Codefest Winter 2018

From Open Bioinformatics Foundation
Jump to: navigation, search

OpenBio Winter Codefest 2018 is Thursday Jan 18th and Friday Jan 19th in Boston, MA. This is a standalone event aimed at getting interested bioinformatics open source community members together before the GCC/BOSC bioinformatics community conference in Portland in June. It will be held at Harvard Medical School in the Longwood Medical area in Boston.

This is an opportunity for anyone interested in open science, biology and programming to meet, discuss and work collaboratively. Everyone is welcome to attend. We will have a mix of experienced developers, newcomers to bioinformatics and everything in between.

Register: add your name to the participants list.

If you're interested in learning more about Codefest, previous fun and successful events were Codefest 2010 in Boston, Codefest 2011 in Vienna, Codefest 2012 in Los Angeles, Codefest 2013 in Berlin, and Codefest 2014 in Boston, Codefest 2015 in Dublin, Codefest 2016 in Orlando and Codefest 2017 in Prague.


The goal of Codefest is to bring open source bioinformatics programmers together to have an enjoyable and productive two days. Practically this results in a number of useful outcomes:

  • Developing new communities working on shared problems. For example, the Common Workflow Language developed from discussions at Codefest 2014.
  • Establishing new friendships, helping to expand the open source bioinformatics community.


Codefest is kindly hosted in the Longwood Medical area of Boston. For both venues enter the Courtyard from Longwood Avenue at the Intersection of Avenue Louis Pasteur:

  • Thursday -- Jeffery Modell Immunology Center, Armenise Building, 100A Fred S. Rosen Lecture Hall 210 Longwood Avenue, Boston MA -- enter from the left side of the courtyard if walking from Longwood. The building says 210 Longwood Avenue, Armenise Building, Alpert Building, Courtyard Cafe outside the door. There is security immediately in front as you enter. They'll have a list of participants but tell them you're going to Codefest and go to the left. There is a lecture hall, atrium area and smaller classroom space. We'll be in the classroom space and atrium.
  • Friday -- Harvard Medical School Countway Library 403 Computer Lab, 10 Shattuck St, Boston MA -- enter through the far end of the quad. There will be security; tell them you're going to Codefest and they'll have a list of participants. Take the elevators on the left side up to the 4th floor.

For people coming from outside of Boston and orienting themselves, the venue is easily accessible via public transport (the T) on the E Green Line Subway (towards Heath Street/VA Medical center). Get off at the Longwood Medical Area stop. When taking the train from the city be sure to get on an E line as there are three other Green Line options (B, C, D) which go to different parts of the city.

Resources for remote (and local) attendees while the hackathon is ongoing:

We plan to have lunch and coffee available for everyone attending thanks to our wonderful sponsors. The rough schedule for the two days (all times EST) is:

  • Thursday Jan 18th 9am: Meet in Modell 100A, introductions, coffee (remote participants)
  • Thursday Jan 18th 10-12:30: Work in groups
  • Thursday Jan 18th 12:30-1: Pre-lunch reports and organization (remote participants)
  • Thursday Jan 18th 1pm: Provided Lunch from El Pelon (Mexican)
  • Thursday Jan 18th 2-5:30: Work in groups
  • Thursday Jan 18th 5:30pm: End of day presentations (remote participants)
  • Thursday Jan 18th 6:30pm: Pay your way group dinner -- Boston Beerworks 61 Brookline Ave, Boston, MA 02215
  • Friday Jan 19th 9am: Meet in Countway Library, provide status updates and organize, coffee (remote participants)
  • Friday Jan 19th 10-12:30: Work in groups
  • Friday Jan 19th 12:30-1: Pre-lunch reports and organization (remote participants)
  • Friday Jan 19th 1pm: Provided lunch from Penguin Pizza
  • Friday Jan 19th 2-5:30: Work
  • Friday Jan 19th 5:30pm: Wrap up presentations (remote participants)
  • Friday Jan 19th 6:30pm: Pay your way group dinner -- Boston Beerworks 61 Brookline Ave, Boston, MA 02215

This is completely flexible based on progress and needs of attendees.

Some housing options:


You are very welcome to attend. There is no cost, we only ask you to register to help organize numbers. Please add yourself if you are interested to this Google spreadsheet We'll coordinate through the Biohackathon mailing list, so please sign up to discuss and receive updates.

If you're not able to physically attend, we're still more than happy to have you participate in Codefest. Please sign up on the the Google spreadsheet and list yourself as remote only. We have a Gitter chat room we can use to coordinate and discuss in real time and will have an open Google Hangout to make it easier to be part of Codefest remotely.

Add your project ideas to the shared google document. The ideas include smaller focused projects and larger work. We want suggestions from everyone and will organize into groups around these during Codefest.

Why attend

  • For current community members: expand your network and strengthen existing relationships. Teach and learn from new community members. Focus on open source work without interruptions. Discuss questions and problems in real time.
  • For everyone: discuss and learn from the community. Teach others what you know. Build new friendships and collaborations.

If you have any questions or thoughts, please get in touch with Brad directly, in the Gitter chat room or on the Biohackathon mailing list.

What to expect

The OpenBio Codefest is a collaborative two day working session. The only requirement for attendance is that you have an interest in open source software and solving scientific problems. We will have contributors to open source bioinformatics tools present to collaboratively work with, and we welcome new attendees who want to learn and contribute to open source code or documentation.

The rough structure of the two days is:

  • Start with introductions from everyone attending about their goals and plans for the two days.
  • Assemble into working groups based on shared interests like programming languages, open source projects or biological questions. We use the collaboratively brainstormed Google document as the basis for setting up groups. Attendees determine the goals for the two days. If you have an idea for a project, please add it before the event. Any and all suggestions are welcome.
  • Work and discuss. Enjoy the productive time.
  • We'll have regular breaks where each group can deliver short reports on their progress.
  • We have informal lunches, dinners and drinks as a way for everyone to get to know each other better.

Please feel free to get in touch with any of the organizers with questions. You are very welcome at Codefest.


Google Cloud

We're grateful to Veritas and the Genomics and Life Sciences Team at Google Cloud for helping sponsor the winter Codefest.

Sponsorship money helps provide food and drink for the Codefest and Open Bioinformatics Foundation Travel Fellowships. If interested in becoming involved with the open source community, please get in touch with Brad Chapman.