Abstract submissions for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010) are now open.

At-a-glance
BOSC is an ISMB 2010 Special Interest Group (SIG)
Date: July 9-10, 2010
Location: Boston, Massachusetts, USA
BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010
Abstract submission via Open Conference System site:  http://events.open-bio.org/BOSC2010/openconf.php
E-mail: bosc@open-bio.org
Bosc-announce list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates
April 15: Abstract deadline
May 5:  Notification of accepted abstracts
May 28: Early Registration Discount Cut-off date
July 8-9:  Codefest 2010
July 9-10: BOSC 2010
August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics

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. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

We have some exciting things planned this year, including:

• Codefest 2010 programming session for the two days preceeding BOSC:  See http://www.open-bio.org/wiki/Codefest_2010 for details.
• OpenBio Solution Challenge:  See session description below and http://www.open-bio.org/wiki/SolutionChallenge for details.
• Student Travel Fellowships:  Through generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2010. Each winner will be awarded $250 to defray the costs of travel to BOSC 2010.  See http://www.open-bio.org/wiki/BOSC_2010#Student_Travel_Awards for details.
• First-ever BOSC Proceedings will be published in the Open Access journal, BMC Bioinformatics.  Manuscripts will be due after BOSC on August 15.  See http://www.open-bio.org/wiki/BOSC_2010#First-ever_Published_BOSC_Proceedings for details.
• Sessions on approaches to analyzing high-throughput ‘omics data, cloud-based approaches to improving software and data accessibility, the semantic web in open source bioinformatics, see below:

We invite abstracts for talks at the following sessions:

OpenBio SolutionChallenge — Bioinformatics library providers: please join us in a friendly competition to solve a shared biological problem, demonstrating the utility of your toolkit alongside other developers. Instead of the traditional Bio* updates that we’ve had at previous conferences, this year, we’re planning to organize these talks around a central theme: the OpenBio Solution Challenge. We start with a biological question of general interest, and the project talks will focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). Specific challenges are being discussed on the SolutionChallenge page and through the various Bio* mailing lists. Alternately, each project could highlight a challenge that they particularly do well, focusing tutorial-style on how to solve a particular problem.

The BOSC 2010 organizing committee is hard at work getting prepared for this
July’s meeting in Boston:

http://www.open-bio.org/wiki/BOSC_2010

One of the items we’ve traditionally had at the conference is a project
update from each of the OpenBio affiliated groups. This year, we’re thinking
about organizing these talks around a central theme: the OpenBio solution
challenge. We start with a biological question of general interest, and each
of the project talks would focus around how you would solve that problem
using your toolkit and programming language.

This is meant to provide a challenge for OpenBio contributors, a nice tutorial
style overview of various projects and approaches for other programmers, and a
fun opportunity to compete and learn from other projects. Conference attendees
will vote on their favorite solution, with the winner receiving fame and
fortune (warning: fortune not guaranteed).

For this to be successful, it of course requires interest and enthusiasm from
y’all fine folks involved with the projects. Specifically:

• Is there interest from your group in participating in the challenge? You’ll
  want at least a few people interesting in working on it, and someone to give
  a presentation at BOSC.
• Do you have suggestions on a good theme or specific biological problem to
  tackle? We’ll hope to pick something in a sweet spot that is challenging
  enough to be of interest, yet reasonable for presentation and preparation.

Let’s discuss ideas and get this together. Since the schedule for BOSC is
developing rapidly, please give us an idea if you’re interested by
February 12th, and copy responses to the BOSC mailing list as a central
place for discussion.

bosc@open-bio.org

BOSC 2010 is currently in the planning stages. It will be held for 2 days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010.  The BOSC 2010 web site can be accessed here:  http://www.open-bio.org/wiki/BOSC_2010.

The BOSC organizing committee is soliciting input on the planning of BOSC 2010 so that we can make it a successful and productive conference for the O|B|F community.  You may send your suggestions to the bosc@open-bio.org e-mail address  or add suggestions to the BOSC 2010 talk/discussion wiki page at: http://www.open-bio.org/wiki/Talk:BOSC_2010. Please respond to any or all of the questions below:

1.  For the last several years BOSC has consisted mainly of one or two keynote presentations, other talks chosen from among the submitted abstracts organized into sessions by topic, updates from the Bio* projects, Lightning Talks, and informal Birds of a Feather sessions.  Would you rather see BOSC continue in this fashion, or would you support changing the format to one or all of the following:

• Tutorials where there were in depth demonstrations and code tutorials. This could be lead off by the OBF projects instead of the traditional update talks, but could feature any open source projects interested. These would be hands on sessions with real code examples, with a focus on teaching people how to leverage various code bases to make real life work easier.  Would you be willing to organize/lead such a session for your project?
• Discussion following the hands on tutorials, these would be interactive sessions focused around dealing with unsolved issues. The “speaker” would be responsible for setting up a set of discussion topics around an issue of interest, and then facilitating ideas and opinions from the attendees. The goals would be to talk through problems and gather a consensus about options for solving them.  Would you be willing to organize/lead such a session for your project?
• Mini-hackathon either before, during, or after the 2-day BOSC.  The subject of the hackathon would need to be organized by the individual project leaders/teams.  Some suggestions would be adding/extending support for next-gen sequencing; organizing bugs/tasks so that new beginners can start contributing to the project easily and working on some of those bugs/tasks; organizing some type of contest like the Genome Annotation Assessment Project (GASP) where solutions from different projects compete on arriving at some type of goal.  Would you be willing to organize/lead this type of session?
• Organizing/creating a LiveCD or Debian download of Bio* projects with documentation to support outreach to the larger bioinformatics community.  Would you be willing to organize/lead this type of session?
• What session topics would you like to see represented for traditional talks?
• Who would you like to hear as a keynote speaker?

2.  The BOSC 2010 organizing committee is in discussion with an open access journal to publish a formal Proceedings for BOSC.  If you are planning on submitting an abstract for BOSC 2010, are you interested in submitting a more formal paper to the BOSC proceedings, given that as the author you would need to pay the page charges that could run between US$500-1000?  We are likely to move ahead with plans to have a proceedings, but it would be helpful to know how many submissions to expect.

3.  Call for volunteers.  Organizing tutorial/hackathons and such will only be possible if individuals step forward to lead these sessions.  Please let us know if you would be willing to serve in any capacity.  We also need volunteers to review abstracts for the more “traditional” sessions, please let us know if you are willing to do this as well.

Timeline: We are planning on putting out the Call for Abstracts in mid-January.  To be on track, we would like to receive your input by Friday, January 8.  If you are willing to step forward to organize a tutorial/discussion/hackathon, you would need to commit by that time, although there would still be some more time to put the actual program together in the new year.

Thanks and Happy Holidays!

Kam Dahlquist
Chair, BOSC 2010 on behalf of the BOSC 2010 Organizing committee:
Brad Chapman, Michael Heur, Darin London, Anton Nekrutenko, Steffen Moeller, Jim Procter
And the O|B|F Board:
Chris Dagdigian, Nomi Harris, Hilmar Lapp, Jason Stajich

The BOSC 2009 schedule of speakers with links to abstracts has been posted at http://www.open-bio.org/wiki/BOSC_2009_Schedule.

Alan Ruttenberg of Science Commons and Robert Hanmer of the Hillside Group have been confirmed as Keynote Speakers for BOSC 2009.  For more information, see the BOSC 2009 web site at http://www.open-bio.org/wiki/BOSC_2009. 

Abstract acceptances went out today–stay tuned for the schedule, which will be posted once the speakers have confirmed their invitations.

The early registration deadline for BOSC is Friday, May 15; don’t forget to take advantage of the discounted fee for early registrants at http://www.iscb.org/ismbeccb2009/registration.php.

Please forward as appropriate and forgive multiple postings.

Call for Abstracts for the 2009 Bioinformatics Open Source Conference (BOSC) 2009

An ISMB 2009 Special Interest Group (SIG)
Date: June 27-28, 2009
Location: Stockholm, Sweden
URL: http://www.open-bio.org/wiki/BOSC_2009
Abstract submission via EasyChair:
https://www.easychair.org/login.cgi?conf=bosc2009

Important Dates
Monday, April 13: Abstract deadline
May 1, 2009: Notification of accepted abstracts
May 15, 2009: Early Registration Discount Cut-off date
June 27-28, 2009: BOSC 2009

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. To be considered for acceptance, software systems representing the central topic in a presentation submitted to BOSC must be licensed with a recognized Open Source License, and be freely available for download in source code form.

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.

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:

1. Descriptions of a particular open source software implementation by a member of the development team, especially in the areas listed below.

2. 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:
Topics
Design Patterns in Bioinformatics
Regulatory Genomics
Multicore and GPGPU computing
Data & Analysis Management (shared session with DAM SIG)
Computational Grids
Visualization
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.

To contact the organizing committee, e-mail bosc at open-bio.org.

To sign up for BOSC-related announcements, subscribe to the Bosc-announce list (http://lists.open-bio.org/mailman/listinfo/bosc-announce).

BOSC 2009 Organizing Committee
Kam D. Dahlquist (Chair)
Lonnie R. Welch (Co-chair)
Hilmar Lapp
Jens Lichtenberg
Frank Drews
Andrew Dalke
Jim Procter
Seán I. O’ Donoghue
Anton Nekrutenko
Steffen Moeller

Belated, and probably most of you knew already, but just in case you didn’t, the 2009 Bioinformatics Open Source Conference (BOSC) was accepted on Dec 16 as a Special Interest Group (SIG) meeting by the respective ISMB 2009 review committee. Special thanks and congratulations to Kam Dahlquist, who agreed again this year to chair the conference, and who pulled the proposal together.

You can follow the organization and the conference taking shape at the BOSC 2009 wiki page. Ideas, preliminary schedules, etc are discussed  on the associated talk page. You are welcome and encouraged to join us there. The blurb for publicizing the event on the ISMB website is due on January 16, in a little more than 1 week. If you have ideas or would like to help, do let us know.

BOSC 2008 will be in Toronto, CANADA this summer July 18 & 19, 2008. There will also be a panel discussion on developing open-source software during ISMB during the lunch break on Tuesday July 22.