Difference between revisions of "BOSC 2010"

Latest revision as of 21:57, 26 September 2016

The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 will be held for two days in conjunction with the 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2010) at the Hynes Convention Center (room 207) in Boston, Massachusetts, USA. The dates of BOSC 2010 are July 9-10; the main ISMB Conference runs July 11-13, 2010. BOSC attendees are also invited to participate in the Codefest 2010 programming session on July 7-8.

ANNOUNCEMENT: Congratulations to the winners of the BOSC 2010 Student Travel Fellowships: Nobuaki Kono, Eric Talevich, and Jens Lichtenberg!

SLIDES for both days' talks are up on SlideShare under the username "bosc2010". Individual links to each talk are posted on the schedule page.

BOSC 2010 Proceedings: The Proceedings have been published as of 21 December 2010 in BMC Bioinformatics.

Overview

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, 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.

Keynote Speakers

Guy Coates

Guy Coates, Group leader of the Informatics Systems Group at the Wellcome Trust Sanger Institute, will be one of our keynote speakers at BOSC 2010. Guy Coates is an expert in large Linux/Unix systems architecture, management and application optimization, next-gen DNA sequencing pipelines, very large database systems (>50TB), and high performance compute clusters (1500+ CPUs). He will lead off the conference, with a talk entitled:

Clouds: all fluff and no substance? Cloud architectures have made plenty of impact in the press over the past 18 months, but have they made any impact in solving real bioinformatics challenges? This talk will detail the Sanger Institute's experiences with the cloud, both good and bad, and ask what needs to be done to prepare the cloud for the era of commodity sequencing and $500 genomes.

Ross Gardler

Our other keynote speaker will be Ross Gardler, Vice President for Community Development at the Apache Software Foundation and Manager for OSS Watch (University of Oxford), which helps institutions and projects in the UK that are using or developing free and open source software. He has also performed Computer Science and Management research and teaching in both the UK and West Indies. Ross will be giving a talk entitled:

Community Development at the Apache Software Foundation The Apache Software Foundation is home to over 100 projects including the famous Apache Web Server. In this talk Ross will discuss how the foundation was created, how ASF projects are managed and how the foundation has scaled from a community of 12 developers to over 3000 active committers and hundreds of thousands of active contributors. Finally Ross will look at new moves to help scale the foundation even further.

Important Dates

• February 26, 2010: Call for abstracts opens
• March 9, 2010: Registration opens
• April 15, 2010: Deadline for submitting abstracts, abstract submission is now closed
• May 6, 2010: Notifications for accepted abstracts were e-mailed to corresponding authors
• May 14, 2010: Deadline for presenters to confirm acceptance of invitation to speak and for authors offered conditional acceptance to come into compliance with requested changes.
• May 28, 2010: Early Registration Discount Cut-off Date (Registration site through ISMB)
• July 7-8, 2010: Codefest 2010 programming session
• July 9-10, 2010: BOSC 2010!

Registration

Registration for BOSC is through the ISMB main conference web site. Please note that you can register for BOSC without registering for the ISMB conference.

The deadline for discounted early registration is May 28, 2010.

Schedule

• The BOSC 2010 Schedule has been posted.
• Alternately, click here to download the BOSC 2010 program and schedule as a PDF file (5 pages, 300k)
• Click here to download all abstracts compiled into one PDF file (36 pages, 2 MB).
• Individual abstracts can be accessed by clicking on the links on the schedule.

Information for Speakers

Audio/Visual

• Please bring your slides on a flash drive and be prepared to load your file onto the podium computer at the break immediately preceeding your session. We want to minimize switching computers between speakers to save time.
• The podium computer is configured as follows:
  • Windows XP SP3
  • Office 2007
  • Media Play 11
  • QuickTime
  • Adobe Reader 9.x
  • IE 8
  • Fire Fox 3.6
• Live demos are possible, but we advise that you also bring screen shots. While we have been promised an internet connection, be prepared for connection problems.

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 on SlideShare.
• After your presentation, please e-mail your slides to bosc@open-bio.org or make other arrangements for transfer of the file.
• For example, see slides from BOSC 2009 or BOSC 2008 on SlideShare.

PLoS Postcards

• Speakers at BOSC are asked to give permission for their talks to be reported as a PLoS Postcard.
• Graduate students and postdocs attending BOSC/ISMB are invited to submit a 1000 word summary of a talk given at BOSC/ISMB which will be published in PLoS Computational Biology. Examples from PSB 2010 can be found here.
• For your talk to be reported as a postcard, this form needs to be filled out and submitted according to the instructions on the form.

Call for Lightning Talks/Birds of a Feather Sessions

Lightning Talks and Software Demonstrations

The program committee is currently seeking speakers for the lightning talks. Call for Lightning Talks is now closed. 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 2010, please e-mail us at bosc@open-bio.org:

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

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 software 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 2010 Birds of a Feather page.

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.
  • (Of course, we would still welcome traditional Bio* Update abstracts, too!)
• Approaches to analyzing high-throughput 'omics data -- Presentation of projects that use the MapReduce framework either for
  1. parallelized analysis of possibly terabyte size data sets from next-gen sequencing and mass spec proteomics or
  2. parallelization of bioinformatics algorithms in general (e.g., the Apache Mahout project).

Projects may involve Hadoop (MapReduce API + HDFS) as well as associated open source toolkits (Hbase, Hive, Pig, Cascading, etc.) or other NoSQL non-relational data stores.

• Cloud-based approaches to improving software and data accessibility -- The emergence of cloud computing has made highly scalable cluster computing available to computational biologists. Services such as Amazon Elastic Compute Cloud combined with publicly available datasets promise to lower the overhead to participate in large scale data analyses. We are interested in talks focused around how the community can build up resources and datasets for cloud infrastructure, as well as the sharing of insights, and the contribution of implemented workflows. Current implementations and initiatives are encouraged to submit abstracts for talks and join in the pre-conference Codefest session.
• The Semantic Web in open source bioinformatics -- Emerging Semantic Web technologies promise to improve data interoperability and accessibility. Seeing these developments as promising for life science researchers who struggle daily with new file formats and incompatible datasets, BioHackathon 2010 focused around current semantic resources and tools for bioinformatics. We solicit session talks from researchers using RDF and related technologies in their research and data analyses, with a special focus on documenting how these tools can contribute to open data access.
• Open Source Software -- Open source software that does not fit neatly into the above categories.
• Lightning Talks -- short, 5 minute talks intended to introduce very recent developments, initiate discussion, or highlight resources of interest to BOSC attendees. Abstracts for Lightning Talks will be accepted up to the first day of BOSC and will be accepted based on space availability and conformance to the Open Source License Requirement.

Student Travel Awards

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.

• To apply for the award, submit your abstract by the April 15 deadline through the Open Conference Systems site.
• Be sure to check the box indicating that you are a graduate student.
• Your abstract will undergo the normal review process for BOSC. In addition, the BOSC Organizing Committee will review the student abstracts and pick the three best abstracts for the Student Travel Awards.
• Notifications have gone out: Congratulations to Nobuaki Kono, Eric Talevich, and Jens Lichtenberg!
• You will still need to make your own travel arrangements for BOSC. The award will take the form of a check or reimbursement to take place at the conference itself.

Abstract Submission Information

The deadline for abstract submissions is Thursday, April 15. Abstract submissions are now closed. Abstract submissions were not accepted via e-mail this year. All abstracts were submitted through our Open Conferences System 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; 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 (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:

• Recognized Open Source Licenses
• Definition of the Open Source Philosophy

First-ever Published BOSC Proceedings

The Proceedings have been published as of 21 December 2010 in BMC Bioinformatics.

More information can be found on the BOSC 2010 Proceedings internal web site.

The BOSC Organizing Committee is pleased to announce that this year we have published the first-ever BOSC Proceedings in the Open Access journal, BMC Bioinformatics.

• Presenters at BOSC 2010 were invited to submit a 4-5 page manuscript for publication in the Open Access journal, BMC Bioinformatics.
• Manuscripts were due after the conference on August 15, 2010 to give authors time to refine their submission based on discussion at BOSC (especially for participants in the OpenBio Solution Challenge).
• Manuscripts for all Session topics were considered.
• Manuscripts were peer-reviewed (abstract acceptance to BOSC did not guarantee publication in the Proceedings).
• Manuscripts conformed to BMC Bioinformatics author guidelines and formatting, although submissions were processed through BOSC, NOT the BMC Bioinformatics submission web site.
• Authors were charged the fee of GBP 550 per article, invoiced by and paid directly to BioMed Central. This fee was payable regardless of any BioMed Central membership arrangements, and it was the responsibility of the author to pay this sum to BioMed Central for inclusion in the Proceedings.

Organizing Committee

Chair

• Kam D. Dahlquist (Loyola Marymount University)

Members

• Brad Chapman (Biopython developer; Mass General Hospital)
• Nomi Harris (OBF Board)
• Michael Heuer (BioJava Developer)
• Darin London (BioPerl Developer)
• Steffen Möller (Institute for Neuro- und Bioinformatics, Lübeck, Germany)
• Jim Procter (University of Dundee, Scotland)
• Ron Taylor (Pacific Northwest National Laboratory)

Ex Officio (Members of the OBF Board)

• Chris Dagdigian
• Hilmar Lapp
• Jason Stajich

Previous BOSCs

The first BOSC was held in 2000. Please see past BOSC conferences for information about the first ten 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.
• The deadline for abstract submissions is Thursday, April 15. Abstract submissions will not be accepted via e-mail this year. All abstracts are to be submitted through our Open Conferences System site.
• For more information about the conference, please contact the organizers at bosc@open-bio.org.

Sponsors

The keynote speakers and student travel fellowships to BOSC 2010 were made possible by Eagle Genomics, Ltd. and an anonymous donor. Thank you.