Get your own Open Humans project up in 5-10 minutes

How can we make it easy to add data to Open Humans?

Open Humans lives through its community of members and the projects they design. That’s why there’s a large number of tools that make the creation of these projects possible: Projects can be run right on-site, use the Python command line interface library or use generic OAuth2-based API-methods to interact with Open Humans. But one simple need remained painful: simply enabling Open Humans members to upload file(s) into your own project.

Doing this needed some fiddling. Even if you code, setting up your own website can be time-consuming and often is something you don’t want to spend a lot of time on. Along with Mad – and the great help of some of our prospective Outreachy interns – I’ve been busy to reduce this pain…

Meet the oh_data_uploader template! All you need to allow Open Humansmembers to upload data into your project, with a one-click deployment to Heroku, for free! All of the project configuration can be done right in your browser, no assembly or coding required.

Now the process boils down to a simple 5-step guide and instead of taking some hours to set up your own data source it should now take between 5-10 minutes. Just use the administrative backend to fill out the configuration parameters, add the file meta data you expect and edit the copy-text of your project website using Markdown in the same way and you’re good to go. You can click here to see how it looks like out of the box (just ask if you want to have the demo password 😊).

I made already good use of this template myself, because it is what I used to quickly deploy the FamilyTreeDNA integration into Open Humans. What new data source will you add to Open Humans today?

2018 Board of Directors candidates

The self-nomination period for our Board of Directors is over and I am happy to announce that 10 eligible candidates are on the ballot!

At our annual meeting on March 26, two board-elected seats will be determined from these candidates. And following this, members of Open Humans will be invited to elect the third “community” seat! We invite you to learn more about the candidates by reading the introductions and further links below.

 

Benyam Alemu

About me

I am a national nonprofit leader, educator and researcher. I bring a
fascination for the applications of computation in biology –
through both bioinformatics and digital health to a an
entrepreneurial background.

My experiences range from leading companies, serving on institutional
steering committees, designing university coursework, creating
research experiences and influencing educational policy.

My vision for Open Humans is for it to also be used as a tool used by
other institutions to expose graduate students, underclassmen and
K-12 students alike to participatory methods of initiating and
conducting collaborative computational research.

Websites / Links

James M. Turner

About me

I have always had a passion for science, especially genetics. I ended up in software instead, but have continued to follow the field as an adult. I joined the Personal Genome Project in January 2011, and have been an activate participant ever since.

I organized and ran the PGP Participant’s Forum. I have also created several tools for the Open Humans API, including the HealthKit Uploader app.

I also have a second career as a freelance writer. I have written for publications such as the Christian Science Monitor, and have also written 3 books on software development. I also am the president and chairman of the board of a 501(c)3 public charity that has raised over $250,000 for cancer research, among other causes.

I think that I could leverage both my experience in journalism and in fundraising to assist the board in it’s duties. I would like to see OH work to expand the number of participants with active datasets so that the statistical power of the data would be increased.

Websites / Links

Dana Lewis

About me

I am passionate about open source and open science efforts. I’m one of the creators and the first users of an open source artificial pancreas (e.g. hybrid closed loop) system to make life with type 1 diabetes easier. My skillset ranges from non-traditional technical skills to communication and strategy. I’m dedicated to taking what we’ve learned in the diabetes community & sharing these lessons learned with all communities. To that end, I’m also a RWJF grant-funded principal investigator, studying the processes of patient-driven and patient-led innovation research, with goals around scaling effective processes and collaborations between traditional and ‘new’ stakeholders. I’ve used OpenHumans for ~2 years now, and believe it plays an integral role in enabling individuals to share data and facilitate new research efforts. My vision is to help support and scale the organization to continue to meet the needs of these new stakeholders and communities.

Websites / Links

Cameron Colby Thomson

About me

I am an entrepreneur, open source advocate, and PGP participant. My interest in open humans centers around the profound impact of genetics on our future as a species. As a board member of the Human Rights Foundation, and with organizations in life and health insurance, I am also deeply interested in the societal impact of sharing information which may allow third parties to predict our traits available in the public domain. I believe my primary contribution, aside from experience in board governance, would be to offer the board due diligence capacities in better understanding these risks and opportunities and communicating them to external stakeholders in stewardship of the foundation. More details and background are available on my website.

Websites / Links

Alexander (Sasha) Wait Zaranek

About me

I am head of quantified biology at Veritas Genetics, the first company to introduce whole genome sequencing and interpretation to consumers and their physicians for under $1,000. My current research is focused on the delivery of real-time, biomedical insights from massive data sets, spanning millions of individuals across collaborating organizations, eventually encompassing exabytes of data. I am also a co-founder of the Harvard Personal Genome Project.

My hope is that Open Humans becomes a central, global hub for participatory research and participant led data sharing much as Wikipedia has become a hub for sharing facts. Specifically, I will use my relationships with the Global Alliance for Genomics and Health (GA4GH), the NIH data commons pilot, the NIST “Genome In a Bottle” reference material consortium, and the global Personal Genome Project (PGP) organizations to further the integration of Open Humans with other local, national and international biomedical data sharing efforts.

Websites / Links

Embriette Hyde

About me

My passion for sharing science with the public started in graduate school, when I realized that scientists do a bad job of explaining their work to the broader community. This is critical — public perception of science has downstream effects on funding. A major roadblock is a misunderstanding of the scientific process and timeline. Citizen science projects help fill this knowledge gap by giving people the opportunity to contribute to science and experience it first hand. One of my most fulfilling experiences was managing the American Gut Project, which is part of Open Humans. Open Humans encourages people to support citizen science, and the dataset integration it promotes is critical for making precision medicine a reality in healthcare. My vision for Open Humans includes establishing educational efforts such as more regular and varied blog posts, short video blogs, and online courses — including a hands-on course on how to interpret scientific papers.

Websites / Links

Richard Sprague

About me

For decades, I’ve managed consumer-focused software products at places like Apple, Microsoft, and numerous startups because I believe technology is a great equalizer, transforming society by putting powerful computing tools within the reach of everyone. An early and active fan of OpenHumans, I think science too can be transformed if we make personal health and self-tracking data openly accessible to all curious people.

Like most OpenHumans users, my background is outside the world of professional science or academia.  As a former product developer, big company exec, and entrepreneur, I want OpenHumans to appeal to all ranges of expertise, in every part of the world, because the ability to do science shouldn’t depend on your background or your current skill level.  To do this, I’d like to help OpenHumans (1) improve its visibility through world-class marketing and promotion, (2) expand internationally and (3) remain the best place for sharing, exploring, and analyzing humans.

Websites / Links

Katarzyna Wac

About me

Katarzyna Wac is an Associate Professor of Computer Science at University of Copenhagen (DK) University of Geneva (CH), affiliated with Stanford University. Her research appears in more than 100 to date peer reviewed proceedings and journals in computer science, human-computer interaction and health informatics. She is a (co)-PI in several European, Swiss and Stanford Medicine projects. Dr. Wac leads Quality of Life Technologies lab researching how emerging sensor/actuator-based mobile and wearable technologies can be leveraged for a personalized assessment of the individual’s behavior and Quality of Life (QoL), as they unfold naturally over time and in context, and improvement of the latter. The vision for Open Humans is to enable individual’s short-term behavior and long-term QoL assessment and improvement based on the crowdsourced efforts of the donors, social and behavioral, as well as data scientists and practitioners leveraging the results for better QoL-enabling services.

Websites / Links

Chris Gorgolewski

About me

My life’s mission is to accelerate the progress of science by making as much data accessible to as many researchers as possible. Most of my work has focused on brain imaging data. I built a platform for sharing results of neuroimaging experiments (https://NeuroVault.org), as well as one for sharing raw neuroimaging data (https://OpenNeuro.org – formerly known as OpenfMRI). I have also been promoting ethical data sharing by providing ready to use text for participant content forms (http://open-brain-consent.readthedocs.io/en/latest/ultimate.html). I would work with the Open Humans Foundation to help integrate it with existing open neuroimaging databases and getting their participants involved in additional follow-up data collection via the Open Humans platform.

Websites / Links

Nomi L. Harris

About me

I have been involved in the world of bioinformatics for decades. I have a master’s degree in Medical AI. Most of my work experience has been in bioinformatics rather than medical informatics, but I would love to get involved with something more directly relevant to health.

I have chaired BOSC (the Bioinformatics Open Source Conference) for the last 8 years. Under my leadership, BOSC has flourished and become more diverse in both content and attendance. I am also a board member for the Open Bioinformatics Foundation.

In addition to helping OHF communicate using social media and other online mechanisms, I’d like to help organize events to bring OHF community members together to exchange ideas and meet face-to-face.

Websites / Links

OHF Board of Directors: Self-nominations invited

Dear Open Humans community,

Our nonprofit organization, Open Humans Foundation, will be having its annual election next month for its Board of Directors. Three of our nine seats will be up for election and, while current board members are invited to re-apply and continue their service, not all are planning to do so.

I’m also delighted to share that we have restructured our organization’s governance to create “community seats”. One of the three seats this round will be chosen by Open Humans members!

Anyone may apply to our board. The process involves a self-nomination, and nominees should be seconded by a current member of the Board of Directors.

Being a director of this organization is a position of trust. While I manage day-to-day operations, the board is our highest tier of governance – our ultimate decision-making authority. Many board members also contribute to the organization as officers, e.g. as secretary or treasurer. As Executive Director, I serve at the board’s behest.

You can learn more about our organization’s governance – including current board members, bylaws, and standing rules – by visiting the organization website here: http://openhumansfoundation.org/

Please self-nominate by completing our self-nomination form. Our deadline for self-nominations is March 12.

We expect our board-elected seats to be determined at our annual meeting on March 26, and we look forward to holding a community election following this. Please stay tuned!

Sincerely,

Mad Price Ball
Executive Director, Open Humans Foundation

Interviewing project grant awardee Kevin Arvai

Today we’re interviewing Kevin Arvai. Kevin is a bioinformatician with an interest in personal genetic data and he was awarded a project grant to implement a project that will bring genotype imputation to the Open Humans community.

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

I am a data scientist at a clinical genetics company in Maryland. My background and formal education is in biology, however I completed a master’s degree in computational biology and bioinformatics. Like many, I’m riding the wave of data that our generation has found itself immersed in by competing in data science competitions and contributing to “open-” (source, science, data) projects. I’m particularly interested in machine learning and human genetics but looking forward to learning new skills by building Imputer.

When and how did you come to Open Humans?

I came to Open Humans in February 2018 after working on a project with the Director of Research, Bastian, at a hackathon hosted by NCBI.

Have you been involved in any projects on Open Humans so far, either as a participant or even running your own

Not only is this my first project working with Open Humans, this is my first project as part of a open source community. Open Humans was a welcoming and collaborative group of people that encouraged my ideas, so it seemed like a perfect fit to start contributing.

Your project Imputer was awarded one of the Open Humans project grants. Can you explain us what the project is about?

The goal of Imputer is to provide users with a more comprehensive picture of their genome. Direct to consumer genetics companies, like 23andMe, only genotype a small fraction of the genome. Researchers are finding new genetic locations associated with traits and diseases at a rapid pace. Users might be interested in knowing their genotype status for these new associations, but the locations may be in regions that direct to consumer tests are not genotyping. Imputer leverages the vast amount of genotype data made available by 1000 genomes project and by the Haplotype Research Consortium to provide Open Humans users with genotype estimates at additional locations in their genome.

How did you come up with the idea behind Imputer?

The genesis of Imputer was spawned from long conversation over lunch with Bastian.

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

I’d like to encourage others who are “interested in, but anxious about” contributing to open source projects to take the leap! If you’ve found this post, Open Humans is a great place to start!

Kevin’s encouragement motivated you to take action? The Open Humans project grants are ongoing and you can apply for one too!

Open Humans, what’s next?

President Bartlet of The West Wing is calling his famous “What’s next” to his secretary after managing a task.

I just defended my PhD last week, and one question from virtually every person who attended and stayed for the after-party: What’s Next? Which initially felt a bit weird. After all, I already took my next step three months ago when I joined Open Humans as the Director of Research. But then I realized that this is a nice opportunity to reflect a bit on my first months and think about what my next goals for Open Humans are.

Where is Open Humans so far?

So far I spent good parts on learning the ropes. First of all, I had to find my way into the technical infrastructure of Open Humans. Learning the code base, the APIs, server setups and so on. And what better way to do this but starting my own projects? I thus integrated two new projects on Open Humans: First I connected my long-standing project openSNP with Open Humans – allowing users of both platforms to re-use their genetic data more easily. Then I started TwArχiv, which not only brings a new data source but also some data-visualization to Open Humans. This integration of Twitter data will hopefully also be a first step towards a more holistic view of personal data that includes non-medical data.

Hand in hand with the technical side of things I also found my way into the community around Open Humans. Learning which projects there are, how to best support them and also how to grow the Open Humans community even more. I not only got to know many of the brilliant individuals inside the Open Humans community, but I also helped them to achieve their goals – be it through bug fixes, relevant connections or finding out how to optimize our website to make it work for their needs. First steps towards a further community growth were also taken: We could announce the first three successful grant applications, all bringing new data sources to Open Humans. And a fourth grant announcement – enhancing existing data sets – will be out soon!

The Open Humans community grows nicely and is becoming more and more engaged. So things are on track. But where should we go from here? And what is the larger vision? Traditional academic research – as well as corporate data silos – put themselves into the center of all data collection. In contrast, Open Humans is very different to this. As Steph laid out in her blog post: Open Humans is a technological platform; a vibrant community; and a paradigm shift to how research is done at the same time. In addition to all these things there is one thing that I always mention when people ask me what Open Humans is: It is empowerment. Putting individuals in control of their own data and of research at large. And to me, this means more than ‘just’ giving people the choice of when and where to share their data.

What should Open Humans be?

Empowerment means giving people the opportunity and chance to explore and understand their own data. Be it on their own – or in collaboration as a community outside the traditional academic research setting. The growth of the independent Open Artificial Pancreas community – which aggregates their own data through Open Humans – is a stellar example for this empowerment. As stewards of the Open Humans ecosystem it is our responsibility to support people to run projects like these. It is up to us to make it easier to create and run projects on Open Humans – empowering more people including those who are not highly programming savvy. Open Humans offers the unique chance to democratize science, enabling people outside academia to do new research that has never existed before. To pull this off we have to become more inclusive in our approach. This means getting everybody on board who has great ideas for research.

First steps towards this direction have been made already: We now have a first data uploader template that allows everyone to create their own, data-collecting Open Humans project while requiring zero programming knowledge. Instead a web browser is enough to do the complete setup. A similar idea for the administration of projects should become a reality in the near future. Furthermore, we are on the way to create shareable analyses notebooks. These can be written and run by everyone – facilitating community-driven data analysis. By increasing our inclusivity more we will not only see more projects on Open Humans, we will also see a much wider diversity in how these projects will use data. I can’t wait to interact with all of them.

I see this diversity reflected in the kinds of data that will be on Open Humans and the kinds of research that will be done with it. Traditionally many of the projects on Open Humans have and had a focus on health. But I don’t see why this should be the sole kind of research that profits by being run with and by highly involved participants. After all, while much of the Quantified Self revolves around health, it is far from the only topic: People are interested in their personal finance data, phone usage, emails and more. And so are social scientists, economists and other academic disciplines. My goal is to get these people on board for Open Humans too, showing them the huge benefit that an engaged study population offers.

Let’s just think of a simple example: Everyone can pay Twitter to get access to their firehose of data or just scrape tweets for keywords from the web. But who but Open Humans can offer potential access to 200 or more full Twitter archives that are available right now? And more importantly, who offers the possibility to get in touch with these people and as such a way to get additional metadata and consent them? The same is true for virtually all kinds of social media data and many other data types. Humans are more than their bodies, and Open Humans should reflect this.

So this is what’s next for Open Humans: Creating an ecosystem that enables the largest possible number of people to do research; that collects and enables the re-use of the most diverse set of data; and that brings together participants and researchers from all disciplines and walks of life – informing each other and creating the most interesting research.

An interview with project grant awardee Anh Nguyet Vu

Today we’re interviewing Anh Nguyet Vu. She is the recipient of one of our Project Grants. With MyFitnessPal Miner she not only brings a new data source to Open Humans, she is also working on visualizing these data and connecting them to genetic data. 

Hey Anh Nguyet, please give our blog readers a quick introduction about who you are! How did you come up with the idea behind MyFitnessPal Miner?

Generally I wouldn’t want to introduce myself by talking about my problems, but in this case it does give you the story behind the project. So when I was a freshman in undergrad, I faced a problem that would eventually lead to the development of MyFitnessPal Miner. This problem, no doubt a familiar one for many others, was weight gain. Since I was (and am) the kind of person who believes that “what cannot be measured cannot be managed”, I started tracking dietary intake. Because I was already tracking what I was eating, I became interested in the quantified self movement, and it wasn’t long before I was convinced that collecting other types of data would be valuable. I experimented with many food logging tools, including MyFitnessPal (which was never my primary app, but it happens to be the most popular one today). I also tried a variety of activity and exercise trackers before Fitbit hit mainstream. Probably my most earnest project was tracking how much time was spent on different activities, down to a minute’s resolution, over a span of three months.

It was inevitable that I would want to incorporate genetic data. To gather all the other kinds of data without considering your personal genetics is to miss out on a crucial part — especially if you wanted to optimize health, as I was a little obsessive about. I had a self-defined area of concentration called “personalized medicine” (also known as “precision medicine”) for my undergraduate major at Stanford. I think more people understand personalized medicine as tailoring drug treatments for an individual’s genetic makeup, but if you believe in “food as medicine”, then it should encompass nutrition as well.

Your project MyFitnessPal Miner was awarded one of the Open Humans project grants. Can you explain us what the project is about?

MyFitnessPal Miner exists with three goals. The first is about making the data more accessible, allowing you to get your own data in a format useful for other projects, including ones on Open Humans. The app ports your data to standard .csv files and does some additional parsing to create potentially useful tags. For example, it tries to recognize instances of fast food by matching records containing restaurant chain names.

The second goal is integrating that data with current genetic resources. There are some really interesting studies on how your genetics influences and interacts with your diet, such as your preferences for salty/sweet/bitter foods, risk for specific food intolerances, and how you’d react to a low-carb versus a high-carb diet. When curating these kinds of studies, I think that many people must also be curious about how the findings apply to them. So if you have 23andMe data and MyFitnessPal data, the app gives you a kind of integrated dashboard of genetics and nutritional behavior. You might, for instance, be able to see that your fast food consumption is greater than average, and that this seems congruent with what a published study has found given your genetic variants. Or next to the summary of your actual sodium intake, you might notice the relevant finding that your genetics predict that your blood pressure is fairly sensitive to how much salt you’re eating. However, because MyFitnessPal doesn’t contain explicit data for vitamins and minerals, not every related published finding can be connected with your real-life dietary data, unless the app can be made to intelligently infer vitamin and mineral intake from the food records.

Beyond comparing existing information, through the app it should be possible to use your real-life dietary data along with your genetic data to suggest something new. This third goal is kind of a reach goal given the limited time frame I have, but it’s the essence of an Open Humans project. I’d still have to think about the questions that are feasible and the methodology for them. Hopefully it won’t be just me, and there will be people in the Open Humans community who’d want to build upon MyFitnessPal Miner.

I do also hope that there will be interest outside of Open Humans. You can recall that all of this started not with my interest in genetics, but with food tracking. Well, it’s the start of a new year, and there will be a lot of people doing that as they pursue a healthier lifestyle. Some will seek understanding of their calorie and macronutrient patterns and then be hungry for additional value from their collected data. Being shown where the genetics tie in to create that additional value can perhaps entice people to bring their genetic data to the project, and therefore to Open Humans.  

When and how did you come to Open Humans?

I consider myself a relatively new member of Open Humans, since I joined in the fall of 2017. Around that time I was doing research for a start-up, where a colleague mentioned Open Humans and said making his genetic data public was something he wouldn’t do. I, on the other hand, was someone who was already quite open, having been to quantified self meetings to hear others share their data and insights and to share mine.

Have you been involved in any projects on Open Humans so far, either as a participant or even running your own?

When I joined Open Humans, I made my data accessible to all studies. I would think more about running my own study after finishing the development of MyFitnessPal Miner.

Genevieve now analyzes private data!

Genevieve Genome Report is a tool that takes genome, exome, or 23andMe data and produces a report comparing your genome to the “ClinVar” database – a public compilation of publish reports and databases.

This might uncover reports about to rare variants with potentially dramatic effects: people typically carry several “recessive diseases”, and this report might uncover some of yours. But it might also uncover mistakes in the literature! Research is messy, and so is this. To help everyone sort through the evidence, Genevieve also invites users to edit collaborative notes regarding reported effects.

As such, the tool is not a clinical tool, no more than Wikipedia is! It’s open source, freely shared, and intended for collaborative learning. It’s my own personal project – and I’ve extended it to enable private data analysis, and empower more folks to explore their data.

Meet the TwArχiv

This is a cross-post from my personal blog, where I also introduced the new Open Humans project I created.

Would you like to analyze your Twitter history? Exactly 5 years ago Twitter started offering the option for users to download their full archive of personal tweets. The archive gives you a change to quickly browse through your personal history and find those funny cat pictures you once posted. But there is additional value in the archive, transcending the trips down to memory lane. For example, by looking into a full Twitter archive one can investigate longitudinal trends in interaction behaviour or geotag-based movement patterns. While Twitter archives come with their own user interface, they are not really designed for such deeper dives into the data. Which is why I have been working on a small tool called TwArχiv that tries to allow for such insights.

Screen Shot 2017-12-21 at 14.08.09

The plot above is a static example of what TwArχiv does. It gives you an idea of how my personal reply behaviour has changed over time. Using a gender-guessing Python library it classifies the users I replied to based on their first names. You can quickly see that I did have an extreme male-bias starting in early 2009 that becomes less pronounced in more recent years. What happened in 2009? I became an active member of the overwhelmingly male German Pirate Party. Go figure.

The plots that the TwArχiv generates include further interesting data. You can see a full, interactive demo done on my personal Twitter archive. The TwArχiv also looks into how your tweet behaviour changes with respect to whether you use Twitter for replying, retweeting or making original posts on your own; at which times of the day you tweet; and even how you move across the globe while tweeting. The gif below gives you a small glimpse into parts of my 2016 movements based on tweets.

If you want to analyse your own Twitter archive please give TwArχiv a try. As it uses Open Humans for the archive storage you can optionally also choose to make that data publicly available. If you have an unprotected Twitter account this data is already public but harder to systematically access (at least for anyone but Twitter itself). So why not help out social media researchers everywhere by giving your data?

If you have ideas for some data analyses that are missing so far: The code of TwArχiv is open source and I’d love to get your contributions and suggestions. And if you have a larger feature/analysis idea that’s not in TwArχiv yet, Open Humans is giving out grants of up to $5,000 for projects that help to grow their eco-system. Improving on TwArχiv is a perfect match for this.

An interview with project grant awardee Benjamin Carr


CarrHeadPier_300

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.

moon

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!