All posts by Madeleine Price Ball

About Madeleine Price Ball

Executive Director of Open Humans Foundation and Shuttleworth Foundation Fellow.

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!

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.

Five new data sources!

We’ve added five new data sources for Open Humans members. We know you have some great stuff to share with science. Get your data in so researchers know it’s there!

Easy links below: you can jump right into adding each source…

  • Connect Fitbit
    Health and fitness devices, including activity trackers that record steps, heartrate, and sleep, as well as a scale.
  • Add Illumina Understand Your Genome
    Whole genome sequencing, generated as part of symposium teaching attendees about their genome data.
  • Connect Moves
    An always-on location logging app for iPhone or Android. It counts steps and classifies activities as walking, cycling, running, and transit.
  • Add uBiome
    Sampling kits for individuals to test gut, mouth, and other locations, performing microbiome sequencing & profiling.
  • Connect Withings
    Health & fitness devices, including a scale and a blood pressure monitor, as well as the Health Mate smartphone app.

These sources are all “in development”. We won’t be able to generate files right away, but we will soon! Add the source and we’ll build our data processing based on what we see.

Sharing is always optional. You choose when to share & who to share with. Data is private by default!


Other data sources…

In case you missed them, here’s all our other data sources (some studies, some commercial). Do any look familiar? Follow the link to add it to your account!

You can also add data files from anywhere using our Data Selfie feature!

GET Labs & GET Conference

As a reminder, Open Humans members are invited to GET Labs & GET Conference in Boston this April 25th and 26th! It’s a unique participatory science event that’s been running since 2010. Registration is still open – read more about it on our previous blog post.

GET Conference & GET Labs

We would like to invite Open Humans members to attend the 2016 GET Conference and GET Labs!

On April 25th and 26th, leading thinkers, scientists, and participatory researchers will gather in Boston at Harvard Medical School for two days of interactive science and amazing talks.

  • Tickets for GET Labs exclusively available to ALL Open Humans members (and ONLY Open Humans members) for a nominal fee of $16! Becoming a member just takes a minute.
  • Tickets for the GET Conference are typically $299, but attendance is FREE for qualifying Open Humans members!

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GET Labs on April 25th

This is an exclusive event for members of the Open Humans community!

What is “GET Labs”? This event is all about advancing science through direct participation. We bring together participants and researchers for a day of interactive labs. If you’ve never been, it’s a unique experience! Our community has helped advance all kinds of research, everything from viral profiling, perfect pitch, ancestry, fitness sensors, user interface design for genome reports, and – probably most popular last year – face mites! (Yep, turns out we all have Demodex mites.)

Fifteen research studies are already planning to attend, and the list is sure to grow. As in years past, the Harvard PGP, GoViral, and American Gut team will attend – and they’re planning to share free microbiome kits with qualifying members!

It’s also a chance to meet other Open Humans members! GET Labs invitations are open to ALL Open Humans members – and ONLY Open Humans members! – for a nominal fee of $16.

Click here to register for GET Labs!

The day will close with our first ever GETy Awards ceremony, honoring excellence in participant-centered research, followed by a reception.

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GET Conference on April 26th

We’ve got amazing talks & discussions lined-up this year! Come learn from leading experts about:

  • Integrated Omics Profiles
  • Microbiomes, Health, and Built Environment
  • AI & Medicine
  • Networked Biology

Part of what makes the GET Conference amazing is how the audience truly bridges researchers and participants. Each year, we reserve around half of the seats for participants from our community, as a thank you for engaging with us and collaborating in the creation of culture of participatory research. For qualified members, registration is free: all we ask is for a donation in the amount you can afford. For everyone else, tickets are $299.

To learn more, click the button below and look at the “special opportunity for Open Humans” on the registration page for how to qualify for your FREE Ticket.

Click here to register for the GET Conference!

As you can see, this year’s events are not to be missed. We hope you can make it! Full agenda here.

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Now Hiring: Back-end Web Developer

Help spread the word! We’re seeking a Senior Software Engineer at PersonalGenomes.org to work on the Open Humans Network, a project that aims to help people aggregate and share their health and trait data to advance scientific, educational and humanitarian causes.

Our model for this initiative is the work we’ve done on the Harvard Personal Genome Project (PGP), which has over 3,000 volunteers publicly sharing extensive biological and trait data, including hundreds of whole genomes, exomes, and genotyping data sets, over 1,000 health records, microbiome datasets from various bodily habitats, device data, brain imaging, etc. This combination of a highly informed and engaged community of volunteers and their contributions of extremely rich biological and health data, along with a network of collaboration-minded researchers, is an incredibly powerful scientific and educational resource that is unrivaled elsewhere. We will build on this momentum with this exciting new initiative that will transform participatory research and advance human health. Check out our recent blog post to see news coverage, videos, and learn more about Open Humans.

Our current hiring position is focusing on someone with back-end web development skills, as we have plans to work with a design firm for initial front-end work. Because we plan to develop open source software used by researchers, we believe Python (which many scientists use) is generally preferred.

We’re looking for someone who…

  • Is interested in building and managing a full-stack website. As the Senior Software Engineer, your expertise will be an important factor in decisions about what kind of technology is used and how it’s deployed.
  • Has used multiple programming languages to build production systems (e.g. Python, JavaScript, Ruby).
  • Is experienced with back-end web development (e.g. Rails or Django).
  • Is comfortable managing Unix servers, cloud-based services and has opinions about how to store and disseminate large datasets (currently around 50TB total, although we would start with managing <10GB).
  • Works well in a small team of developers and scientists.
  • Loves science, participatory research, and free/open source ideals.
  • Believes in our mission!

About PersonalGenomes.org
PersonalGenomes.org is a 501(c)(3) nonprofit organization working to generate, aggregate and interpret human biological and trait data on an unprecedented scale. PersonalGenomes.org’s mission is to make a wide spectrum of data about humans accessible to increase biological literacy and improve human health. Its efforts are informed by values encouraging greater transparency and collaboration between researchers and participants. The organization supports the Personal Genome Project (PGP) global network. The first PGP research study was founded at Harvard Medical School in 2005, and PGP sites now exist at leading institutions in four countries. We also produce the annual Genomes, Environments and Traits (GET) Conference.

About Open Humans
We have years of practical experience, thousands of participants, and diverse data sets accrued. What we need now is an experienced developer to help us build a site for participants and researchers to manage and publicly share this data. Think of this as a nonprofit startup project!

Location
We strongly prefer for the software engineer to be based in Boston, Massachusetts. We can be flexible on geography with the right person, and might also be interested in engineers based in New York City. We collaborate with people all over the globe.

Your experience
In addition to your resume or CV, please feel free to share any open source projects, side projects, and development experiences you are proud of.

Compensation
We offer a competitive salary, commensurate with experience.

Contact
Jason Bobe, jason@personalgenomes.org
Madeleine Price Ball, madeleine@personalgenomes.org

What is Open Humans?

What is Open Humans? Open Humans is about science, sharing, and community. To kick off our blog, we’d like to open with some links to various media about Open Humans from the past couple months.

Personal Genome Project Participants at GET Labs. Aurelien Dailly for PersonalGenomes.org, CC-BY.

New platforms aim to obliterate silos of participatory science

(Article) GET Labs and Open Humans are discussed in this article by Elie Dogen at Nature Medicine News, including some quotes from Jason and the context of GET Labs. Also some quotes from researchers we plan to work with at American Gut and Flu Near You (Daniel McDonald and Rumi Chunara).

By opensource.com, CC BY-SA license.

Some patients are eager to share their personal data

(Article) An interview of Madeleine by Shauna Gordon-McKeon, posted at opensource.com. Madeleine gives some background on motivation for the project, reflecting on lessons learned by the Personal Genome Project at Harvard.

2014bitsbiology_screenshotOpen Data, Open Humans

(Video, 9 min) Madeleine’s talk about Open Humans at the Bits ↔ Biology meeting at MIT. Human research generates identifiable data, creating a tension between privacy and data sharing. Participant-mediated data sharing has the potential to unlock that data and transform how we research ourselves.

From Volunteers, a DNA Database

(Article) In April, the New York Times Science Section featured GET Labs, the Personal Genome Project, and other Open Humans collaborators. Quotes from Jason, Open Humans adviser Abigail Wark, and participant Beau Gunderson.

screenshot_QSPHS-2014_Jason-talkParticipant Centered Research Design

(Video, 10 min) Jason discusses the concept of “participant-centeredness” at the Quantified Self Public Health Symposium at the Qualcomm Institute at UCSD.