| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2011"
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[[Image:Pear.png|right|The Bosc Pear]] | [[Image:Pear.png|right|The Bosc Pear]] | ||
| − | The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) | + | '''Planning for [[BOSC 2012]] is now underway!''' |
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| + | The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) was held immediately before the 19th Annual [http://www.iscb.org/ismbeccb2011 International Conference on Intelligent Systems for Molecular Biology (ISMB 2011)] at the Austria Center in Vienna, Austria. BOSC 2011 took place July 15-16; the main ISMB Conference is July 17-19, 2011. [[Codefest 2011]] was held right before BOSC 2011 (July 13-14, 2011). | ||
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| + | '''The [[BOSC_2011_Schedule|BOSC schedule]] can be viewed [[BOSC_2011_Schedule|as html]] or downloaded [[Media:BOSC2011_schedule.pdf | as a PDF file]].''' You can also download the [http://www.oboedit.org/BOSC2011/BOSC2011-program.pdf complete proceedings]. This large (6 Mb) PDF file includes the schedule and all of the talk and poster abstracts. | ||
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| + | '''Slides for the BOSC talks are now linked (where available) from the [[BOSC_2011_Schedule|BOSC schedule]].''' | ||
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| + | Congratulations to the winners of the BOSC 2011 Student Travel Fellowships: Florian P. Breitwieser, Kerensa McElroy, and Konstantin Okonechnikov! | ||
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| + | Congratulations to the winners (tied) of the Audience Favorite Talk: Andreas Hildebrandt and Konstantinos Krampis! | ||
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== Overview == | == Overview == | ||
| − | The Bioinformatics Open Source Conference (BOSC) is sponsored by the Open Bioinformatics Foundation ( | + | __NOTOC__ |
| + | <div style="float: left; margin-right:20px; maxwidth: 200px">__TOC__</div> | ||
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| + | 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 | + | 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 ongoing 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. | + | Please spread the word about BOSC to interested developers; all are welcome. On Twitter, we recommend the hash tag #bosc2011 ([http://twitter.com/#!/search?q=%23bosc2011 see tweets]). |
| − | [[BOSC 2010]] was held in Boston, MA, from July 9-10. Selected peer-reviewed papers from BOSC 2010 were | + | [[BOSC 2010]] was held in Boston, MA, from July 9-10. Selected peer-reviewed papers from BOSC 2010 were published in [http://www.biomedcentral.com/1471-2105/11?issue=S12 BMC Bioinformatics] on 21 December, 2010. |
<div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_CMYK.jpg|120px|right|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]</div> | <div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_CMYK.jpg|120px|right|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]</div> | ||
| Line 18: | Line 29: | ||
== Sponsors == | == Sponsors == | ||
| − | We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] and an anonymous donor for sponsoring three | + | We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] and an anonymous donor for sponsoring three Student Travel Awards at BOSC 2011. |
== Keynote Speakers == | == Keynote Speakers == | ||
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=== Lawrence Hunter === | === 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 well known for contributions in a broad range of problems in computational biology. | + | 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. |
| − | 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 | + | 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 his lab, some of the socio-political barriers that remain, and what you can do to overcome them. |
=== Matt Wood === | === Matt Wood === | ||
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published author and an advocate of research productivity. | 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 | discussion of the constraints of working with the size, scope and | ||
| − | complexity of modern research data, and how cloud computing can help | + | 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 == | == Important Dates == | ||
* March 1, 2011: Call for abstracts opens | * March 1, 2011: Call for abstracts opens | ||
| − | * | + | * April 18, 2011: Deadline for submitting talk abstracts |
| − | * May 9, 2011: Notifications | + | * May 9, 2011: Notifications of accepted talk abstracts emailed to authors |
| − | * May | + | * May 20, 2011: Deadline for presenters to confirm acceptance of invitation to speak and for authors offered conditional acceptance to come into compliance with requested changes |
| + | * June 3, 2011: [http://www.iscb.org/ismbeccb2011-registration#1daysig Early registration deadline for SIGs (including BOSC)]. | ||
* '''July 13-14, 2011: [[Codefest 2011]] programming session''' | * '''July 13-14, 2011: [[Codefest 2011]] programming session''' | ||
* '''July 15-16, 2011: BOSC 2011''' | * '''July 15-16, 2011: BOSC 2011''' | ||
| − | + | == Open Source License Requirement == | |
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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. | 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. | ||
| − | See the following | + | See the following pages for further information: |
* [http://www.opensource.org/licenses/ Recognized Open Source Licenses] | * [http://www.opensource.org/licenses/ Recognized Open Source Licenses] | ||
* [http://www.opensource.org/docs/definition.php Definition of the Open Source Philosophy] | * [http://www.opensource.org/docs/definition.php Definition of the Open Source Philosophy] | ||
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== Sessions == | == Sessions == | ||
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* '''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 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 and datasets for cloud infrastructure, as well as the sharing of insights, and the contribution of implemented workflows. | * '''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 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 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''' -- | + | * '''The Semantic Web in open source bioinformatics''' -- Existing databases such as UniProt are now being made fully available in [http://dev.isb-sib.ch/projects/uniprot-rdf/ RDF] format, and new repositories such as [http://bio2rdf.org/ 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. | * '''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. | * '''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. | * '''Tools for next-generation sequencing''' -- Practical approaches to analyzing next generation sequencing data, focusing on flexible tools that combine existing software and algorithms. | ||
| + | * '''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. | ||
* '''Open Source Software''' -- Open source bioinformatics software that does not fit neatly into the above categories. | * '''Open Source Software''' -- Open source bioinformatics software that does not fit neatly into the above categories. | ||
| − | * | + | * '''Meeting the challenges of inter-institutional collaboration''' (panel discussion) -- 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. |
| − | + | * '''Poster session''' -- This year, BOSC attendees will have the opportunity to present posters about their work. There are spots available for last-minute posters. | |
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== Organizing Committee == | == Organizing Committee == | ||
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* [http://bcbio.wordpress.com Brad Chapman] ([http://biopython.org Biopython developer]; Mass General Hospital) | * [http://bcbio.wordpress.com Brad Chapman] ([http://biopython.org Biopython developer]; Mass General Hospital) | ||
| − | * [http://www.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; 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) |
* Erwin Frise (Lawrence Berkeley National Laboratory) | * Erwin Frise (Lawrence Berkeley National Laboratory) | ||
* [http://www.bioperl.org/wiki/Darin_London Darin London] (BioPerl Developer, Duke University) | * [http://www.bioperl.org/wiki/Darin_London Darin London] (BioPerl Developer, Duke University) | ||
* Ron Taylor (Pacific Northwest National Laboratory) | * Ron Taylor (Pacific Northwest National Laboratory) | ||
| − | '''Ex Officio (Members of the | + | '''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] | ||
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* 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 [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 wish to be on 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@ | + | * If you have questions about the conference, please contact the organizers at [mailto:bosc@open-bio.org bosc@open-bio.org]. |
| + | |||
| + | [[Category:BOSC]] [[Category:Conferences]] | ||
| + | [[Category:BOSC Conferences]] | ||
Latest revision as of 18:14, 7 September 2015
Planning for BOSC 2012 is now underway!
The 12th Annual Bioinformatics Open Source Conference (BOSC 2011) was 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 took place July 15-16; the main ISMB Conference is July 17-19, 2011. Codefest 2011 was held right before BOSC 2011 (July 13-14, 2011).
The BOSC schedule can be viewed as html or downloaded as a PDF file. You can also download the complete proceedings. This large (6 Mb) PDF file includes the schedule and all of the talk and poster abstracts.
Slides for the BOSC talks are now linked (where available) from the BOSC schedule.
Congratulations to the winners of the BOSC 2011 Student Travel Fellowships: Florian P. Breitwieser, Kerensa McElroy, and Konstantin Okonechnikov!
Congratulations to the winners (tied) of the Audience Favorite Talk: Andreas Hildebrandt and Konstantinos Krampis!
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 ongoing 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 (see tweets).
BOSC 2010 was held in Boston, MA, from July 9-10. Selected peer-reviewed papers from BOSC 2010 were 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 his 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 talk abstracts
- May 9, 2011: Notifications of accepted talk abstracts emailed to authors
- May 20, 2011: Deadline for presenters to confirm acceptance of invitation to speak and for authors offered conditional acceptance to come into compliance with requested changes
- June 3, 2011: Early registration deadline for SIGs (including BOSC).
- July 13-14, 2011: Codefest 2011 programming session
- July 15-16, 2011: BOSC 2011
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 pages for further information:
Sessions
- 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 -- 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.
- 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.
- Open Source Software -- Open source bioinformatics software that does not fit neatly into the above categories.
- Meeting the challenges of inter-institutional collaboration (panel discussion) -- 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.
- Poster session -- This year, BOSC attendees will have the opportunity to present posters about their work. There are spots available for last-minute posters.
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; James Hutton Institute, formerly 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 OBF Board)
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.
