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

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA - BMC Bioinformatics (2014)

Bottom Line: However, this does not scale well when the number of technologies or research groups is large.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.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.

View Article: PubMed Central - HTML - PubMed

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.

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Related in: MedlinePlus

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..
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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..

Mentions: Other frameworks exist to encourage interactions, such as the concept of a Summer of Code (as run, for example, by Google or the European Space Agency), combining remote collaborations with a summit at the end. Many if not most of the contributors to the events we have discussed here also mentor for the Google Summers of Code and find it complementary to the self-organised events - much like extra resources for the researchers' interest and, if attending the summit, an opportunity to look deeply beyond one's personal area of expertise [26]. The events described here focus on the science and easier access to technology in an intense way that is open to everyone (Figure 1). This underscores the Sprints' direct effect on the activity of the projects, both in terms of the number of patches submitted and, on the social side, the number of emails distributed on the mailing list (Figure 2).


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

Möller S, Afgan E, Banck M, Bonnal RJ, Booth T, Chilton J, Cock PJ, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA - BMC Bioinformatics (2014)

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..
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4255748&req=5

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..
Mentions: Other frameworks exist to encourage interactions, such as the concept of a Summer of Code (as run, for example, by Google or the European Space Agency), combining remote collaborations with a summit at the end. Many if not most of the contributors to the events we have discussed here also mentor for the Google Summers of Code and find it complementary to the self-organised events - much like extra resources for the researchers' interest and, if attending the summit, an opportunity to look deeply beyond one's personal area of expertise [26]. The events described here focus on the science and easier access to technology in an intense way that is open to everyone (Figure 1). This underscores the Sprints' direct effect on the activity of the projects, both in terms of the number of patches submitted and, on the social side, the number of emails distributed on the mailing list (Figure 2).

Bottom Line: However, this does not scale well when the number of technologies or research groups is large.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.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.

View Article: PubMed Central - HTML - PubMed

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.

Show MeSH
Related in: MedlinePlus