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.

Personal Data Notebooks: Explore and analyze your data right in your browser

With Open Humans we are not only working to empower you to decide with whom to share your personal data – but also to explore your own data. With our latest project addition – the Personal Data Notebooks – we are taking a further step in that direction. Based on the increasingly popular Jupyter Notebooks they bring together data analysis code, documentation and data visualization. With the added twist that the Personal Data Notebooks also easily provide simple and private access to your personal data that is stored in Open Humans. Which not only makes it easy to write and use a data analysis – it also makes it easy to share your results without having to share your personal data with someone else. That way you can not only learn about yourself and your data, but also about how data analyses are performed.

If you want to write your own data analysis for the notebooks from scratch you can get started in Python, R or Julia. Or if you want to tweak or run existing data analysis you can use and adapt existing notebooks. In the simplest case you don’t even have to write/edit any code, as the input data are standardized according to their Open Humans data source. So for example you can easily run a Fitbit analysis notebook written by someone else right away on your own Fitbit data. To get you started we have a step-by-step guide on how to use the Personal Data Notebooks, along with a set of ready-to-use data analysis notebooks for Fitbit, Apple Health, Moves, 23andMe and Twitter archive data.

But this is just the start. We can’t wait to see what kind of analysis notebooks the community will come up with. To kick off the development of additional notebooks we are running a small competition. Submit your own personal data notebooks until May 27th and our judges will select the most interesting submissions to add them to our example notebooks. For this competition Steven Jonas, Azure Dominique and Gary Wolf of QuantifiedSelf.com have agreed to be our judges! If you need an inspiration for your notebooks you can take a look at already proposed notebook ideas and discuss your ideas on Slack.

Announcing our new Directors for Open Humans Foundation!

With an enormous thank you to all our candidates – and the members that voted –  I’m thrilled to share our three new members of the Board of Directors for Open Humans Foundation!

Community Seat: Dana Lewis

As the first winner of the Community Seat election, we’re thrilled to have Dana representing the interests of the Open Humans community. Dana is a pioneer in open source and health, including her leadership of the inspiring OpenAPS community and work connecting this community to research. You can read more about this – and how Dana has used Open Humans – in her post on our blog: “Why Open Humans is an essential part of my work to change the future of healthcare research”

Full vote tallies of the community election were as follows: Dana M Lewis (92), Alexander (Sasha) Wait Zaranek (60), Embriette Hyde (53), James M Turner (33), Katarzyna Wac (28), Richard Sprague (23), Chris Gorgolewski (16)

We are also thrilled to introduce two new board-elected directors!

Board-elected Seat: James Turner

James is one of the earliest and most active members of the Open Humans community, and has been profiled on our blog as well! Having joined through participation in the Personal Genome Project, James went on to create some of the first projects in our site – including an Apple Health import app that has been used in downstream academic research. In addition to his long commitment to this community, James brings valuable practical experience in managing nonprofit organizations, having created and managed his own charitable 501(c)3 for several years.

Board-elected Seat: Chris Gorgolewski

Chris is an academic in the field of neuroscience, interested in expanding the use of Open Humans among traditional researchers. Chris has promoted neurological research data sharing through his work with Neurovault, OpenNeuro, and reusable data sharing language for consent forms. Chris brings to the board a new facet of research, and an interest in promoting the use of Open Humans in studies — including the return of valuable data to participants to enable both individual access as well as re-use in new research.

Finally, I want to thank the candidates who volunteered to become members of our board. Candidates took time to communicate with us and with the community, and we are honored by the visions you shared with us. There were more excellent candidates than we had seats to fill! But there will be seats again, and we hope you continue to be part of Open Humans as some of our most brilliant members, colleagues, and advocates.

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?

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

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!