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[Gofriends] BOSC 2010 Abstracts due April 15

Dahlquist, Kam D. Kam.Dahlquist at
Thu Apr 8 08:36:48 PDT 2010

Call for Abstracts for the 11th Annual Bioinformatics Open Source Conference (BOSC 2010)

An ISMB 2010 Special Interest Group (SIG)
Date: July 9-10, 2010
Location: Boston, Massachusetts, USA
BOSC 2010 web site:
Abstract submission via Open Conference System site:
E-mail: bosc at
Bosc-announce list:

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 for details.

-- OpenBio Solution Challenge:  See session description below and 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 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 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.  (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 parallelized analysis of possibly terabyte size data sets from next-gen sequencing and mass spec proteomics or 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.

BOSC 2010 Organizing Committee:
Kam D. Dahlquist (Chair), Brad Chapman, Nomi Harris, Michael Heuer, Darin London, Steffen Möller, Anton Nekrutenko, Jim Procter, Ron Taylor, Chris Dagdigian, Hilmar Lapp, Jason Stajich

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