Chapman, Brad A.

Cock, Peter J. A.

Goecks, Jeremy

Harris, Nomi L.

Hotz, Hans-Rudolf

Lapp, Hilmar

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Vol. 31 no. 2 2015, pages 299–300BIOINFORMATICS MESSAGE FROM THE ISCB doi:10.1093/bioinformatics/btu413Advance Access publication July 14, 2014The Bioinformatics Open Source Conference (BOSC) 2013Nomi L. Harris1,*, Peter J. A. Cock2, Brad A. Chapman3, Jeremy Goecks4,Hans-Rudolf Hotz5 and Hilmar Lapp61Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS 972R525, Berkeley, CA 94720, USA,2Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK, 3Bioinformatics Core,Harvard School of Public Health, Boston, MA 02115, USA, 4The Computational Biology Institute, George WashingtonUniversity, Washington, DC 20052, USA, 5Bioinformatics Department, Friedrich Miescher Institute for BiomedicalResearch, Maulbeerstrasse 66, 4058 Basel, Switzerland and 6National Evolutionary Synthesis Center (NESCent),Durham, NC 27705, USAContact: nlharris@lbl.govIn July 2013, more than 100 bioinformatics researchers, devel-opers and users of Open Source Software gathered in Berlin,Germany, to attend the 14th Annual Bioinformatics OpenSource 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 forumfor communicating the results of their latest efforts to thewider research community, and a focused environment for de-velopers and users to interact and share ideas about standards,software development practices and practical techniques for sol-ving bioinformatics problems. BOSC includes a 2 day ‘CodeFest’preceding the formal conference, which provides a venue fordevelopers to meet in person to work on or plan joint projects(M €oller et al., 2013).The session topics at BOSC 2013 included Cloud and ParallelComputing, Visualization, Software Interoperability, Genome-scale Data Management, a session for updates on ongoingOpen Source projects and two new sessions: Open Science andReproducible Research and Translational Bioinformatics, recog-nizing the growing use of computational biology in medical ap-plications. Slides from all of the presentations are available onthe BOSC Web site, along with some of the posters and videorecordings for selected talks, including the keynotes and paneldiscussion.Open Science is a movement dedicated to making all aspects ofscientific knowledge production freely available for reuse andextension, including scientific data, methods and analyses. Inresponse to the increasing traction that this movement hasgained, BOSC 2013 featured a new session devoted explicitlyto Open Science. One of the objectives of Open Science is thewider issue of making published research reproducible. Asidefrom openness in software licensing, this also includes opennessof data and unhindered access to scientific papers themselves(Open Access). When researchers can freely access publicationsand the source code and data that support them, it becomespossible for them to recreate the steps that the authors wentthrough to reach their conclusions and to then go beyondthem. In this way, Open Science not only stands to provide thevalue of validating published results by recreating them but alsoto accelerate the pace of scientific discovery, by enabling re-searchers to more effectively build on the results of previouswork, rather than having to reinvent tools and reassembledatasets.Each day of BOSC traditionally starts off with a keynotetalk by a person of influence in Open Source bioinformatics.BOSC 2013’s first keynote speaker was Cameron Neylon,the Advocacy Director for the Public Library of Science, whois a prominent advocate for open science. Neylon discussed thecultural issues that are hindering open science, and spoke aboutthe potential of openness in scientific collaborations for generat-ing impact. Our second keynote speaker was Sean Eddy, a groupleader at the Howard Hughes Medical Institute’s Janelia Farm,who is perhaps best known as the author of the HMMER soft-ware suite (Eddy, 2011). He discussed how his own experienceand practices show that dedicating effort to thorough engin-eering in tool development—which is often shunned as uninter-esting and unpublishable—can be a key to creating a lastingimpact.To stimulate discussion on controversial ormultifaceted topics, BOSC includes a panel, in which panelistsrepresenting a range of viewpoints, answer questions from theaudience. This year’s panel was on Strategies for Funding andMaintaining Open Source Software. To secure continuedfunding for a software project, researchers must be able todemonstrate its impact. The panelists explored ways toquantify usage of one’s software as a measure of impact.They agreed that traditional publications, and tracking theircitations, still play an important role in publicizing and demon-strating the use of one’s software, but they are not the onlymetric.With the increasing reliance of more and more fields of biol-ogy on computational tools to manage and analyze their data,BOSC seems assured to stay relevant to life science, and thus tolife scientists.Additional InformationPlan to join us for BOSC: 15th Annual Bioinformatics OpenSource Conference in Boston, USA, July 11–12, 2014. For*To whom correspondence should be addressed.Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US. 299more information visit http://www.open-bio.org/wiki/BOSC_2014.ACKNOWLEDGEMENTSThe authors thank all the current and past members of the BOSCorganizing and abstract review committees, the Codefest organi-zers and hosts and their panelists, speakers and delegates formaking every BOSC a stimulating and informative meeting.They are grateful to Eagle Genomics for repeatedly sponsoringstudent travel awards and to ISCB and the ISMB meeting orga-nizers—especially Steven Leard—for their part in making BOSChappen.Funding: NLH was supported by the U.S. Department ofEnergy, Office of Biological and Environmental Researchunder Contract DE-AC02-06CH11357. PJC was supported bythe Scottish Government Rural and Environmental Researchand Analysis Directorate. BC has no external funding toreport. JG was supported in part by grant number HG005542from the National Human Genome Research Institute, NationalInstitutes of Health, as well as grants HG005133 and HG006620.HRH was supported by the Novartis Research Foundation HLwas supported by the National Evolutionary Synthesis Center(NESCent), NSF #EF-0905606.Conflicts of interest: none declared.REFERENCESEddy,S. (2011) Accelerated Profile HMM Searches. PLoS Comput. Biol., 7.e1002195. http://dx.doi.org/10.1371/journal.pcbi.1002195 (14 July 2014, datelast accessed).Harris,N. et al. (2013) The Bioinformatics Open Source Conference (BOSC) 2013.PeerJ PrePrints, 1, e83v1. http://dx.doi.org/10.7287/peerj.preprints.83v1 (14 July2014, date last accessed).M €oller,S. et al. (2013) Sprints, Hackathons and Codefests as community gluons incomputational biology. EMBnet.J., 19, 40–42. http://journal.embnet.org/index.php/embnetjournal/article/view/726/998 (14 July 2014, date last accessed).300N.L.Harris et al.

The Bioinformatics Open Source Conference (BOSC) 2013

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