The Bioinformatics Open Source Conference (BOSC) 2013

Abstract

The 14th annual Bioinformatics Open Source Conference (BOSC) was held in Berlin in July 2013, bringing together over 100 bioinformatics researchers, developers and users of open source software. Since its inception in 2000, BOSC has been organised as a Special Interest Group (SIG) satellite meeting preceding the large International Conference on Intelligent Systems for Molecular Biology (ISMB), which is the annual meeting of the International Society for Computational Biology (ISCB). BOSC provides bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community, and a focused environment for developers and users to interact and share ideas about standards, software development practices, and practical techniques for solving bioinformatics problems. As in previous years, BOSC 2013 was preceded by a Codefest, a two day hackathon that brings together bioinformatics open source project developers and members of the community and allows them to work collaboratively and achieve greater interoperability between tools developed by different groups. The session topics at BOSC 2013 included several that have been popular in previous years, including Cloud and Parallel Computing, Visualization, Software Interoperability, Genome-scale Data Management, and a session for updates on ongoing open source projects, as well as two new sessions: Translational Bioinformatics, recognizing the growing use of computational biology in medical applications, and Open Science and Reproducible Research. Open Science, a movement dedicated to making all aspects of scientific knowledge production freely available for reuse and extension, not only validates published results by allowing others to reproduce them, but also accelerates the pace of scientific discovery by enabling researchers to more efficiently build on previous work, rather than having to reinvent tools and reassemble data sets. BOSC typically features two keynote talks by researchers who are influential in some aspect of open source bioinformatics. Our first keynote talk this year was by Cameron Neylon, the Advocacy Director for the Public Library of Science (PLOS), who is a prominent advocate for open science. He discussed the cultural issues that are hindering open science, and how openness in scientific collaborations can generate impact. Our second keynote speaker, Sean Eddy, who is perhaps best known as the author of the HMMER software suite, began his keynote talk with an inspiring history of how he got involved in bioinformatics and proceeded to argue that dedicating effort to thorough engineering in tool development, which is often shunned as incremental, can become the key to creating a lasting impact. With the increasing reliance of more and more fields of biology on computational tools to manage and analyze their data, BOSC is well positioned to stay relevant to life science, and thus life scientists, for many years to come.

The Bioinformatics Open Source Conference (BOSC) 2013

“…In July 2013, more than 100 bioinformatics researchers, developers and users of Open Source Software gathered in Berlin, Germany, to attend the 14th Annual Bioinformatics Open Source Conference (BOSC, http://www.open-bio.org/wiki/ BOSC_2013, Harris et al, 2013). Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community, and a focused environment for developers and users to interact and share ideas about standards, software development practices and practical techniques for solving bioinformatics problems.…”