Difference between revisions of "BOSC 2012"

Revision as of 22:30, 1 March 2012

The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) will take place July 13-14, 2012, in Long Beach, CA, right before ISMB 2012.

Submit your abstract now! The deadline for submitting abstracts for talks is April 13, 2012.

Important Dates

• March 1, 2012: Call for Abstracts opens
• April 13, 2012: Deadline for submitting abstracts for talks
• May 7, 2012: Notification of accepted talk abstracts emailed to authors
• July 11-12, 2012: Codefest 2012 (in planning phase as we secure space)
• July 13-14, 2012: BOSC 2012 (Long Beach, California)
• July 15-17, 2012: ISMB 2012 (Long Beach, California)
• July 19-20, 2012: EU-codefest 2012 (Lodi, Italy)

Overview

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.

Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC (Bioinformatics Open Source Conference) was held in 2000, there were already a number of popular open source bioinformatics packages, and the number and range of these projects has increased dramatically since then. Many open source bioinformatics packages are widely used by the research community across a wide variety of applications. Open source bioinformatics software has facilitated rapid innovation, dissemination, and wide adoption of new computational methods, reusable software components, and standards.

BOSC brings together bioinformatics open source developers from all over the world so they can forge connections each other (both within and across projects), increase the visibility of their work, and collaborate to build shared resources. Participants can work together to create use cases, prototype working code, or run hands-on tutorials in new software packages and emerging technologies. For those who are bioinformatics software users rather than developers, BOSC introduces or updates them on a wide array of projects that they might find useful.

Please spread the word about BOSC to interested developers; all are welcome. On Twitter, we recommend the hash tag #bosc2012.

Sessions

• Cloud and Parallel Computing -- This session will cover 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's Elastic Compute Cloud combined with publicly available datasets promise to lower the overhead to participate in large scale data analyses. Talks will focus on how the community can build up resources, datasets, and workflows for making the best use of cloud infrastructure. We will also include talks on data-parallel approaches to analyzing massive data sets, such as those resulting from next-generation sequencing and mass spec proteomics, and reports on the parallelization of bioinformatics algorithms in general.
• Linked Data -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and RDF in particular) to expose, share, and connect data, information, and knowledge online. Linked Data principles are increasingly being embraced by bioinformatics resources. For example, UniProt is now being made fully available in RDF , and collaborative initiatives such as Bio2RDF aim to expose many commonly used database resources to data integration through RDF and its query language, SPARQL. This session is devoted to reports on software that works with such new data stores, or aids in their development, including technologies for interoperable web services, and tools for ontology building or maintenance.
• Genome-scale Data Management -- This session will focus on processes and technologies that support the creating, managing and reporting of genomic data. This session is appropriate for discussion of systems that involve components such as (but not limited to) Ensembl and GMOD/Chado data stores, Taverna and Galaxy analysis workflows, and BioMart and InterMine warehouses.
• Data Visualization and Imaging -- This session will address visualization techniques and tools that provide insight into large and highly complex biomedical data sets , as well as biological image processing, analysis and data management. Talks that address the development of frameworks and communities are particularly welcome.
• Translational Bioinformatics -- This session will explore applications of biological and medical informatics to the development of personalized healthcare, therapies, and a better understanding of human health and disease. Topics include the analysis of human microarray and other 'omics data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases.
• Software Interoperability (possibly a joint session with BSI-SIG, the Software Interoperability SIG) -- Open Source approaches to integrating the latest bioinformatics tools. Examples of interoperability environments include Galaxy, Cytoscape, caBIG, and myGrid.
• Bioinformatics Open Source Project Updates -- This session will feature short talks from ongoing projects describing their recent progress. Abstracts will be solicited from open source projects affiliated with the O|B|F (see http://www.open-bio.org/wiki/Projects), including the Bio* projects, DAS, BioMOBY, EMBOSS, and GMOD, but any other open-source project will be equally eligible to submit presentations for this session.
• Panel: Interfacing with Industry -- Companies are more and more seeing the benefits of working with open source code and making their own code open; meanwhile, academics frequently partner with companies on their research projects. We encourage submissions from companies that work with open source software, as well as developers from non-commercial organizations who collaborate with companies. We anticipate a broadly useful conversation about the benefits and pitfalls of academic/commercial interaction.

Submitting Abstracts

The deadline for abstract submissions is Friday, April 13, 2012.

Abstracts must be one page in length and submitted as a PDF (preferred) or Microsoft Word file only. Please observe the following formatting guidelines:

• Use 1 inch (2.5 cm) margins on the top, sides, and bottom of the page.
• Include the following pieces of information 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 printed "as is" in the program booklet; please help your all-volunteer Organizing Committee by following the formatting guidelines above.

Accepted talks will be 5-20 minutes. You will be notified of the length of your talk upon abstract acceptance.

Click here to submit your abstract

Open Source License Requirement

The Open Bioinformatics Foundation, which sponsors 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

Posters at BOSC

BOSC includes poster sessions. All accepted speakers will also have the opportunity to present posters. In addition, abstracts for which there is not enough time to allocate a talk may be selected for poster presentation. Finally, there will be a few spots reserved for last-minute posters.

Student Travel Awards

Thanks to generous sponsorship from Eagle Genomics and an anonymous donor, we are pleased to announce the competition for three Student Travel Awards for BOSC 2012. Each winner will be awarded $250 to defray the costs of travel to BOSC.

• To apply for the award, submit your abstract by the April 13 deadline.
• Be sure to indicate that you are a student on the abstract submission form.
• Your abstract will undergo the normal review process for BOSC. The BOSC Organizing Committee will select the three best abstracts for the Student Travel Awards.
• You will still need to make your own travel arrangements for BOSC. The award will take the form of a reimbursement check after the conference.

Keynote Speakers

Jonathan Eisen

Dr. Eisen is a professor of evolutionary biology at U. C. Davis, and also has an adjunct position at the Department of Energy Joint Genome Institute in Walnut Creek, CA. His research focuses on the origin of novelty (how new processes and functions originate). Dr. Eisen is heavily involved in the Open Access publishing movement and is Academic Editor in Chief of PLoS Biology. In 2011, he was awarded the 2012 Benjamin Franklin Award for Open Access in the Life Sciences.

His talk is entitled "Science Wants to Be Open - If Only We Could Get Out of Its Way":

Scientific research and education is inherently an open activity. Yet the culture of scientific practice has inserted barriers in the way of this openness in every conceivable area from peer review, to publishing, to sharing resources, to education. I will argue that most or even all of these barriers are unnecessary and should be eliminated for scientific progress to be most efficient.

Suzanna Lewis

Suzanna Lewis is the head of the Berkeley Bioinformatics and Open Source Projects and a founder of the Gene Ontology Consortium. In addition to the Gene Ontology, she is involved in the OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project.

Her talk is entitled "Fun with Standards":

The Web is a wonderful soapbox for publishing data of all kinds. Labs of all sizes are using it to distribute their results and conclusions to the entire world. As DNA sequencers and other lab instruments continue to improve, the sheer volume of this information is going to continue to increase super-linearly. Providing open access to it is straightforward from a technical standpoint, but if you are a consumer, trying to locate particular data, then trolling the Web is not much better than rolling dice. Zipf’s law applies, and the things you are most interested in can only be found in a tiny minority of the items available on the Web.

Standards, as a topic, do not make a heart flutter with excitement or chills go up your spine. Despite this, in order to find the data I was after, I have been involved in designing a number of controlled vocabularies and ontologies such as the Gene Ontology and the Phenotypic Quality Ontology, and I have learned from these experiences. In this talk I will discuss: information space as a graph made up of simple relationships between things; what physical centralization can offer; standards as a way to enable interoperability which in turn can drive innovation; and the relative (in)effectiveness of top-down standardization committees.

Organizing Committee

Chair

• Nomi L. Harris (Lawrence Berkeley National Laboratory)

Members

• Jan Aerts (Katholieke Universiteit Leuven)
• Brad Chapman (Biopython developer; Harvard School of Public Health)
• Peter Cock (Biopython developer; James Hutton Institute, formerly Scottish Crop Research Institute)
• Christopher Fields (National Center for Supercomputing Applications)
• Erwin Frise (Lawrence Berkeley National Laboratory)
• Peter Rice (European Bioinformatics Institute)

Ex Officio (Members of the O|B|F Board)

• Chris Dagdigian
• Kam D. Dahlquist
• Hilmar Lapp
• Jason Stajich

Open Source License Requirement for Talks at BOSC

The Open Bioinformatics Foundation, which sponsors 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 (including source code) for download as a tar/zip file accessed through ftp/http or through a widely used version control system like cvs/subversion/git/bazaar/Mercurial.

More information on Open Source:

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

Previous BOSCs

• The first BOSC was held in 2000.
• BOSC 2011 took place in Vienna in July 2011.
• Information about the first 12 conferences

Contact Us

• If you'd like to join the mailing list for BOSC-related announcements, including the call for abstracts and deadline reminders, please subscribe to the Bosc-announce list. This list has low traffic, and your address will be kept private.
• If you have questions about the conference, please contact the organizers at bosc@open-bio.org.