Category Archives: Open Humans

Help us resurrect OpenPaths!

Four days ago Facebook announced it is killing Moves, a smartphone app that lets you collect your continuous GPS data. People could download their location data, donate it to research, and connect it to other apps.

Soon Moves will be dead – and there is no obvious replacement. But there could be.

OpenPaths is a similar tool, developed seven years ago by a team at the New York Times Research & Development Group. It had an ethos that matched our own – it empowered its users, gave them access to their data, and the ability to share with projects. The NYT team handed OpenPaths to an academic group at UCSD. And late last year, UCSD gave it to us.

OpenPaths was like Open Humans before we existed – and by some amazing act of fate, we have inherited it. It could be something better than Moves: a nonprofit, open source tool that strives to empower the community that maintains it.

But OpenPaths is broken, and we need help to fix it!

We need an iOS developer, and an Android developer. We’re also seeking a full time Django developer for our main site, who might also help build a new OpenPaths server.

Please help and spread word! Come chat with us in our community Slack, and share our jobs page to help us find developers that can help.

Outreachy: My journey so far

We are happy that Open Humans will have four Outreachy interns this summer. Our interns are working on their own Open Humans related projects and will regularly blog about their internship experience. Read Manaswini Das’s post about their way to Outreachy and their first two weeks as an Outreachy intern:

Open-source… I was a bit obnoxious about this term until a year ago, when I was not familiar with this new world of outstanding work done by millions across the globe. It’s been a year now and the journey has been more than rewarding.

My journey started with contributions to repositories as a part of Hacktoberfest 2017. I got a limited edition Hacktoberfest T-shirt too, as promised. The thought of contributing to something that will be utilized by the world intoxicated me and inspired me to dive deep into this. I started looking for other ways to find repositories that kindled my interest.

Going through several blog posts over the internet, I came across Outreachy, an open source internship program for people from marginalized groups. I had applied for Winter term 2017 (Round 15). But then, it was already nearing the deadline when I started contributing. So, I knew I stood a slim chance of getting accepted.

This time, I didn’t commit the same mistake. Once Round 16 was announced, I started exploring organizations and projects. I concentrated on ‘Adding data sources to Open Humans’ project under Open Humans Foundation and began my contributions right away! Two months hence, I found my name among the accepted interns. I am overwhelmed and looking forward to making the most of this internship period.

For those who haven’t come across this open source internship program, let me enlighten you.

What is Outreachy all about?

Well, Outreachy is an open source internship program for individuals belonging to groups traditionally underrepresented in technology. This program is similar to Google Summer of Code, except for the fact that it is not limited to students and it happens twice a year, May through August and December through March cohorts.

For those who want to probe deeper into this, find the details here.

Now, some tips for the ones preparing for the upcoming rounds:

Start early

To make it into the internship program, you should begin as soon as possible. It takes time to comprehend the code base. It may seem intimidating at first but select your projects wisely.

In case you are not comfortable with a project even after contributing, you still have time and liberty to switch to projects matching your interest. Keep in mind that you can apply to a maximum of two projects.

Subscribe to the announcement mailing list here.

Ask questions

In case you have questions, don’t hesitate to ask questions to your mentors. Don’t be afraid of being judged.

Asking questions doesn’t reveal your ignorance. It is a sign that you are learning.

Don’t be shy. Shed your cocoon and feel free to ask even the silliest of questions. But remember, do your research too. Try to work out the problem on your own first. If you are still stuck, then reach out to the community. You never know, it might be a bug!

Don’t doubt your abilities

If you think you don’t fit in, then, trust me you are the right person to apply for this internship program. You won’t be able to explore this new you unless you do it.

Be consistent

Don’t aim at a huge last-minute contribution. Make small but consistent contributions till the end of the application period. This creates a good impression.

Another golden tip: In case you are not into contributions for some time, be in touch with your mentors. Discuss your ideas about the project and know more about the organization.

Imposter Syndrome

At times, you may feel that you could achieve everything only due to luck and that you lack potential.

You may also feel that you won’t be able to make it even after you get accepted. Well, my friend, you are suffering from the imposter syndrome. This happens when you focus on the big picture of what you are trying to do in a project. To overcome this, follow the divide and conquer rule.

Have faith in yourself. Don’t let the imposter syndrome grip you.

Proposal time

This is the final dash to the race. Discuss your ideas with your mentors and come up with a suitable timeline. Work out your schedule and make sure your proposal is precise. Submit your proposal for review to your mentors. Trust me, your proposal will get better with each review. And yes, don’t wait till the last minute for this.

Updates

It’s been more than two weeks into this internship period now. I am working on adding Github and Twitter API integrations under the mentor-ship of  Mike Escalante. First three weeks, I have been getting familiar with the codebase and the workflow that is to be followed for the integrations, taking some help from the existing integrations. Apart from that, I have been exploring the Github API and setting up the app on Heroku.

My mentor, Mike has been very supportive and encouraging throughout, checking-in almost everyday and clearing all my doubts in a jiffy.

What’s next?

I’m planning to get the Github integration up and running by this week and then, I will be working on creating data explorations of this integration for the next two weeks.

I’ll be coming up with the technical details of this Github integration in the upcoming posts.

Cheers!

 

 

Open Humans + Outreachy : Weeks 1-2

We are happy that Open Humans will have four Outreachy interns this summer. Our interns are working on their own Open Humans related projects and will regularly blog about their internship experience. Read Rosy Gupta’s post about their first two weeks as an Outreachy intern:

What is Outreachy? What are the do’s and don’ts for your application if you are interested?  How did I find such an apt gig? What have I been and will be doing this non-vacation summer? Read on to find it out.

Outreachy is an amazing opportunity for underrepresented folks in Open Source Software Development. It allows you to work with tech organizations through a remote internship. It is somewhat similar to (the more heard of companion) Google Summer of Code (GSOC) but Outreachy happens twice a year and you don’t have to be a student to be eligible for it. Like most people, I didn’t know about Outreachy until I heard about it from former interns at an open source meetup. I was delighted to know that a remote and paid internship existed for non-students – seemed like an interesting way out to spend summers at home before starting my Masters in the fall.

So how do you get in?

Decide that you really really want to go for it

Getting onboard with Outreachy isn’t an overnight thing. You need to be involved with the organization that you intend to work with for a couple of months (hard truth). I started making contributions for Open Humans in February itself. Read up about the organization and the project nicely and THINK if you’d actually be able to spend your summer doing that. My fellow intern, Tarannum has some really good points on the organization and project selection in her blog post. Check it out here.

Code Communicate Sleep Repeat

Start with small contributions, even trivial bugs maybe and you’ll be able to make a major impactful one gradually as you get the hang of the code and the language. It’s good to raise your doubts in the common group (there’s no such thing as a stupid question). Having said that, it’s equally important to make a sincere effort before poking mentors and community with low-hanging fruit kind-of questions. The mentors in my case were damn helpful and pretty quick in solving our doubts, reviewing the code and merging the pull requests. Thanks for all the sweet help – Bastian Greshake Tzovaras (my mentor), Mad Price Ball and Mike Esclante.

Show Time – The Proposal

Unless you know about the project well, it will be difficult to come up with improvement suggestions for the project. Last minute stint usually doesn’t work – so it’s good to start with your proposal application ahead of the deadline. Keep it succinct.

 

After being chosen from a competitive pool of applicants, now, I am working with Bastian Greshake Tzovaras on Creating a stand-alone web application to manage and administer projects on Open Humans using Django. For the next three months, I will be adding some new features and enhancing the user experience for this project management application.

The first two weeks of my internship have flown by. I spent them going through unread pieces of code in the repo. Here, I learned that I need to comment the code a lot and since the project is in its infant stage, this quote would be a handy reminder 😀

“Always code as if the guy  who ends up maintaining your code will be a violent psychopath and knows where you live”

The application uses Django framework, so I’ve been trying to get my head around Python lately. One of the initial weird things was HTML with a bunch of curly brackets containing Python code. This turned out to be the templating engine, Jinja. I have also been learning more about designing the dashboards to deliver a good user experience. The work is giving me the opportunity to sharpen my Git skills too and I’m learning to make NEAT git pulls now.

The first few weeks have mostly been trying to fit in the remote work setting and understanding the timeline of the project. Luckily, my wonderful mentor, Bastian has been great putting my nerves at ease. He’s always encouraging me to communicate often (the key to remote work) and is quick with the doubt-solving sessions. Despite our contrasting time zones, it has been a smooth sail so far and his guidance has been really valuable.

My upcoming task is to work on building annotations for the dashboard. This would make the user experience more interactive. I’d also be working on adding a feature to download files in customizable ways.

I’d include more about my first two weeks’ work in the next blog post. Well yes, we need to blog every two weeks as a part of the internship. The good part is I’m writing my first blog post ever! Need more motivation?  Hit me up 😀

Good luck!

The road to Outreachy

We are happy that Open Humans will have four Outreachy interns this summer. Our interns are working on their own Open Humans related projects and will regularly blog about their internship experience. Read Tarannum Khan’s first post about how they came to join Open Humans as an Outreachy intern:

Four months ago, my amazing journey with Outreachy started. Ever since I see a tremendous growth in me regarding not only the open source development field but also a great boost in my will to continue and succeed, interact with a new bunch of people easily and learn from them.

Just clearing the fog, Outreachy is a great program for the people out there traditionally underrepresented in tech who are interested in open source development and don’t know where to start or try hands in this area. This is the right place to get started. Outreachy community provide an immense support for beginner like you and me and nurture our development skills by providing a superb platform to work in a collaborative environment with the mentors and other Outreachy participants.

I am working with the Open Humans organization and my project is on “Writing an Python module for the Open Humans API & a self-contained, modular Django app”. Open Humans community have been very supportive throughout. I would like to thank Mad Price Ball(mentor), Bastian Greshake Tzovaras and Mike Esclante for being always there to clear my doubts. And the best thing about them is that they has been a major support in this process of learning by sharing their development knowledge which is pretty cool.

I got to know about Outreachy through my friends of my institute and took my first big step in this area.

START(very important)

Organisation and project selection

Select the perfect organisation with the perfect project and the perfect language to work on(But life is not so perfect). So let’s go practical. On the outreachy website, once the projects get floated, look for each and every project of every organisation. Take a look at the repository provided by them. For the beginners, do check on the issue tagged with beginners or good first issue. If it looks understandable after having a look at the repository, you are good to go and start contributing to it.

Initially you can contribute to two or three repositories but with time you would know which one to really pick and focus on. Every mentor has a different interaction style which is mentioned in the outreachy website from which you will get an idea, how to reach the mentors. I suggest that your decision to choose a project should majorly depend on the project repository, it’s issue and then on the language. Don’t hesitate to pick a language in which you are not much comfortable but you should know the basics at the least, rest assured learning with this amazing community.

Bug fixing

Once the project is selected, take an issue, if you think you can do it, get it assigned and start working. If you are having any trouble feel free to either raise your doubts in the organisation forum or you can contact mentors. Someone will be always there to git pull you ahead from where you were stuck. You would love the feeling when your first pull request will be merged. 🙂

Patience is the key

Sometimes things might get a little tough as you are a new player in this field. Just keep up with patience, keep reading documentations, keep discussing with your mentors, keep coding and you will solve the issue(BA-AM). After solving each issue from beginner friendly to moderate to hard level, your self-confidence will be boosted immensely. In this great learning curve, you will learn a lot of new and interesting development stuff and your stamina to read documentations will increase drastically. (Life of a developer: Birth, find bug, read documentation, code, death)

Outreachy proposal

Now it’s time for the big show: PROPOSAL. Think clearly and meticulously about the project, the problem it’s trying to solve and make a clear plan of how you will solve the problem with the proper timeline and technical details. You can see a link to my proposal here. Start at least two weeks before the deadline to write the proposal.

Done and dusted. After the outreachy application period, keep on contributing. Whether you get selected or not, but the road to Outreachy is totally amazing. Your knowledge and confidence will boost immensely. And maybe not immediately but definitely, you will get a project to work with the Outreachy community as Outreachy programme is held in winters as well as in summers, so just keep on coding. I was lucky enough to get selected in my first attempt and work with Open Humans. Just be ready to give your time and energy to Outreachy and keep on working. 😀

Some pre-internship suggestions will be to learn git. It really helps and will save a lot of your time. The earlier you start contributing, the better your chances will be to spend your summer or winter non-vacation.

Feel free to contact me at tkhaniitr@gmail.com. I will be there to clear the doubts and even interact with you, given that I am not that boring 😀.

Keep your enthusiasm up and keep coding.

Meet Andrew Riha, our next project grant awardee

Today we’re introducing Andrew Riha who recently was awarded one of our project grants for his tool lineage. With lineage Andrew will make the genetic data you store on Open Humans even more useful, by enabling Ancestry analyses!

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

IMG_6353

I’m a systems engineer at an aerospace company in Southern California. I studied at Iowa State University, the University of Newcastle, and Delft University of Technology, and I have a B.S. and M.S. in computer engineering. A few years ago, I became interested in direct-to-consumer DNA testing after a friend told me about his experience with 23andMe. This interest developed into a passion, and I’m currently pursuing a graduate certificate in bioinformatics. My hobbies include running, traveling, and backpacking.

When and how did you come to Open Humans?

Director of Research, Bastian, introduced me to the Open Humans platform in early 2018. I had mentioned to Bastian that I wanted to turn my hobby open source Python project lineage into a web app, so he suggested I consider applying for a project grant.

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

This is my first project with Open Humans. I’m looking forward to learning from others and further developing and integrating lineage into the Open Humans ecosystem as a great open source web app!

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

lineage is a framework for analyzing genotype files (e.g., raw data files from 23andMe, Ancestry, etc.), primarily for the purposes of genetic genealogy and ancestry analysis. It can identify DNA and genes shared between individuals, and it provides other useful capabilities such as merging raw data files from different testing companies, identifying discrepant and discordant SNPs, and remapping SNPs to different assemblies / builds.

How did you come up with the idea behind lineage?

After my friend told me about his experience with 23andMe, I started researching how to get tested and found the International Society of Genetic Genealogy’s wiki very helpful and informative. The wiki led me to an excellent paper by Whit Athey that discussed using genotype files to phase the chromosomes of a family group and “reverse engineer” the DNA of a missing parent in the process! So, for a CS50 final project, I challenged myself to implement Whit’s algorithm in Python, using scientific libraries and vectorized programming in order to efficiently handle and analyze the large datasets involved.

The initial algorithm implementation was successful, and lineage had begun. But, I soon realized the need for other capabilities, such as comparing / merging files from different testing companies and determining what DNA is shared between individuals so that it could be used to guide the phasing algorithm. So, lineage grew into the framework that exists today, and I eventually want to return to implementing Whit’s algorithm, applying the bioinformatics and visualization concepts that I’ve learned along the way.

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

lineage wouldn’t have been possible without the knowledge and help graciously provided by so many people. It is in that spirit that I’d like to encourage others to create and contribute to open source projects – sharing your ideas and passions with the world can be a very rewarding endeavor!

Oh, and thanks Mom, Dad, grandmas, and grandpas for the genes. 🙂

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?

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.