ANNOUNCING THE PGP HACKATHON 1.0
We’ll be holding our first PGP Hackathon in Boston, MA this summer on the weekend of July 21 & 22, 2018. We’ll also hold a reception with informal talks including ‘Introduction to human genetics’ and ‘Introduction to genome sequencing and data file types’ on the evening of Friday, July 20 (full schedule is below).
NOTE: SPACE IS LIMITED. THE APPLICATION DEADLINE WAS JULY 6, 2018; WAITLIST applications will be reviewed in the order received.
WHAT IS A HACKATHON?
Hackathons are events that bring people of diverse backgrounds together in teams to problem-solve and spur development of interesting computer programs, applications, or websites in a short period of time – usually over a single weekend (more info on Hackathons can be found here). A cursory online search will reveal hundreds of hackathons around the world with a variety of goals. The PGP Hackathon will focus on things you can do with personal genomes, especially when connected with other information about individuals such as their traits, health and environmental exposure data.
WHY IS THE PGP HAVING A HACKATHON?
One of the great strengths of the PGP is the uniquely open data provided by our participants in the project. Participants stay engaged, and not only want to learn about their own genomes and health, but wish to share their data freely for the benefit of society. This level of data sharing and participant involvement does not exist anywhere else in the global research community!
The data for the PGP is rich, but underutilized. Companies like 23andMe, and Illumina (via their Understand Your Genome program), provide a degree of interpretation of individual genomes. However, that analysis is usually private, and doesn’t provide an opportunity for others to test and verify new ways to analyze data. Approximately 500 participants in the PGP have now published their Whole Genome Data Sequences. Data at this resolution can be used to answer questions not possible with other types of less complete genomic data.
Basically, the PGP is the best genome sequencing sandbox in the world, and we want the PGP community and fans of the PGP to explore and help us discover what is possible! As a Hackathon attendee, you can bring your questions and ideas to the event, and pitch them to other attendees on Saturday morning. Attendees with similar interests will then form teams with diverse skills to find solutions together over the weekend.
Hackathon team participants will use public PGP genomes and associated data to demonstrate what can be learned from analysis of genome data, like: Can you take a genome sequence data file and find genes that determine blood type? Ancestry? Propensity for diseases? Rare ancestral variants? What about compatibility for organ transplant, known as the Human Leukocyte Antigen (HLA) type? NOTE: The PGP is NOT a clinical study but for research use only.
WHO CAN PARTICIPATE?
Everyone!!…but priority will be given to existing PGP participants. Because you will be on a team with other Hackathon attendees, in fairness to your teammates, we ask you to commit to spend all day, 9am-6pm on Saturday and Sunday with your team.
Concerned that you don’t know how to program or code? Don’t be. There will be fellow attendees who know how to. Concerned that you don’t know about genomics and genetics? There will be attendees who do. If you’ve had ideas about what can be done with genomic data, we want to hear them and help make you part of a team to implement them.
Bring your curiosity and your questions! You don’t need to be a computer programmer to participate, just have a willingness to learn and contribute your enthusiasm.
Teams will be provided with data sets from the PGP and computer resources if needed (though please bring a laptop if you have one). You can also bring your own data for analysis. This is a chance to meet and collaborate with other like-minded people who want to take on the challenge of bringing genomic data to life.
Some simple examples will be provided to get you started using individual genomes, pairs of genomes or beyond. At the end of the weekend, teams will demonstrate their progress, and there will be opportunities to post your code for use by others within and outside of the PGP community.
SCHEDULED MENTORS AND LEADERSHIP
Throughout the weekend, we will have several mentors circulating in the meeting space amongst teams to offer guidance by helping formulate questions, provide constructive feedback, and give advice. Here are some of the mentors who will have generously volunteered their time to help out:
Ahmet Raşit Öztürk
Sarah Wait Zaranek
Sasha Wait Zaranek
(If you are a professional who works in bioinformatics and genomics, you may want to sign up for a few hours as a Hackathon mentor, and help empower dozens of citizen scientists! Please email us at firstname.lastname@example.org and use the words Hackathon Mentor in the subject.)
To make the PGP Hackathon fun and productive, we will form teams with diverse and complementary expertise, skills, and interests. Space is limited. The application deadline was July 6, 2018. If you are still interested in participating, please complete the waitlist application – There are no wrong answers; we’ll use information in your applications to help balance skills of attendees.
Due to the limited space, application does not guarantee an invitation. Priority will be given to PGP participants. Accepted applications will result in an invitation to join on or before July 9, 2018, after which you will need to confirm your attendance using the link provided in the invitation, by July 12, 2018.
Harvard Medical School, Boston, MA
(Disabled accessible location to be announced)
Friday, July 20 (attendance optional)
6:30 pm – 9:30 pm Reception/Mixer plus short talks
7:00 pm Introduction to human genetics
8:00 pm Introduction to genome sequencing and data file types
Saturday, July 21
8:30 am Breakfast (provided)
9:00 am Welcome to the Hackathon, Keynote address
9:30 am Orientation demo and presentation: “Hello Genome!”
10:15 – 11:00 am 1-Minute pitches from the participants and Group Introductions
11:00 – Noon Brainstorming and idea development
Noon – 1:00 pm Lunch (provided)
1:00 – 6:00 pm Hacking in groups (mentor interactions)
6:00 pm Officially adjourn for the day
Sunday, July 22
8:30 am Breakfast (provided)
9:00 am – Noon Hacking in groups (mentor interactions)
Noon – 1:00 pm Lunch (provided)
1:00 – 5:00 pm Hacking
5:00 – 6:00 pm Final demos and wrap-up
WHAT WE’LL PROVIDE
- PGP genomes and ancillary data with which to build & test handy new tools (you can also bring your own vcf format/AncestryDNA/23andme data or we can help download it).
- Brain fuel (breakfast and lunch, healthful snacks, hot tea/coffee, and cold drinks)
- Computer accounts for writing code and running analysis
- Relevant data in accessible directories
- Simple example programs to get you started (for computer aficionados, think ‘Hello world!’ for genomes)
- Bioinformatics and graphics libraries for Python/R/other standard environments
- Working space with Wi-Fi (teams may also roam elsewhere on the campus)
- Expert mentors to provide guidance
WHAT YOU WILL NEED
- Enthusiasm, ideas, team spirit, and commitment to join a team for the entire weekend. This is a team-oriented event, and all members will be working together to reach their goals together!
- A laptop with a charger (tell us ahead of time if you lack one and we can try to accommodate you)
If you would like to volunteer for a few hours to help with the event, please email us at email@example.com and use the words Hackathon Volunteer in the subject.
The hackathon would not be possible without the generous support of our sponsors:
An Anonymous Donor
If you would like an opportunity to be a sponsor of this Hackathon or future PGP Hackathons, please send an email to firstname.lastname@example.org and use the words Hackathon Sponsorship in the subject.
CODE OF CONDUCT
The Harvard PGP is a welcoming endeavor. We honor diversity in age, gender, gender identity or expression, culture, ethnicity, language, national origin, political beliefs, profession, race, religion, sexual orientation, socioeconomic status, disability, or technical ability. We have a zero-tolerance policy for any type of harassment, emotional, physical, or otherwise. See full policy here.
QUESTIONS & MEDIA INQUIRIES
Please email email@example.com and use the word Hackathon in the subject.