Monthly Archives: October 2017

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”.