BOSC 2009

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Revision as of 13:18, 29 May 2009 by Kdahlquist (talk) (Robert S. Hanmer: added talk title)
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The Bosc Pair

BOSC 2009 will be held for 2 days in conjunction with the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2009) in Stockholm, Sweden (which itself will be held jointly with the 7th European Conference on Computational Biology, ECCB 2009). The dates of BOSC 2009 are June 27 - 28; the main ISMB/ECCB Conference runs June 29 - July 2, 2009.

Please see past BOSC conferences for the previous 9 conferences.


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.

Important Dates

  • February 16, 2009: Registration for ISMB and BOSC Opens
  • Monday, April 13: Abstract deadline: Submissions are now closed.
  • May 13, 2009: Notification of accepted abstracts
  • May 15, 2009: Early Registration Discount Cut-off date
  • Saturday, June 27 and Sunday, June 28, 2009: BOSC 2009!

Keynote Speakers

The BOSC 2009 Organizing committee is pleased to announce our two Keynote Speakers:

Alan Ruttenberg

Alan Ruttenberg is a Principal Scientist at Science Commons. He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results. He is currently involved in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences. He is also an active participant in W3C Semantic Web activities. In 2006 and 2007 he was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. He is a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry. His graduate work was at the MIT Media Lab in the Music and Cognition Group, and he has an undergraduate degree in Physics and Mathematics from Brandeis University.

Robert S. Hanmer

Robert S. Hanmer is a Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area. He is based in Naperville, Illinois, USA. Current responsibilities include developing software-sourcing strategies for middleware and open source software. Previous positions within Lucent and Bell Laboratories have included development, architecture and evaluation of highly reliable systems focusing especially on the areas of reliability and performance. He is active in the software patterns community, including serving as program chair at several pattern conferences. He has authored or co-authored 14 journal articles, several book chapters and the book Patterns for Fault Tolerant Software. He is a member of the IEEE Computer Society, a Senior Member of the ACM and current President of The Hillside Group, the organization that sponsors the PLoP conference. He received his B.S. and M.S. degrees in Computer Science from Northwestern University in Evanston, Illinois.

His talk at BOSC will be entitled "Software Patterns for Reusable Design".


The list of confirmed speakers can be found by following the link. The final schedule of talks will be posted on June 1.


This year’s conference will mark the 10th anniversary of BOSC. To celebrate the special occasion, the theme of this year’s conference is “Looking Back and Looking Ahead: Open Source Solutions to Grand Challenges in Bioinformatics.” We are inviting abstracts for two different types of talks:

  • Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below
  • Reviews of open source software that compares and contrasts different solutions to the same bioinformatics problem.

In addition, we are asking all speakers to come prepared to lead an informal tutorial on their software during a Birds of a Feather/hackathon session. This year’s topics include:

  • Design Patterns in Bioinformatics (topic organizer: Lonnie Welch)
    • Various recurring patterns have emerged in the field of bioinformatics. The open source community has created many of these patterns, and this session will feature presentations that analyze and codify bioinformatics patterns. See for definitions and examples of patterns.
  • Regulatory Genomics (topic organizer: Lonnie Welch)
    • This session will focus on open source software that is designed for decoding the regulatory aspects, i.e., the control systems, of the genomes.
  • Multicore and GPGPU computing (topic organizer: Frank Drews)
  • Data & Analysis Management (topic organizer: Anton Nekrutenko)
    • Shared session with DAM SIG for introduction of cutting edge applications that mold data sources and analysis tools into a singular medium benefitting both extremes on the user spectrum: experimentalists and computational researchers
  • Computational Grids (topic organizers: Steffen Möller, Frank Drews)
    • Presentation of projects in computational biology that adapted grid technologies for their research or services. The speaker should explain how heterogeneous resources from multiple geographical locations were brought together to achieve what barely could have been achieved alone.
  • Visualization (topic organizers: Jim Procter)

There will also be updates from O|B|F-sponsored projects, and as always, abstracts may be submitted for open source software that does not fit neatly into the above categories. Lightning Talks will also highlight very recent developments.

Abstract Submission Information

The deadline for abstract submissions is Monday, April 13. Abstract submissions will not be accepted via e-mail this year. All abstracts are to be submitted through our EasyChair conference site.

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

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 (length ~5 minutes) will be accepted up until the 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:

Post-conference Slide Availability

  • In the spirit of openness, we would like to make the presentation slides publicly available after the conference.
  • The organizers will be requesting an electronic copy of the slides for posting.
  • For example, see slides from BOSC 2008 on SlideShare.

Publication of Post-conference Proceedings

The BOSC 2009 Organizing Committee is currently working out an agreement with an Open Access bioinformatics journal to publish a Post-conference Proceedings based on this year's presenations. Details will be available here on the BOSC web site as they become available.

Organizing Committee

The organizing committee can be contacted by email at




  • Hilmar Lapp (O|B|F, BioPerl, BioSQL, and NESCent)
  • Jens Lichtenberg (Ohio University)
    • Publications Chair (responsible for managing the EasyChair site, making the abstract program, organizing proceedings)
  • Frank Drews (Ohio University)
    • Multicore and gpgpu computing
  • Andrew Dalke (Dalke Scientific, Goteborg, Sweden)
  • Jim Procter (University of Dundee, Scotland)
    • Visualization
  • Anton Nekrutenko (Penn State University)
    • Overlap with Data Management & Analysis SIG
  • Steffen Möller (Institute for Neuro- und Bioinformatics, Lübeck, Germany)
    • Computational grids

How to participate & contact

  • If you wish to join the BOSC 2009 Organizing Committee, please send an e-mail to Conference planning is being discussed on the Discussion page, you are welcome to add your ideas.
  • 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.
  • For more information about the conference or the call for abstracts, please contact the organizers at