Community-driven development for computational biology at Sprints, Hackathons and Codefests

Abstract

Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together.

Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities.

Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.

Figure 1

Forms of academic exchange. The most common opportunities for scientists to meet separated by their drive for novelty and development (Y axis) and their duration (X axis), the former as a subjective consensus among the authors. Sprints, Codefests and Hackathons dominate for their focus on joint new developments, the transfer of expertise for new scientific questions, the distribution of infrastructure and a network of trust between the contributors. Longer programs like the Summer of Code combine many types of interactions over a long time, with the difference that those participating may be assigned different, specific roles - say as mentor and learner.

Figure 2

Number of uploads to Debian Med per individual. The figure from http://blends.debian.net/liststats/ indicates the activity of team members with upload privileges. One clearly sees the increased breadth since the first Sprint in early 2011..