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

Steffen Möller*, Enis Afgan, Michael Banck, Raoul J.P. Bonnal, Timothy Booth, John Chilton, Peter J.A. Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján, Eri Kibukawa, David R. Powel, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Clare Sloggett & 8 others Stian Soiland-Reyes, William Spooner, Sascha Steinbiss, Andreas Tille, Anthony J. Travis, Roman Valls Guimera, Toshiaki Katayama, Brad A. Chapman

*Corresponding author for this work

Research output: Contribution to journalArticle

18 Citations (Scopus)
4 Downloads (Pure)

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.

Original languageEnglish
Article numberS7
JournalBMC Bioinformatics
Volume15
Issue numberSuppl. 14
DOIs
Publication statusPublished - 27 Nov 2014

Fingerprint

Social Planning
Computational Biology
Technology
Feathers
Birds
Coffee
Workflow
Strengthening
Atmosphere
Interaction
Work Flow
Join
Community
Consensus
Appointments and Schedules
Schedule
Coding
Joints
Research
Range of data

Keywords

  • open source
  • synthetic biology
  • open source tool
  • commercial service provider
  • open source software developer

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

Möller, S., Afgan, E., Banck, M., Bonnal, R. J. P., Booth, T., Chilton, J., ... Chapman, B. A. (2014). Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics, 15(Suppl. 14), [S7]. https://doi.org/10.1186/1471-2105-15-S14-S7

Community-driven development for computational biology at Sprints, Hackathons and Codefests. / Möller, Steffen; Afgan, Enis; Banck, Michael; Bonnal, Raoul J.P.; Booth, Timothy; Chilton, John; Cock, Peter J.A.; Gumbel, Markus; Harris, Nomi; Holland, Richard; Kalaš, Matúš; Kaján, László; Kibukawa, Eri; Powel, David R.; Prins, Pjotr; Quinn, Jacqueline; Sallou, Olivier; Strozzi, Francesco; Seemann, Torsten; Sloggett, Clare; Soiland-Reyes, Stian; Spooner, William; Steinbiss, Sascha; Tille, Andreas; Travis, Anthony J.; Guimera, Roman Valls; Katayama, Toshiaki; Chapman, Brad A.

In: BMC Bioinformatics, Vol. 15, No. Suppl. 14, S7, 27.11.2014.

Research output: Contribution to journalArticle

Möller, S, Afgan, E, Banck, M, Bonnal, RJP, Booth, T, Chilton, J, Cock, PJA, 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, RV, Katayama, T & Chapman, BA 2014, 'Community-driven development for computational biology at Sprints, Hackathons and Codefests', BMC Bioinformatics, vol. 15, no. Suppl. 14, S7. https://doi.org/10.1186/1471-2105-15-S14-S7
Möller S, Afgan E, Banck M, Bonnal RJP, Booth T, Chilton J et al. Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics. 2014 Nov 27;15(Suppl. 14). S7. https://doi.org/10.1186/1471-2105-15-S14-S7
Möller, Steffen ; Afgan, Enis ; Banck, Michael ; Bonnal, Raoul J.P. ; Booth, Timothy ; Chilton, John ; Cock, Peter J.A. ; Gumbel, Markus ; Harris, Nomi ; Holland, Richard ; Kalaš, Matúš ; Kaján, László ; Kibukawa, Eri ; Powel, David R. ; Prins, Pjotr ; Quinn, Jacqueline ; Sallou, Olivier ; Strozzi, Francesco ; Seemann, Torsten ; Sloggett, Clare ; Soiland-Reyes, Stian ; Spooner, William ; Steinbiss, Sascha ; Tille, Andreas ; Travis, Anthony J. ; Guimera, Roman Valls ; Katayama, Toshiaki ; Chapman, Brad A. / Community-driven development for computational biology at Sprints, Hackathons and Codefests. In: BMC Bioinformatics. 2014 ; Vol. 15, No. Suppl. 14.
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title = "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.",
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author = "Steffen M{\"o}ller and Enis Afgan and Michael Banck and Bonnal, {Raoul J.P.} and Timothy Booth and John Chilton and Cock, {Peter J.A.} and Markus Gumbel and Nomi Harris and Richard Holland and Mat{\'u}š Kalaš and L{\'a}szl{\'o} Kaj{\'a}n and Eri Kibukawa and Powel, {David R.} and Pjotr Prins and Jacqueline Quinn and Olivier Sallou and Francesco Strozzi and Torsten Seemann and Clare Sloggett and Stian Soiland-Reyes and William Spooner and Sascha Steinbiss and Andreas Tille and Travis, {Anthony J.} and Guimera, {Roman Valls} and Toshiaki Katayama and Chapman, {Brad A.}",
note = "All scientific groups that support contributions to Open Source software are thanked. The events' hosting institutions are thanked for providing facilities and support. O'Reilly, Electric Genetics, Apple Asia, the Debian project, UK Natural Environment Research Council, the participants' employing institutions and their funding agencies are thanked for contributing to the travel costs of the events. Participants contributing to this paper who were financed by grants received those from the DFG (EXC 306/2), the EU (COST {"}SeqAhead{"} BM 1006, STREP {"}Wf4Ever{"} FP7-ICT-2007-6 270192) and the Research Council of Norway ({"}ELIXIR.NO{"}, 208481). The anonymous reviewers are thanked for their constructive comments. The authors are listed alphabetically by surname, with the exception of the first and last authors who initiated the meetings.",
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AU - Afgan, Enis

AU - Banck, Michael

AU - Bonnal, Raoul J.P.

AU - Booth, Timothy

AU - Chilton, John

AU - Cock, Peter J.A.

AU - Gumbel, Markus

AU - Harris, Nomi

AU - Holland, Richard

AU - Kalaš, Matúš

AU - Kaján, László

AU - Kibukawa, Eri

AU - Powel, David R.

AU - Prins, Pjotr

AU - Quinn, Jacqueline

AU - Sallou, Olivier

AU - Strozzi, Francesco

AU - Seemann, Torsten

AU - Sloggett, Clare

AU - Soiland-Reyes, Stian

AU - Spooner, William

AU - Steinbiss, Sascha

AU - Tille, Andreas

AU - Travis, Anthony J.

AU - Guimera, Roman Valls

AU - Katayama, Toshiaki

AU - Chapman, Brad A.

N1 - All scientific groups that support contributions to Open Source software are thanked. The events' hosting institutions are thanked for providing facilities and support. O'Reilly, Electric Genetics, Apple Asia, the Debian project, UK Natural Environment Research Council, the participants' employing institutions and their funding agencies are thanked for contributing to the travel costs of the events. Participants contributing to this paper who were financed by grants received those from the DFG (EXC 306/2), the EU (COST "SeqAhead" BM 1006, STREP "Wf4Ever" FP7-ICT-2007-6 270192) and the Research Council of Norway ("ELIXIR.NO", 208481). The anonymous reviewers are thanked for their constructive comments. The authors are listed alphabetically by surname, with the exception of the first and last authors who initiated the meetings.

PY - 2014/11/27

Y1 - 2014/11/27

N2 - 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.

AB - 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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