BOSC 2011

The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) will be held immediately before the 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2011) at the Austria Center in Vienna, Austria. BOSC 2011 will take place July 15-16; the main ISMB Conference will be July 17-19, 2011. Participants are also invited to Codefest 2011, July 13-14.

The deadline for submitting abstracts is April 18, 2011.

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.

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.

Please spread the word about BOSC to interested developers; all are welcome. On Twitter, we recommend the hash tag #bosc2011.

BOSC 2010 was held in Boston, MA, from July 9-10. Selected peer-reviewed papers from BOSC 2010 were be published in BMC Bioinformatics on 21 December, 2010.

Sponsors

We thank Eagle Genomics, Ltd. and an anonymous donor for sponsoring three Student Travel Awards at BOSC 2011.

Keynote Speakers

Lawrence Hunter

Lawrence Hunter is Professor of Pharmacology and Computer Science at the University of Colorado and director of the Computational Bioscience Program at the School of Medicine. He is one of the founders of ISMB, a fellow of the ISCB, and is well known for contributions in a broad range of problems in computational biology.

Dr. Hunter will be giving a talk entitled The role of openness in knowledge-based systems for biomedicine. Knowledge-based approaches to the analysis to genome-scale data require the extraction, sharing and use of very large amounts of knowledge about biomedicine. Developments such as the open source software movement, the Open Biomedical Ontologies, Semantic Web standards such as OWL and SPARQL, and the spread of open access publishing are creating the potential for powerful knowledge-based computer systems that may play an important role in the future of biomedical research. Yet several critical challenges remain before this vision can be realized. Dr. Hunter will discuss some relevant recent resources developed in my lab, some of the socio-political barriers that remain, and what you can do to overcome them.

Matt Wood

As the Technology Evangelist for Amazon Web Services, Matt discusses the technical and organisational aspects of cloud computing across the world. With a background in the life sciences, Matt is interested in helping teams of all sizes bring their ideas to life through technology. Before joining Amazon he built web-scale search engines at Cornell University, sequenced DNA in Hinxton and developed scientific software in Cambridge. He is a frequent speaker at international conferences, a blogger, published author and an advocate of research productivity.

Matt's talk, entitled Into the Wonderful, will feature a discussion of the constraints of working with the size, scope and complexity of modern research data, and how cloud computing can help accelerate academic research. We'll take a look at the current state of the art, the role cloud computing plays in increasing the impact of open source tools, the use of public hosted data in the cloud and how academic cloud platforms can help promote collaboration, reproducibility and reuse across disciplines.

Important Dates

• March 1, 2011: Call for abstracts opens
• April 18, 2011: Deadline for submitting abstracts
• May 9, 2011: Notifications for accepted abstracts e-mailed to corresponding authors
• May 16, 2011: Deadline for presenters to confirm acceptance of invitation to speak and for authors offered conditional acceptance to come into compliance with requested changes.
• July 13-14, 2011: Codefest 2011 programming session
• July 15-16, 2011: BOSC 2011

Abstract Submission Information

Submit your abstract here!

The deadline for abstract submissions is Monday, April 18, 2011.

Abstracts must be one page in length and submitted as a PDF 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
  • Whether you would like your abstract to be considered for a talk, a poster, or both.
• 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.

This year, BOSC will include a poster session. Please indicate in the header section of your abstract whether you'd like to be considered for a talk, a poster, or both. (All speakers will also have the opportunity to present posters.)

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

Sessions

• Approaches to parallel processing -- This session will cover data-parallel approaches to analyzing the massive data sets from next-generation sequencing and mass spec proteomics, or reports on the parallelization of bioinformatics algorithms in general.
• 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. Talks will focus on 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.
• The Semantic Web in open source bioinformatics -- Software that employs semantic web technology: Existing databases such as UniProt are now being made fully available in RDF format, and new repositories such as Bio2RDF are being built upon RDF and are allowing RDF-based query language use (e.g., SPARQL). This session is devoted to reports on software that works with such new data stores, or aids in their development, as well as descriptions of software that pertains to ontology building or maintenance. We also solicit talks about projects that employ information management architectures/frameworks such as UIMA, an open source project in Apache Incubator status, that facilitate integration of semantic analysis and search components.
• Genome content management -- 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-- Approaches to presenting large biomedical datasets with visual aids that make the data easier to understand and analyze.
• Tools for next-generation sequencing -- Practical approaches to analyzing next generation sequencing data, focusing on flexible tools that combine existing software and algorithms.
• Open Source Software -- Open source bioinformatics software that does not fit neatly into the above categories.
• Shared topics with other SIGs: A session in which participants in other ISMB SIGs can make brief presentations about open source software to a wider audience, allowing BOSC attendees to hear about open source projects in other biology-related areas, and for participants in specialized SIGs to meet other open source developers and form collaborations.

In addition to the above sessions, there will be a panel discussion about Meeting the challenges of inter-institutional collaboration. Many open source projects involve collaborators from organizations all over the world. Participants in this panel discussion will comment on how their projects have dealt with the challenges that arise from these multi-institution collaborations. Please let us know if you would like to be a panelist.

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 2011. Each winner will be awarded $250 to defray the costs of travel to BOSC 2011.

• To apply for the award, submit your abstract by the April 18 deadline.
• Be sure to check the box indicating that you are a student.
• 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.

Organizing Committee

Co-Chairs

• Nomi L. Harris (Lawrence Berkeley National Laboratory)
• Peter Rice (European Bioinformatics Institute)

Members

• Brad Chapman (Biopython developer; Mass General Hospital)
• Peter Cock (Biopython developer; Scottish Crop Research Institute)
• Erwin Frise (Lawrence Berkeley National Laboratory)
• Darin London (BioPerl Developer, Duke University)
• Ron Taylor (Pacific Northwest National Laboratory)

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

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

Previous BOSCs

The first BOSC was held in 2000. Please see past BOSC conferences for information about the first 11 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. 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.