Monthly Archives: March 2018

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!

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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?

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