Community-driven development for computational biology at Sprints, Hackathons and Codefests
Community-driven development for computational biology at Sprints, Hackathons and Codefests
复制标题
Sprints、Hackathon 和 Codefest 上社区驱动的计算生物学开发
作者：
Steffen Möller;E. Afgan;M. Banck;R. Bonnal;Tim Booth;J. Chilton;P. Cock;M. Gumbel;N. Harris;Richard C. G. Holland;Matúš Kalaš;L. Kaján;Eri Kibukawa;David R. Powell;P. Prins;Jacqueline Quinn;Olivier Sallou;F. Strozzi;T. Seemann;Clare Sloggett;S. Soiland;W. Spooner;Sascha Steinbiss;A. Tille;A. Travis;R. Guimera;Toshiaki Katayama;Brad A. Chapman
计算生物学包含广泛的技术和方法。如果提供数据或提供数据解读工具的人员能够达成相互理解和共识，多种技术就可以结合起来创建更强大的工作流程。为了确定和实施最佳方法，需要大量的交流和共同研究。传统上，科学会议以展示新技术或见解的报告为特色，随后在茶歇期间进行非正式讨论。在多机构合作中，为了就实施细节达成一致，或者传递对一项技术更深入的见解和实用技能，一个小组的代表通常会访问另一个小组。然而，当技术或研究小组的数量很大时，这种方式的扩展性不佳。会议通过引入同好（BoF）会议环节来应对这一问题，同好会议为有共同兴趣的个人提供了加强互动的机会。然而，并行的同好会议常常使参与者难以参加多个同好会议并在不同技术之间找到共同点，而且同好会议通常时间太短，参与者没有时间一起编程。本报告总结了我们在计算生物学代码节、黑客马拉松和冲刺活动方面的经验，这些都是互动式开发者会议。它们通过加强同行之间的互动并让参与者确定日程和主题，来减少上述传统科学会议的局限性。这些会议通常作为安排宽松的“非传统会议”（参与者和会议主题的自组织确定）进行，至少持续两天，首先有开场介绍性报告来欢迎和组织参与者，随后是紧张的协作编程环节。我们总结了这些会议的一些显著成果，并描述了它们在组织方式、针对受众的方式以及对各自社区的推广方面的差异。黑客马拉松、代码节和冲刺活动都有一种激励氛围，鼓励参与者在自我驱动的积极环境中共同集思广益，解决共同感兴趣的问题，并为新参与者提供参与协作项目的机会。
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. 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. 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.
短期努力的巨大影响：开源科学软件中的指导和代码集成
影响因子：
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作者：
Trainer, Erik;Chaihirunkarn, C.;Herbsleb, J.
通讯作者：
Herbsleb, J.
影响因子：
7
作者：
Earl, Dent;Bradnam, Keith;Paten, Benedict
通讯作者：
Paten, Benedict
影响因子：
7
作者：
Stajich, JE;Block, D;Birney, E
通讯作者：
Birney, E