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Difference between revisions of "BOSC 2012"

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[[Image:Pear.png|right|The Bosc Pear]]
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[[Image:Pear.png|left|The Bosc Pear]]
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__NOTOC__
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<div style="float: right; margin-left:20px; margin-right:10px; maxwidth: 150px">__TOC__</div>
  
−
The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) will take place July 13-14, 2012, in Long Beach, CA, right before [http://www.iscb.org/ismb2012 ISMB 2012].
+
The 13th Annual Bioinformatics Open Source Conference (BOSC 2012) was held July 13-14, 2012, in Long Beach, CA, right before [http://www.iscb.org/ismb2012 ISMB 2012].
  
−
The deadline for submitting abstracts has passed, but there will be openings for last-minute lightning talks and last-minute posters at the conference.
+
The conference schedule is available '''[[BOSC_2012_Schedule|here as HTML]]''' (with links to the slide presentations) and '''[[Media:BOSC2012_schedule.pdf | here as a PDF file]]'''.
−
__NOTOC__
+
You can also download the [http://www.open-bio.org/bosc2012/BOSC2012-program.pdf complete program], which includes the schedule and all of the talk and poster abstracts.
−
<div style="float: left; margin-right:20px; maxwidth: 150px">__TOC__</div>
 
  
 
== Important Dates ==
 
== Important Dates ==
  
−
* '''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]] ([http://www.lmu.edu/ Loyola Marymount University], Los Angeles, California)
 
* July 11-12, 2012: [[Codefest 2012]] ([http://www.lmu.edu/ Loyola Marymount University], Los Angeles, California)
−
* '''July 13-14, 2012:  BOSC 2012''' (Long Beach, California)
+
* '''July 13-14, 2012:  BOSC 2012''' (Long Beach, California)--[[BOSC_2012_Schedule|schedule]]
 
* July 15-17, 2012: [http://www.iscb.org/ismb2012 ISMB 2012] (Long Beach, California)
 
* July 15-17, 2012: [http://www.iscb.org/ismb2012 ISMB 2012] (Long Beach, California)
 
* July 19-20, 2012: [[EU_Codefest_2012|EU-codefest 2012]] (Lodi, Italy)
 
* July 19-20, 2012: [[EU_Codefest_2012|EU-codefest 2012]] (Lodi, Italy)
 +
* July 19-20, '''2013''': [[BOSC 2013]] (Berlin, Germany)
  
 
== Overview ==
 
== Overview ==
  
−
The Bioinformatics Open Source Conference (BOSC) is a satellite of [http://www.iscb.org/ismb2012 ISMB]. It 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.  
+
The Bioinformatics Open Source Conference (BOSC) is a satellite of [http://www.iscb.org/ismb2012 ISMB]. It 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.  
  
 
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.
 
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.
Line 24: Line 24:
 
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.  
 
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.
+
Please spread the word about BOSC to interested developers; all are welcome. On Twitter, follow @BOSC2012 and use hash tag #bosc2012.
−
 
 
−
<div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_CMYK.jpg‎|120px|right|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]</div>
 
−
 
 
−
== Sponsors ==
 
−
 
 
−
We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] and an anonymous donor for sponsoring three Student Travel Awards at BOSC 2012.
 
  
 
== Sessions ==
 
== Sessions ==
 +
The conference schedule is available '''[[BOSC_2012_Schedule|here as HTML]]''' and '''[[Media:BOSC2012_schedule.pdf | here as a PDF file]]'''.
  
 
* '''Cloud and Parallel Computing''' -- This session will cover cloud-based approaches to improving software and data accessibility. The emergence of [http://en.wikipedia.org/wiki/Cloud_computing cloud computing] has made highly scalable cluster computing available to computational biologists. Services such as [http://aws.amazon.com/ec2/ Amazon's Elastic Compute Cloud] combined with [http://aws.amazon.com/publicdatasets/#1 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.
 
* '''Cloud and Parallel Computing''' -- This session will cover cloud-based approaches to improving software and data accessibility. The emergence of [http://en.wikipedia.org/wiki/Cloud_computing cloud computing] has made highly scalable cluster computing available to computational biologists. Services such as [http://aws.amazon.com/ec2/ Amazon's Elastic Compute Cloud] combined with [http://aws.amazon.com/publicdatasets/#1 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.
 
* '''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.
 
* '''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.
−
* '''Linked Data''' -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and [http://dev.isb-sib.ch/projects/uniprot-rdf/ 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 [http://dev.isb-sib.ch/projects/uniprot-rdf/ RDF] , and collaborative initiatives such as [http://bio2rdf.org/ 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.
+
* '''Linked Data and Translational Knowledge Discovery''' -- Linked Data is an emerging set of conventions on using basic Semantic Web standards (HTTP URIs and [http://dev.isb-sib.ch/projects/uniprot-rdf/ RDF] in particular) to expose, share, and connect data, information, and knowledge online. This session will explore the application of Linked Data and other knowledge-discovery techniques and paradigms to help advance our understanding of human health and disease.
−
* '''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''' -- Open Source approaches to integrating the latest bioinformatics tools. Examples of interoperability environments include Galaxy, Cytoscape, caBIG, and myGrid.
−
* '''Software Interoperability''' (joint session with [http://www.broadinstitute.org/software/bsi-sig/ 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 OBF (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.
−
* '''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: Bioinformatics Paper Reviews: Open Standards and Standards of Openness''' -- This panel will cover two interrelated types of openness in bioinformatics paper reviews:
−
* '''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.
+
<ul><ul><li>Shared standards/criteria that all reviewers could use when judging bioinformatics papers.
 +
<li>The requirement that authors make their software/methods/data available so that reviewers can replicate and evaluate the work described in the paper.</ul>Should bioinformatics reviewers be encouraged--or required--to use a standardized set of review criteria? (Some possible criteria are described [http://ivory.idyll.org/blog/may-12/blog-review-criteria-for-bioinfo.html in this blog post].)  Should bioinformatics journals require authors, as a condition for publication, to release their tools and scripts? Can we develop procedures for fairly and systematically testing bioinformatics software, and should this testing be done openly (rather than secretly by anonymized paper reviewers)? These and other related topics will be discussed by a panel of experienced and opinionated bioinformatics researchers, in conversation with members of the audience.</ul>
  
−
== Submitting Abstracts ==
+
== Keynote Speakers ==
  
−
The deadline for abstract submissions was '''Friday, April 13, 2012'''. There will be openings for last-minute lightning talks and last-minute posters at the conference.  
+
[[Image:Eisen.jpg|130px|left|Jonathan Eisen]]
 +
=== Jonathan Eisen ===
  
−
Abstracts must be '''one page''' in length and submitted '''as a PDF (preferred) or Microsoft Word file only'''.  Please observe the following formatting guidelines:
+
Dr. Eisen is a professor at the University of California, Davis,
−
* Use 1 inch (2.5 cm) margins on the top, sides, and bottom of the page.
+
where he holds appointments in the Genome Center, the Department of
−
* Include the following pieces of information in order from the top of the page:
+
Evolution and Ecology and the Department of Medical Microbiology and
−
** Title
+
Immunology.  In addition, he has an adjunct position at the Department
−
** Authors, with the presenting author's name underlined.
+
of Energy Joint Genome Institute in Walnut Creek, CA. Prior to moving
−
** Author affiliations, including the e-mail address of the presenting author.
+
to UC Davis he was on the faculty at The Institute for Genomic
−
** URL for the overall project web site
+
Research (TIGR) for eight years.  His research focuses on the genomic
−
** URL for accessing the code
+
basis for the origin of novelty (how new processes and functions
−
** The particular Open Source License being used
+
originate), in particular in microbes. Dr. Eisen is heavily involved
−
* The abstracts will be printed "as is" in the program booklet; please help your all-volunteer Organizing Committee by following the formatting guidelines above.
+
in the Open Access publishing movement and is Academic Editor in Chief
 +
of PLoS Biology.  He is also an active and award-winning blogger and microblogger (e.g.,
 +
see [http://phylogenomics.blogspot.com phylogenomics.blogspot.com] and
 +
[http://twitter.com/phylogenomics twitter.com/phylogenomics]). In 2011, Eisen was awarded the [http://www.bioinformatics.org/franklin/ Benjamin Franklin Award (Bioinformatics)] for promoting open access in the life sciences.
  
−
Accepted talks will be 5-20 minutes. You will be notified of the length of your talk upon abstract acceptance.
+
His talk is entitled '''Science Wants to Be Open - If Only We Could Get Out of Its Way''':
  
−
=== Open Source License Requirement ===
+
''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.''
  
−
The [[OBF|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.
+
[[Image:Goble.jpg|150px|right|Carole Goble]]
  
−
See the following websites for further information:
+
=== Carole Goble ===
−
* [http://www.opensource.org/licenses/ Recognized Open Source Licenses]
+
Carole Goble is a full professor in the School of Computer Science at the University of Manchester, UK, where she co-leads the Information Management Group. She has an international reputation in Semantic Web, Distributed computing, and Social Computing for scientific collaboration. She is the Director of the myGrid project, which has produced the widely-used Taverna open source software; myExperiment, a social web site that enables researchers to share scientific workflows; and the Biocatalogue of web services for the life sciences.
−
* [http://www.opensource.org/docs/definition.php Definition of the Open Source Philosophy]
 
  
−
=== Posters at BOSC ===
+
In 2008 Carole was awarded the inaugural Microsoft Jim Gray award for outstanding contributions to e-Science. In 2010 she was elected a Fellow of the Royal Academy of Engineering for her contributions to e-Science. In 2012 she was nominated for the Benjamin Franklin award for open science in Biology.
  
−
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.
+
Carole's talk is entitled '''If I build it will they come?''':
  
−
== Student Travel Awards ==
+
''Over the years I have built a bunch of open source software and services for researchers: the Taverna workflow system, myExperiment for workflow sharing, BioCatalogue for services, SEEK for Systems Biology data and models, and most recently MethodBox for longitudinal data sets. As well as building software we built communities: development communities and user communities. So what drives/hinders adoption? What do I know now that I wished I had known before? How do we sustain communities on time-limited grants? How do we build it so they come, stay and join in?''
  
−
Thanks to generous sponsorship from [http://www.eaglegenomics.com/ 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.
+
=== Open Source License Requirement ===
−
* To apply for the award, [http://events.open-bio.org/BOSC2012/author/submit.php 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 ==
+
The [[OBF|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.
  
−
=== Jonathan Eisen ===
+
See the following websites for further information:
 +
* [http://www.opensource.org/licenses/ Recognized Open Source Licenses]
 +
* [http://www.opensource.org/docs/definition.php Definition of the Open Source Philosophy]
  
−
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.
+
<div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_CMYK.jpg‎|120px|right|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]</div>
  
−
His talk is entitled "Science Wants to Be Open - If Only We Could Get Out of Its Way":
+
== Sponsors ==
−
 
 
−
''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 ===
+
We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] for sponsoring three Student Travel Awards at BOSC 2012. Each student winner will get free admission to BOSC.
  
−
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
+
== BOSC Organizing Committee ==
−
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'''
 
'''Chair'''
Line 112: Line 98:
 
* [http://www.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; James Hutton Institute, formerly Scottish Crop Research Institute)
 
* [http://www.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; James Hutton Institute, formerly Scottish Crop Research Institute)
 
* Christopher Fields (National Center for Supercomputing Applications)
 
* Christopher Fields (National Center for Supercomputing Applications)
−
* Erwin Frise (Lawrence Berkeley National Laboratory)
+
* [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp] (National Evolutionary Synthesis Center)
 
* Peter Rice (European Bioinformatics Institute)  
 
* Peter Rice (European Bioinformatics Institute)  
  
−
'''Ex Officio (Members of the O|B|F Board)'''
+
'''Ex Officio (Members of the OBF Board)'''
 
* [http://www.bioperl.org/wiki/Chris_Dagdigian Chris Dagdigian]
 
* [http://www.bioperl.org/wiki/Chris_Dagdigian Chris Dagdigian]
 
* [http://myweb.lmu.edu/kdahlqui Kam D. Dahlquist]
 
* [http://myweb.lmu.edu/kdahlqui Kam D. Dahlquist]
−
* [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp]
 
 
* [http://www.bioperl.org/wiki/Jason_Stajich Jason Stajich]
 
* [http://www.bioperl.org/wiki/Jason_Stajich Jason Stajich]
−
 
−
== Open Source License Requirement for Talks at BOSC ==
 
−
 
−
The [[OBF|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:
 
−
* [http://www.opensource.org/licenses/ Recognized Open Source Licenses]
 
−
* [http://www.opensource.org/docs/definition.php Definition of the Open Source Philosophy]
 
  
 
== Previous BOSCs ==
 
== Previous BOSCs ==
Line 137: Line 114:
 
== Contact Us ==
 
== Contact Us ==
  
 +
* [http://twitter.com/#!/BOSC2012 Follow BOSC on Twitter]: @BOSC2012, #bosc2012
 
* 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 [http://lists.open-bio.org/mailman/listinfo/bosc-announce Bosc-announce] list.  This list has low traffic, and your address will be kept private.
 
* 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 [http://lists.open-bio.org/mailman/listinfo/bosc-announce 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 [mailto:bosc@open-bio.org bosc@open-bio.org].
 
* If you have questions about the conference, please contact the organizers at [mailto:bosc@open-bio.org bosc@open-bio.org].

Latest revision as of 18:15, 7 September 2015

The Bosc Pear

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

The conference schedule is available here as HTML (with links to the slide presentations) and here as a PDF file. You can also download the complete program, which includes the schedule and all of the talk and poster abstracts.

Important Dates

Overview

The Bioinformatics Open Source Conference (BOSC) is a satellite of ISMB. It 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.

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, follow @BOSC2012 and use hash tag #bosc2012.

Sessions

The conference schedule is available here as HTML and here as a PDF file.

  • 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.
  • 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.
  • Linked Data and Translational Knowledge Discovery -- 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. This session will explore the application of Linked Data and other knowledge-discovery techniques and paradigms to help advance our understanding of human health and disease.
  • Software Interoperability -- 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 OBF (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: Bioinformatics Paper Reviews: Open Standards and Standards of Openness -- This panel will cover two interrelated types of openness in bioinformatics paper reviews:
    • Shared standards/criteria that all reviewers could use when judging bioinformatics papers.
    • The requirement that authors make their software/methods/data available so that reviewers can replicate and evaluate the work described in the paper.
    Should bioinformatics reviewers be encouraged--or required--to use a standardized set of review criteria? (Some possible criteria are described in this blog post.) Should bioinformatics journals require authors, as a condition for publication, to release their tools and scripts? Can we develop procedures for fairly and systematically testing bioinformatics software, and should this testing be done openly (rather than secretly by anonymized paper reviewers)? These and other related topics will be discussed by a panel of experienced and opinionated bioinformatics researchers, in conversation with members of the audience.

Keynote Speakers

Jonathan Eisen

Jonathan Eisen

Dr. Eisen is a professor at the University of California, Davis, where he holds appointments in the Genome Center, the Department of Evolution and Ecology and the Department of Medical Microbiology and Immunology. In addition, he has an adjunct position at the Department of Energy Joint Genome Institute in Walnut Creek, CA. Prior to moving to UC Davis he was on the faculty at The Institute for Genomic Research (TIGR) for eight years. His research focuses on the genomic basis for the origin of novelty (how new processes and functions originate), in particular in microbes. Dr. Eisen is heavily involved in the Open Access publishing movement and is Academic Editor in Chief of PLoS Biology. He is also an active and award-winning blogger and microblogger (e.g., see phylogenomics.blogspot.com and twitter.com/phylogenomics). In 2011, Eisen was awarded the Benjamin Franklin Award (Bioinformatics) for promoting 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.

Carole Goble

Carole Goble

Carole Goble is a full professor in the School of Computer Science at the University of Manchester, UK, where she co-leads the Information Management Group. She has an international reputation in Semantic Web, Distributed computing, and Social Computing for scientific collaboration. She is the Director of the myGrid project, which has produced the widely-used Taverna open source software; myExperiment, a social web site that enables researchers to share scientific workflows; and the Biocatalogue of web services for the life sciences.

In 2008 Carole was awarded the inaugural Microsoft Jim Gray award for outstanding contributions to e-Science. In 2010 she was elected a Fellow of the Royal Academy of Engineering for her contributions to e-Science. In 2012 she was nominated for the Benjamin Franklin award for open science in Biology.

Carole's talk is entitled If I build it will they come?:

Over the years I have built a bunch of open source software and services for researchers: the Taverna workflow system, myExperiment for workflow sharing, BioCatalogue for services, SEEK for Systems Biology data and models, and most recently MethodBox for longitudinal data sets. As well as building software we built communities: development communities and user communities. So what drives/hinders adoption? What do I know now that I wished I had known before? How do we sustain communities on time-limited grants? How do we build it so they come, stay and join in?

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:

Eagle Genomics logo

Sponsors

We thank Eagle Genomics, Ltd. for sponsoring three Student Travel Awards at BOSC 2012. Each student winner will get free admission to BOSC.

BOSC Organizing Committee

Chair

  • Nomi L. Harris (Lawrence Berkeley National Laboratory)

Members

Ex Officio (Members of the OBF Board)

Previous BOSCs

Contact Us

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