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BOSC 2011

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The Bosc Pear

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) will be held immediately before the 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2011) at the Austria Center in Vienna, Austria. The dates of BOSC 2011 are July 15-16; the main ISMB Conference runs July 17-19, 2011. Participants are also invited to Codefest 2011, July 13-14.

The deadline for submitting abstracts is April 18, 2011.

Overview

The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (O|B|F), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development within the biological research community.

Many open source bioinformatics packages are widely used by the research community across many application areas and form a cornerstone in enabling research in the genomic and post-genomic era. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards. One of the hallmarks of BOSC is the coming together of the open source developer community in one location to meet face-to-face. This creates synergy where participants can work together to create use cases, prototype working code, or run bootcamps for developers from other projects as short, informal, and hands-on tutorials in new software packages and emerging technologies. In short, BOSC is not just a conference for presentations of completed work, but is a dynamic meeting where collaborative work gets done and attendees can learn about new or on-going developments that they can directly apply to their own work.

BOSC 2010 was held in Boston, MA, from July 9-10. Selected peer-reviewed papers from BOSC 2010 will be published in BMC Bioinformatics.

Keynote Speakers

Lawrence Hunter

Lawrence Hunter is Professor of Pharmacology and Computer Science at the University of Colorado and director of the Computational Bioscience Program at the School of Medicine. He is one of the founders of ISMB, a fellow of the ISCB, and well known for contributions in a broad range of problems in computational biology. Dr. Hunter will be giving a talk entitledThe role of openness in knowledge-based systems for biomedicine.

Knowledge-based approaches to the analysis to genome-scale data require the extraction, sharing and use of very large amounts of knowledge about biomedicine. Developments such as the open source software movement, the Open Biomedical Ontologies, Semantic Web standards such as OWL and SPARQL, and the spread of open access publishing are creating the potential for powerful knowledge-based computer systems that may play an important role in the future of biomedical research. Yet several critical challenges remain before this vision can be realized. Dr. Hunter will discuss some relevant recent resources developed in my lab, some of the socio-political barriers that remain, and what you can do to overcome them.

Second Keynote Speaker TBA

Important Dates

  • February 28, 2011: Call for abstracts opens
  • April 18, 2011: Deadline for submitting abstracts
  • May 9, 2011: Notifications for accepted abstracts e-mailed to corresponding authors
  • May 16, 2011: Deadline for presenters to confirm acceptance of invitation to speak and for authors offered conditional acceptance to come into compliance with requested changes.
  • July 13-14, 2011: Codefest 2011 programming session
  • July 15-16, 2011: BOSC 2011

Abstract Submission Information

The deadline for abstract submissions is Monday, April 18, 2011.

Abstracts must be one page in length and submitted as a PDF file only. Please observe the following formatting guidelines:

  • Use 1 inch (2.5 cm) margins on the top, sides, and bottom of the page.
  • List the following elements in order from the top of the page:
    • Title
    • Authors, with the presenting author's name underlined.
    • Author affiliations, including the e-mail address of the presenting author.
    • URL for the overall project web site
    • URL for accessing the code
    • The particular Open Source License being used
  • The abstracts will be presented "as is" in the program booklet; please help your all-volunteer Organizing Committee by following the formatting guidelines above.
  • NOTE: upload your one-page, PDF-formatted abstract to the Open Conference System site as the File. The text box for the Abstract is optional; the PDF file is what will be reviewed.

Accepted talks will be 10-20 minutes, depending on the session. You will be notified of the length of your talk upon abstract acceptance.

Submissions for Lightning Talks (5 minutes) will be accepted up until the first day of the conference, though submission to the program following the above guidelines is strongly encouraged to facilitate better planning. The open-source license requirement (see below) applies equally to lightning talks.

Open Source License Requirement

The Open Bioinformatics Foundation, which is the sole sponsor of BOSC, is dedicated to promoting the practice and philosophy of Open Source Software Development within the biological research community. For this reason, if a submitted talk proposal concerns a specific software system for use by the research community, then that software must be licensed with a recognized Open Source License, and be available for download, including source code, by a tar/zip file accessed through ftp/http or through a widely used version control system like cvs/subversion/git/bazaar/Mercurial.

See the following websites for further information:

Organizing Committee

Co-Chairs

  • Nomi L. Harris (Lawrence Berkeley National Laboratory)
  • Peter Rice (European Bioinformatics Institute)

Members

Ex Officio (Members of the O|B|F Board)

Previous BOSCs

The first BOSC was held in 2000. Please see past BOSC conferences for information about the first 11 conferences.

Contact Us

  • If you wish to be on the mailing list for BOSC-related announcements, including the call for abstracts and deadline reminders, please subscribe to the Bosc-announce list. This list has low traffic, and your address will be kept private.
  • If you have questions about the conference, please contact the organizers at bosc@open-bio.org.
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