PGP HACKATHON 1.0 – Info for Participants Only
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: THIS DOCUMENT MAY BE UPDATED REGULARLY, SO PLEASE CHECK BACK OFTEN!
Please also refer to this folder containing important documents that will also probably change during the event: https://goo.gl/wD97Lq
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.
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. A huge thanks to all of them!
Here are some of the mentors who will have generously volunteered their time to help out:
- Brad Chapman
- Jie He
Ahmet Raşit Öztürk
- Keldin Sergheyev
Sarah Wait Zaranek
Sasha Wait Zaranek
AGENDA AND LOCATIONS
All events will take place at Harvard Medical School in the Longwood Medical Area of Boston, MA 02115. Every building is wheelchair accessible. Please note, that the Friday night reception and Saturday/Sunday are in different locations. You will find a map in the shared folder.
Friday, July 20 (attendance optional)
Location: Harvard New Research Building, Room NRB 350, 77 Avenue Louis Pasteur, Boston, MA 02115
Upon arrival at the entrance to 77 Avenue Louis Pasteur, you will be on level ‘G’. Please ascend the stairs or take the elevator 1 flight up to level ‘1’ and go forward to the security desk, and tell the guard that you are going to the PGP Hackathon event in NRB350. You will have to show ID.
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
Location: Harvard Tosteson Medical Education Center, 2nd floor Atrium and TMEC 227, 260 Longwood Avenue, Boston, MA 02115
Upon arrival at the entrance to at 260 Longwood Avenue. Tell the security guard that you are going to the PGP Hackathon event. You will have show ID. Ascend 2 flights of stairs or take the elevator up to flight ‘2’.
8:30 am Breakfast (provided)
9:00 am Welcome to the Hackathon, Keynote address by George Church
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
Location: Same as Saturday.
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 WILL 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.
Unfortunately, we cannot cover accommodations for our out of town guests. The closest hotels are:
- Inn at Longwood Medical, 342 Longwood Ave, Boston, MA (617) 731-4700
- Courtyard Marriott @ Coolidge Corner, 40 Webster St, Brookline, MA (866) 296-2296
- Holiday Inn Brookline, 1200 Beacon St., Brookline, MA (617) 277-1200
There is a longer list of hotels in a PDF in the shared folder. In addition, there are a few B&Bs in the area including:
Beech Tree Inn, Bertram Inn, Samuel Sewall Inn and Longwood Inn …and of course Airbnb and other similar options.
There are many local garages within blocks of either location including:
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.