BOSC 2008

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The Bosc Pear

The 9th annual Bioinformatics Open Source Conference (BOSC 2008) will take place in Toronto, Ontario, Canada, as one of several Special Interest Group (SIG) meetings occurring in conjunction with the 16th annual Intelligent Systems for Molecular Biology Conference (ISMB 2008).

Keynote Speaker

This year our Keynote speaker will be Julian Lombardi, Senior Research Scholar with Duke University. The title of his presentation will be:

Croquet: An Open Collaboration Architecture for Scientific Visualization and Simulation


The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation (OBF), 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 and dissemination of new computational methods as well as informatics infrastructure. Since the work of the Open Source Bioinformatics Community represents some of the most cutting edge of Bioinformatics in general, the overall theme for the conference this year is "Tackling Hard Problems with Emerging Technologies". Topics under this umbrella include cyberinfrastructure, grid computing and workflow management and discovery, and visualization. We will also have a series of update talks about the main Open Source Bioinformatics Software suites.

One of the hallmarks of BOSC is the coming together of the open source developer community in one location. A face-to-face meeting of this community 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.

Important Dates

March 10: Call for speakers and abstracts is open.

May 11: Abstract submission deadline. All abstracts must be submitted through our Open Conference Systems site.

June 2: Notification of accepted talks.

June 4: Early registration discount cut-off.

June 6: Authors of accepted talks must notify the Program Committee of their acceptance by e-mailing bosc@open-bio.org (revised abstracts must be posted to the Open Conference Systems site.

June 9: Schedule for BOSC 2008 posted. Call for lightning talks and Birds of a Feather sessions opens.

July 18-19: BOSC 2008!


Abstract submissions for full presentations were closed as of May 11, 2008, and the current schedule has been posted.

You may also download the entire BOSC program with the schedule and all abstracts as a PDF file (1971KB).

Important Information for Presenters

Audio/Visual Resources

  • Presenters are encouraged to bring their own laptops for their presentations.
  • If a presentor does not bring a laptop, he/she will be able to borrow one from one of the organizers. In this case, please contact the organizing committee at bosc@open-bio.org to confirm arrangements.
  • A high speed internet connection will be available.

Slide Availability

  • Slides from BOSC2008 have been posted on SlideShare. See links to slides from the schedule.
  • Presenters, if you have not already done so, please e-mail your slides to the organizers at bosc@open-bio.org.

Call for Lightning Talks/Demos/Birds of a Feather Sessions

Lightning Talks and Software Demonstrations

The program committee is currently seeking speakers for the lightning talks. Lightning talks are quick - only five minutes long - and a great opportunity for you to give people a quick summary of your open source project, code, idea, or vision of the future. Or, if you are involved in the development of novel Open Source Software, you could use the time to give a quick demonstration of your work.

If you are interested in giving a Lightning Talk or Software Demonstration at BOSC 2008, please e-mail us at bosc@open-bio.org:

  • a brief title and summary (one or two lines)
  • a URL for the project page, if applicable
  • the specific open source license used for your software or your release plans (NOTE: the Open Source License Requirement also applies to Lightning talks).

We will accept entries on-line until BOSC starts, but space for demos and lightning talks is limited.

Birds of a Feather Sessions

One of the more popular activities at BOSC are the Birds-of-a-Feather sub-meetings that people organize at the end of each days session. These are free-form meetings organized by the attendees themselves. Traditionally, some BOF's have been formed to allow developers and users of individual OBF to meet each other face-to-face to discuss the project, but other meetings have been formed to discuss completely new ideas. These meetings offer a unique opportunity for individuals to explore more about the activities of the various Open Source Projects, and, in some cases, even take an active role influencing the future of Open Source Software development. If you would like to create a BOF, just sign up for a wiki account, login, and edit the BOSC_2008/Birds-of-a-Feather page.

Main Session Topics

This year, BOSC is accepting abstract submissions on the conference theme "Tackling Hard Problems with Emerging Technologies". The conference theme reflects that there are new technologies emerging on both the scientific front (new sequencing technologies, etc.) and the IT front (workflows, mash-up, web 2.0, improvements in all of the major programming languages, etc.), which may allow the open source community to solve problems that were previously intractable. Abstracts may be submitted for the following topics.

1. Cyberinfrastructure - We are interested in presentations on topics dealing with the development of infrastructure on the web to facilitate software and data re-use (mashups, or traditional), interoperability and inter-process communication, system/service discovery, and data movement and modeling in distributed systems. This may include peer-to-peer systems of data transfer, Web Services, various flavors of data representation (SOAP, JSON, XML, others), and technologies commonly referred to under the Web 2.0 paradigm (e.g. folksonomies/tagging, user-based content generation, content feeds, and Social Networking).

2. Grid Computing and Workflow Management and Discovery - We particularly invite talks that report progress in making workflow systems easier to use and on how to do distributed-collaborative research , e.g. workflows that encompass the coordination of systems running in different parts of the world.

3. Visualization - Visualization is a maturing area of open source software development. We particularly invite talks that demonstrate innovative visualization systems, especially those which work in the context of workflows.

4. Open Source Software - Speakers are invited to present talks on the use, development, or philosophy of open source software in bioinformatics.

5. Bio* Open Source Project Updates - We invite abstracts from the representatives of the open source projects sponsored by or affiliated to the OBF (see Projects).

Notes on Submissions

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, in order to be considered for acceptance, any talk submitted to be presented at BOSC which concerns a specific software system to be used by the research community must be licensed with a recognized Open Source License, and be available for download by anyone using ftp, cvs/subversion, or as a tar/zip file from the Project Website.

See the following websites for further details:

How Do I Submit?

The deadline for abstract submissions for full presentations was May 11, 2008. Abstract submissions were not accepted via e-mail this year. All abstracts were submitted through our Open Conference Systems site. Note: the BOSC 2008 OCS site has been taken down. If you need to access this site, you should contact the current BOSC organizers at bosc@open-bio.org. — Kdahlquist; 00:42, 4 December 2009 (UTC)

You will need to prepare a short, 50-word abstract, and a full abstract to upload as a PDF file or plain text file. Full abstracts must be one page in length. Place the title and authors of the abstract at the top of the page and use 1 inch (2.5 cm) margins on the top, sides, and bottom of the page.

NOTE: The Open Conference Systems abstract submission system will tell you to upload a "paper". This refers to your one-page full abstract. The one-page abstract will appear in the SIG booklet distributed by ISMB and no other papers will be published from this conference. There will not be a poster session at BOSC, only presentations.

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


Please see the ISMB registration site for details. Online registration opened March 6, 2008.

Feedback on BOSC 2008 and Planning for BOSC 2009

Give us your feedback on BOSC 2008 so we can plan for BOSC 2009, the 10th Annual BOSC! Sign up and login to the discussion page and give us your suggestions, and volunteer for BOSC 2009.


Chair of the conference and of the organizing committee is Kam Dahlquist. Aside from Dr. Dahlquist, the 2008 BOSC Organizing Committee consists of Chris Dagdigian, Hilmar Lapp, Darin London, and Jason Stajich. For more information about the conference or the call for abstracts, please contact the organizers at bosc@open-bio.org.

NOTE: Abstract submissions will not be accepted via e-mail this year. All abstracts must be submitted through our Open Conference Systems site which will open Monday, March 10, 2008.


The keynote speaker and student travel fellowships to BOSC 2008 were made possible by Helicos Biosciences Corporation and an anonymous donor. Thank you. Helicos Logo