All posts by Bastian

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!

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.

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”.