Codefest Winter 2018

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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 at:

Harvard Medical School Countway Library 403 Computer Lab, 10 Shattuck St, Boston MA

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.

Some housing options:

We plan to have lunch and coffee available for everyone attending thanks to our wonderful sponsorts. The rough schedule for the two days is:

  • Thursday Jan 18th 9am: Meet, introductions, coffee
  • Thursday Jan 18th 10-1: Work in groups
  • Thursday Jan 18th 1pm: Provided Lunch
  • Thursday Jan 18th 2-6: Work in groups
  • Thursday Jan 18th 6pm: End of day presentations
  • Thursday Jan 18th 7pm: Pay your way group dinner
  • Friday Jan 19th 9am: Meet, provide status updates and organize, coffee
  • Friday Jan 19th 10-1: Work
  • Friday Jan 19th 1pm: Provided lunch
  • Friday Jan 19th 2-6: Work
  • Friday Jan 19th 6pm: Wrap up presentations
  • Friday Jan 19th 7pm: Pay your way group dinner

This is completely flexible based on progress and needs of attendees. Some resources while the hackathon is ongoing:

  • Feel free to ask in the Gitter Chat channel if you're wondering about the current status at any time.


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 the Genomics and Life Sciences Team at Google Cloud, and Veritas 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.