects individuals who want to participate in research with research studies and projects that can be run by academic and “citizen” scientists alike. As I make this transition, I’d like to take the opportunity to reflect a bit on path into all things open* and what my vision for future is.

Digging into the old archives of my first (German language) science blog I find what must be my first public writing about Open Access back in April of 2009 and it’s been quite a ride since then. Back then I was a frustrated life sciences undergrad student, annoyed by not being able to read all the primary literature that sounded interesting enough to read. Frustrated enough even to run for state parliament on the platform of the Pirate Party in 2010, campaigning for both Open Access in the narrow sense and open access to education in the broader sense. While I ultimately didn’t end up in parliament, little did this to deter me from being more involved in opening up how research can be conducted. After moving on to doing a master’s degree in ecology and evolution it wouldn’t be too long before the next hobbyist open* project should start.

Only a year later, in the summer of 2011, Philipp Bayer and I started to work on openSNP, an open source repository that allows people from around the world to donate their genetic and phenotypic information into the public domain. Thanks to the magic of open source we were quickly joined by the ever talented Helge Rausch. Being frustrated was yet again a big driver in the process. Ironically, my frustration at that time was with the same people who started Open Humans. I wanted to donate my 23andMe data to its intellectual predecessor, the Personal Genome Project, only to discover that accepted donors had to be US citizens or residents. What else could one do in such a situation but start an alternative data repository, right? And ultimately our completely unfunded grassroots approach of “people just doing things in their spare time” did pay off: So far over 3,700 data sets have been donated through openSNP – making it the largest open* data source for personal genomics data. Along the way this work has led to many fun collaborations and interesting data uses, including work on the ethics of participant-led research, studies on genomic privacy, crowdsourced machine learning competitions based on genetic data and even art installations.

My own work in open* over the years has focused a lot on how to break down barriers to participation in research at large, be it in who’s getting access to publications, supporting people who want to start their own open* projects or evaluating how we can improve research by including participants more in the process. But while open science may be slowly winning in who is getting access to publications and data, there is still a long way to go when it comes to who will actually participate in doing research: For a large part research is still heavily confined to the realm of academia, with all the biases that this entails that lead to a growing divide between researchers and the “general public” at large. We need to take the next step in opening up science, this time to larger audiences, involving people much earlier in the research process, transforming “citizen science” into an endeavour that’s actually participatory and gives participants much more agency.

And to me Open Humans is doing just that: Offering a space that is open to everyone or – as Madeleine Ball put it so succinctly in her introductory blogpost as the Executive Director of the Open Humans Foundation – an empty garden with everyone of you being the gardeners. As such, Open Humans allows you to design and execute research projects, regardless of whether you are coming from Academia or not. I think the big success of the Quantified Self movement is testament to the wish of people to study themselves and do research. The great idea is that by increasing inclusivity we will all win. When academic and participant-led research come together – informing each other in the process – we will all end up with new and better research, asking more relevant questions and getting more satisfactory answers. So, if you have an interesting idea you would like to research, then please go ahead and give it a try!

Now that I just handed in my PhD thesis (obviously doing some meta-research on my thesis writing that’s fully in the spirit of Open Humans along the way), I want to put all of my energy into making the shift to more inclusive and grassroots-style research happen. This is made possible by Madeleine Ball, who has years of experience leading this field. She was not only instrumental in the success of the Personal Genome Project, but also co-founded Open Humans. She is herself a fellow of the Shuttleworth Foundation, and it is funding from this fellowship – along with her own co-investment! – that gives me the chance to fully pursue this. I am extremely grateful for this and her guidance will offer an excellent learning opportunity for me. I also have to thank Chris Mungall and the whole Berkeley Bioinformatics Open Source Project (BBOP) group for their great support. Through it I will be able to do all of this in a great and supportive environment at the Lawrence Berkeley National Lab. My role during the fellowship will be to help you tend to this garden in the best way possible, hopefully building many new collaborations, projects, studies and friendships along the way. So, let’s together get the democratization of science started.


A note on the term “citizen science”: The term sucks. Of course true inclusivity needs to mean that everyone – regardless of their immigration status – should be able to be an active agent in the research process. While I think that “participatory science” makes for an excellent replacement for the activity itself, I still struggle to find a replacement for “citizen scientist”.

Announcing Bastian joining Open Humans!

IMG_9708_editI am thrilled and honored to announce an expansion to the Open Humans team!

Bastian Greshake Tzovaras will join us starting November 1 as Director of Research at the Open Humans Foundation. He is funded by a fellowship from the Open Humans Foundation to support his work pursuing our shared vision of advancing citizen science and open approaches to health and human subjects research. Before Bastian starts, I’d like to to tell you more about him – even if you think you know him well!

To many Bastian is best known for openSNP, a project he co-founded in 2011 with Philipp Bayer – and joined soonafter by Helge Rausch. OpenSNP invites individuals to donate and publicly share their genetic data (e.g. from 23andMe and AncestryDNA). OpenSNP members can also contribute additional data, including crowd-sourced trait surveys. It is a community and platform that matches the themes of the Personal Genome Project and Open Humans.

I think OpenSNP has been an impressive success. On a small crowd-funded budget, Bastian, Philipp, and Helge helped more than 3,700 individuals to publicly share their genotyping data. I believe this is more publicly shared human genotyping data than all other projects combined!

Finding some way to join forces with Bastian seemed obvious and overdue. And so, I reached out. Because for Open Humans to succeed as a shared vision, it needs more than just me.

And as I got to know Bastian better, I realized how profoundly dedicated he is to broad and resonant themes – of personal data sharing, citizen science, participatory research, open access, and open science. He has published research about personal data sharing behavior, participant-led research, analyses of Sci-Hub usage, open peer review, and open science tools – in addition to his thesis work with lichen metagenomics! He serves on the committees for the Bioinformatics Open Source Conference (BOSC), OpenCon Berlin, and a FORCE11 workgroup. He has worked with with Mozilla Science Lab to mentor open science projects, run workshop sessions, and teach participatory/open science approaches. He attends, speaks, and presents at numerous events and meetings – BOSC, MozFest, Creative Commons, Sage Assembly, OpenCon, and more.

In summary, OpenSNP was just one facet of Bastian’s prolific and wide-ranging dedication to open approaches and social change in how we perform research. His vision matches that of Open Humans, and his strengths complement mine.

Bastian’s work with Open Humans will focus on the following areas: sustainable approaches for citizen science and patient-engaged research, collaborations and outreach for participatory research projects, mentorship and support for projects, and academic engagement via collaborations, publications, and meetings. I suspect he’ll get involved in almost everything, as his skills and interests are so diverse!

It is an honor to have Bastian joining Open Humans. I am eager for him to begin, and I look forward to his work with Open Humans in the coming year – and, if all goes well, years to come. Together we can endeavor to grow an open ecosystem – one that is thriving, sustained, and expands the world with something powerful and new.

Introducing myself as Executive Director.

Today is my first day as Executive Director of Open Humans Foundation. I am honored and thrilled to be taking the helm! As Open Humans co-founder I’m a familiar face, but I’d like to take this opportunity to re-introduce myself – and to share my vision.

How I got here probably begins with my love for creating and sharing knowledge.

As an early biotech graduate student, I stumbled into Wikipedia. I edited articles, created diagrams, and improved knowledge. Genetics was a theme: a reflection of my graduate work, and a topic I’d loved since high school. I gave the Genetics page a complete remodel – featured article in 2008! I helped One Laptop per Child create an offline Wikipedia for hundreds of thousands of children. I also created a page for my favorite mutation, a thing of history and beauty: Double-flowered.

This love for knowledge sharing – and for genetics – drew me, belatedly, to another project in the lab: George Church’s Personal Genome Project (PGP). (I was already in George’s lab. My thesis was mostly about DNA methylation.) George’s vision for the PGP was radical: open sourcing ourselves. He invited individuals to publicly share their genomes, health records, cell lines, and more. Participants took on strange, unknown risks. It was provocative and transgressive, and George had volunteered as its pilot participant: PGP #1.

In the years that followed, the Harvard PGP publicly released hundreds of genomes and enrolled thousands of participants. I became Director of Research for George’s project, and I was involved in every facet of operations. I created the project’s trait surveys, rewrote its entrance exam, fielded a multitude of inquiries, and helped organize sample collection events. I evaluated hundreds of genomes to create the “research reports” participants received, which explained the potential impact of variants in their genome. I was also first author on key papers for the project.

In addition, I became a liaison for the Harvard PGP and other projects that wished to work with it. When Jason Bobe expanded the GET Conference to add “GET Labs”, I was there as an interface between the researchers, the PGP, and the participants. My ongoing collaborations, through GET Labs and otherwise, have included American Gut (Rob Knight, UCSD), GoViral (Rumi Chunara, NYU), Critical Assessment of Genome Interpretation (Steven Brenner, UC Berkeley & John Moult, U of Maryland), the Personal Genomics Human Computer Interaction group (Orit Shaer, Wellesley & Oded Nov, NYU), and the PeopleSeq Consortium (Robert Green, Partners).

Through these, I started to see the bigger picture of what it means to study ourselves.

Genomes hold larger lessons. We have entered a world of data, where personal and meaningful information is being aggregated about us. But data sharing is foundering on privacy concerns. Silos of control have divorced individuals from their data, and reinforce a divide between the roles of participant and researcher.

This matters, because our data matters – it has the potential to make discoveries, to improve our health, and to empower us. But achieving these visions has begun to seem like an unreachable mirage.

By Michael Gwyther-Jones, CC-BY-SA.

I see a design problem. Our system for research was built in a pre-digital world. Open Humans is a redesign, restructuring how we aggregate data and perform research.

In Open Humans, individuals are the aggregators and data sharers.

And anyone can create a project on the site to work with members.

Projects can be citizen-led as well as traditional academic studies. Projects can provide data analysis tools, or can add new data. Data can come from anywhere – from research studies to third party APIs. A project can also invite members to share data broadly, e.g. in a “commons”, managed by a trusted entity. Researchers can build upon existing data streams. And studies can return their data – where it becomes a resource for personal discovery and future research.

It unlocks new opportunities for longitudinal research, for citizen science, for individual exploration, and for innovations that transcend any single study.

Our role is to be stewards: we have built an empty garden. You are its gardeners.

In this role, I hope you can trust us. Open Humans Foundation is a nonprofit, and my work as steward is supported by my Shuttleworth Foundation Fellowship. This funds me as an individual – and more – it grants me access to $250,000 in project funding each year. But for each $10 in project funding I seek from the Shuttleworth Foundation, I must give $1 of my own income. This is their bargain, and I’m taking it. I’m investing in this dream, and in this community garden.

What has grown already is full of serendipity and innovation. When we started, we seeded this with data we supported: genomic, microbiome, activity tracking, GPS. But now it grows beyond us. James Turner – a PGP participant – created an open source app to add Apple iOS “HealthKit” data. Continuous glucose monitor data has come from the Nightscout Project, a type 1 diabetes community. The Nightscout Foundation is creating a patient-led “data commons”. And Dana Lewis invites data donations from her own amazing community – the Open Artificial Pancreas System (OpenAPS) – and is bringing aggregated OpenAPS data to research teams at Stanford and Johns Hopkins. Newcomers wander in regularly now, bearing the seeds of nascent projects.

And so I invite you. Come, build. Plant your seeds – your data – your projects and ideas. Let’s grow something amazing together.

Announcing our new Executive Director: Madeleine Ball

A message from George Church, President of Open Humans Foundation Board of Directors, and Misha Angrist, John Cammack, Esther Dyson, Juan Enriquez, Steven Keating, and Michelle Meyer.

Photo of Madeleine Ball

On behalf of the Open Humans Foundation Board of Directors we are thrilled to announce a new Executive Director for the Open Humans Foundation: Madeleine Ball.

Madeleine Ball is co-founder of Open Humans, and our previous Director of Research. In recognition of her vision for opening human health data – and her talents in pursuing this vision – Madeleine was recently awarded a Shuttleworth Foundation Fellowship. We are thrilled with her recognition with this award, as it publicly confirmed what we privately knew: Madeleine is an enormously talented individual that balances thoughtful strategy with bold vision. We are confident that she will lead OHF to new innovations and achievements.

Our organization has undergone exciting changes in recent years, and we have had a rich history since our start. Founded by Jason Bobe and George Church in 2008, our organization was originally called “PersonalGenomes.org” to reflect its focus on George Church’s Personal Genome Project.

Jason, our organization’s co-founder and outgoing Executive Director, was pivotal in reifying George’s pioneering vision for open science, genomes, and health data. After helping to establish the Harvard Personal Genome Project (PGP), Jason set-up a global network including sites at Sick Kids Hospital in Toronto, Canada; University College London in the United Kingdom; and Center for Molecular Medicine in Vienna, Austria. Simultaneously, Jason’s support for the pilot PGP site – at George’s lab in Harvard Medical School – helped it achieve many noteworthy successes.

Jason organized the Harvard PGP’s study protocols, consents and operations, including an innovative quiz format for testing and improving understanding in the informed consent process. He also led the effort to integrate the Harvard PGP platform with Google Health (sadly discontinued), and, with Jason’s guidance, Harvard PGP was the first participatory study to adopt “Creative Commons Zero” for public domain human health data, releasing an unprecedented set of public genome and health data, cell lines, and official “genome reference material“, as well as sparking numerous ground-breaking papers.

In 2010, Jason’s work extended to the Genomes Environment and Traits conference (GET), an annual conference exploring the frontiers of understanding about human biology that uniquely brought together research participants and scientists to debate the technical, commercial, and societal impacts of advances in our ability to measure and understand people and their traits. (At the first conference, a dozen pioneers of personal genomes – like James Watson, Esther Dyson and Skip Gates – were interviewed by Robert Krulwich and Carl Zimmer, while a desktop DNA sequencer hummed away in the back, analyzing the microbial DNA extracted from a dollar bill donated by a conference participant.) In recent years, the conference itself became a laboratory: GET Labs invited attendees to participate directly with studies. This led to some interesting shared experiences – like armpit swabs, sampling face mites, and the sounds of sterile kit packaging being unwrapped in the restrooms stalls.

Most recently, in March 2015 Jason and Madeleine launched a new program, Open Humans, with support from the Robert Wood Johnson Foundation and the John S. and James L. Knight Foundation. Its transformative, participant-centered approach unlocks new opportunities for research – including longitudinal data aggregation and a cohort shared between studies. The success of this program led us to change the organization’s name to “Open Humans Foundation” in 2016. While we continue to support PGP and GET programs, we believed this new name would better reflect the organization’s overarching vision, as well as expressing our confidence in the Open Humans program itself.

Madeleine is expected to begin as Executive Director on June 1. We are sorry to see Jason leave the Executive Director position, as he shifts to focus more on his work with the Icahn Institute at Mount Sinai where he leads the Resilience Project and other cutting edge clinical research endeavors at the newly formed Institute for Next Generation Healthcare. Jason will continue his leadership of the organization by joining the Board of Directors later this year.

New GoViral website + get a prize for contributing!

ONE OF OUR FIRST PARTNERS HAS UNDERGONE A REBOOT!

GoViral.
Using crowdsourcing to track the spread of viruses.

Join now to help impact the future of public health.
If you haven’t been to their new site, check it out
– it went live in September 2016! –
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Meet a GoViral Team Member

Ingrid Spielman is the research associate and data scientist who built GoViral’s new website.

Hope: Why did you think GoViral would benefit from having a new website? 14379714_10211042321037579_7715615894899053292_o (1)

Ingrid: GoViral, as it stood, had a website interface without any means to interact with users. The new site makes it easy for us to engage with participants. We can remind them to submit kits, and also show them more of the data they input in the form of cool, interactive visualizations.

Hope: Can you describe your typical workday?

Ingrid: While working on the website, I kept a detailed list of project goals. I took a certain amount of time to learn how to accomplish each goal, then went ahead and implemented it. Basically, it broke down to 40% search, 20% asking smart people for help, 40% trying … That adds up right? … If I had known exactly what we needed to do when I started, I bet this project would have happened much more quickly!

Hope: You received your Master’s in Material Science in 2012. What exactly is ‘material science’ and how does it relate to your current work?

Ingrid: It’s a multidisciplinary field where we look at material failure, and discover and engineer materials that have very specific and/or enhanced properties. By looking at how materials degrade over time due to stress, strain failure, or corrosion from sunlight or chemicals, we learn how to improve them. So you have people in material science who are engineering composites that are made up many types of materials – your shoes, for example. Others look at ways to use PTFE (poly tetra fluoro ethylene) – which most people know of as Gore-Tex – in clothing.

Some material scientists look at biomaterials specifically, and solve polymer problems – in which case they’re half chemist! They apply fundamental physics and chemistry to understand the properties of materials and how they change over time. Practical applications are solar cells – how we improve their efficiency – or building computers with smaller, more delicate circuits. They might discover alloys with interesting electronic properties or design lightweight materials that respond better under stress – think of carbon fiber bikes. Perhaps they build materials with interesting reflective properties – which would be considered metamaterials.

Basically, as my professor used to say and probably still does, everything boils down to a materials science question!

With my research-oriented background, GoViral was a natural fit. But I’m so lucky Rumi said I could work on the website. I had to learn most of everything I did for it from scratch!

Hope: Is there another project you’ve worked on that you found to be particularly interesting and/or fulfilling?

Ingrid: Before I decided to focus on data science, I worked in a microbiology lab where we studied how bacteria move and adhere to surfaces. In particular, we studied the bacteria that causes gonorrhea. I used a software called ‘matlab’ to build a user interface so students could easily upload videos of the bacteria, track them, and then find out how fast they moved and how much they were able to pull on the elastic surface they were sitting on. Data like this has implications for how we sterilize surfaces, and also how we treat bacterial infections – which is obviously very important!

Hope: On your LinkedIn page, you mention that you participate in triathlon racing. How did you get involved in this, and what makes it so enjoyable to you?

Ingrid: Cool that you looked! This summer, I did an olympic distance triathlon race at Lake George. I started triathlons while I was in graduate school. I love all three sports – swimming, biking, and running. On weekends, I go out to Coney Island to do laps and to Piermont for cycling trips. The cycling is by far the most fun of the three – if you like exploring and feeling wind in your face!

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

Ingrid: There are so many wristwatch tools for tracking health related things. I’d like to measure people’s gate (walking) by putting sensors in the soles of their shoes that could help improve both posture and running / walking techniques.

It would be cool to track insulin levels without actual blood samples. It will be great when the cost of sequencing is low enough that people can have in-home devices, and start measuring their gut microflora and skin microflora on a daily basis. If we also keep track of what we eat, this can probably lead to many discoveries in how foods affect our immune system and health.

Additionally, I’d like us to be able to track cortisol levels so we can see how stressed we are at any given point in time.

Hope: I bet lots of people would track that. Thanks, Ingrid!


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