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Difference between revisions of "BOSC 2013"
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|[[Image:Pear.png|left|The Bosc Pear]] | |[[Image:Pear.png|left|The Bosc Pear]] | ||
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| − | |The 14th Annual Bioinformatics Open Source Conference (BOSC 2013) | + | |The 14th Annual Bioinformatics Open Source Conference (BOSC 2013) took place July 19-20, 2013, in Berlin, Germany, right before [http://www.iscb.org/ismbeccb2013 ISMB/ECCB 2013]. |
| + | The '''[[BOSC_2013_Schedule|conference schedule is available here as HTML]]''' (including links to presentations) and '''[[Media:BOSC2013_schedule.pdf | here as a PDF file]]''' (A4 format). | ||
| + | The '''[http://www.open-bio.org/bosc2013/BOSC2013-program.pdf complete program]''', including all accepted talk and poster abstracts, is '''[http://www.open-bio.org/bosc2013/BOSC2013-program.pdf here]'''. | ||
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| + | Conference report preprint: [https://peerj.com/preprints/83/ Harris et al. (2013) The Bioinformatics Open Source Conference (BOSC) 2013. PeerJ PrePrints 1:e83v1]; abridged formal report: [http://dx.doi.org/10.1093/bioinformatics/btu413 Harris et al. (2014) The Bioinformatics Open Source Conference (BOSC) 2013. Bioinformatics (in press)] | ||
| + | |} | ||
== Important Dates == | == Important Dates == | ||
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* July 17-18, 2013: [[Codefest 2013]], Berlin | * July 17-18, 2013: [[Codefest 2013]], Berlin | ||
| − | * July 19-20, 2013: '''BOSC 2013''', Berlin | + | * July 19-20, 2013: '''BOSC 2013''', ICC Berlin, Berlin -- '''[[BOSC_2013_Schedule|schedule]]''' |
| − | * July 19-23, 2013: [http://www.iscb.org/ismbeccb2013 ISMB/ECCB 2013], | + | * July 19-23, 2013: [http://www.iscb.org/ismbeccb2013 ISMB/ECCB 2013], ICC Berlin, Berlin |
| − | + | * July 11-12, 2014: [[BOSC 2014]], Boston, MA | |
== Overview == | == Overview == | ||
| − | The Bioinformatics Open Source Conference (BOSC) is a two-day Special Interest Group of [http://www.iscb.org/ismbeccb2013 ISMB]. It is sponsored by the Open Bioinformatics Foundation ( | + | The Bioinformatics Open Source Conference (BOSC) is a two-day Special Interest Group of [http://www.iscb.org/ismbeccb2013 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. BOSC covers the wide range of open source bioinformatics software packages that have been successfully developed and adopted by the community, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of open source bioinformatics software and open science, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. | 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. BOSC covers the wide range of open source bioinformatics software packages that have been successfully developed and adopted by the community, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of open source bioinformatics software and open science, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics. | ||
| − | Please spread the word about BOSC--all are welcome. On Twitter, follow @ | + | Please spread the word about BOSC--all are welcome. On Twitter, [https://twitter.com/OBF_BOSC follow @OBF_BOSC] and use [https://twitter.com/search?q=%23BOSC2013 hash tag #bosc2013]. |
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== Keynote Speakers == | == Keynote Speakers == | ||
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This year's keynote speakers will be Sean Eddy of the Howard Hughes Medical Institute's Janelia Farm, and Cameron Neylon of the Public Library of Science. | This year's keynote speakers will be Sean Eddy of the Howard Hughes Medical Institute's Janelia Farm, and Cameron Neylon of the Public Library of Science. | ||
| + | [[Image:SeanEddy.jpg|150px|Sean Eddy]] | ||
| + | [[Image:Neylon.jpg|90px|Cameron Neylon]] | ||
[[BOSC_Keynote_Speakers|More information about BOSC 2013 Keynote Speakers]] | [[BOSC_Keynote_Speakers|More information about BOSC 2013 Keynote Speakers]] | ||
== Session Topics == | == Session Topics == | ||
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| + | The conference schedule is available '''[[BOSC_2013_Schedule|here as HTML]]''' and '''[[Media:BOSC2013_schedule.pdf | here as a PDF file]]''', including [[BOSC_2013/BOFs|Birds of a Feather (BoF) meetings]]. | ||
* '''Open Science and Reproducible Research''' -- New this year, this session encompasses the theory and practice of open science, including open notebook science, open data, transparent and reproducible workflows, and shared standards for reviewing and publishing research papers. | * '''Open Science and Reproducible Research''' -- New this year, this session encompasses the theory and practice of open science, including open notebook science, open data, transparent and reproducible workflows, and shared standards for reviewing and publishing research papers. | ||
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* '''Software Interoperability''' -- This session covers Open Source approaches to integrating the latest bioinformatics tools. Building flexible, reproducible workflows with connected tools is essential to modern bioinformatics. The goal of this session is to investigate how we can increase tool connectivity and help communities work better together. | * '''Software Interoperability''' -- This session covers Open Source approaches to integrating the latest bioinformatics tools. Building flexible, reproducible workflows with connected tools is essential to modern bioinformatics. The goal of this session is to investigate how we can increase tool connectivity and help communities work better together. | ||
* '''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 large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases. We especially welcome work that bridges the gap between research and patients, making analysis tools available and understandable for non-scientists. | * '''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 large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases. We especially welcome work that bridges the gap between research and patients, making analysis tools available and understandable for non-scientists. | ||
| − | * '''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 | + | * '''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 abstracts for this session. |
* '''[[BOSC_Panel_2013|Panel: Strategies for funding and maintaining open source software]]''' | * '''[[BOSC_Panel_2013|Panel: Strategies for funding and maintaining open source software]]''' | ||
== Submitting Abstracts == | == Submitting Abstracts == | ||
| − | The deadline for abstract submissions for talks was April 12, 2013. | + | The deadline for abstract submissions for talks was April 12, 2013. Late poster abstracts were accepted until June 7. We have reserved a few spaces for walk-in posters, which [[BOSC_Abstract_Submission|must meet the BOSC requirements of open source and recognized license]]. The ISMB staff specify that posters should not exceed the following dimensions: 0.95 m wide x 1.30 m high. |
| − | [[BOSC_Abstract_Submission| | ||
| − | <div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_2013. | + | <div style="float:right; background-color: #FFFFFF">[[File:Eagle_logo_2013.jpg|120px|right|Eagle Genomics logo|link=http://www.eaglegenomics.com/]]</div> |
== Sponsor == | == Sponsor == | ||
We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] for helping to sponsor three Student Travel Awards at BOSC 2013. Each student winner will receive $250 towards travel expenses. In addition, the Open Bioinformatics Foundation will grant these three students free admission to the conference. | We thank [http://www.eaglegenomics.com/ Eagle Genomics, Ltd.] for helping to sponsor three Student Travel Awards at BOSC 2013. Each student winner will receive $250 towards travel expenses. In addition, the Open Bioinformatics Foundation will grant these three students free admission to the conference. | ||
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== BOSC Organizing Committee == | == BOSC Organizing Committee == | ||
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* [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp] (National Evolutionary Synthesis Center) | * [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp] (National Evolutionary Synthesis Center) | ||
| − | '''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://www.bioperl.org/wiki/Jason_Stajich Jason Stajich] | * [http://www.bioperl.org/wiki/Jason_Stajich Jason Stajich] | ||
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== Contact Us == | == Contact Us == | ||
| − | * [http://twitter.com/#!/BOSC2012 Follow BOSC on Twitter]: @ | + | * [http://twitter.com/#!/BOSC2012 Follow BOSC on Twitter]: @OBF_BOSC, #bosc2013 |
* 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, or would like to volunteer to help out, please contact the organizers at [mailto:bosc@open-bio.org bosc@open-bio.org]. | * If you have questions about the conference, or would like to volunteer to help out, please contact the organizers at [mailto:bosc@open-bio.org bosc@open-bio.org]. | ||
Latest revision as of 16:47, 26 February 2016
 |
The 14th Annual Bioinformatics Open Source Conference (BOSC 2013) took place July 19-20, 2013, in Berlin, Germany, right before ISMB/ECCB 2013.
The conference schedule is available here as HTML (including links to presentations) and here as a PDF file (A4 format). The complete program, including all accepted talk and poster abstracts, is here.
|
Important Dates
- July 17-18, 2013: Codefest 2013, Berlin
- July 19-20, 2013: BOSC 2013, ICC Berlin, Berlin -- schedule
- July 19-23, 2013: ISMB/ECCB 2013, ICC Berlin, Berlin
- July 11-12, 2014: BOSC 2014, Boston, MA
Overview
The Bioinformatics Open Source Conference (BOSC) is a two-day Special Interest Group 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. BOSC covers the wide range of open source bioinformatics software packages that have been successfully developed and adopted by the community, and encompasses the growing movement of Open Science, with its focus on transparency, reproducibility, and data provenance. We welcome submissions relating to all aspects of open source bioinformatics software and open science, including new computational methods, reusable software components, visualization, interoperability, and other approaches that help to advance research in the biomolecular sciences. Two full days of talks, posters, panel discussions, and informal discussion groups will enable BOSC attendees to interact with other developers and share ideas and code, as well as learning about some of the latest developments in the field of open source bioinformatics.
Please spread the word about BOSC--all are welcome. On Twitter, follow @OBF_BOSC and use hash tag #bosc2013.
Keynote Speakers
This year's keynote speakers will be Sean Eddy of the Howard Hughes Medical Institute's Janelia Farm, and Cameron Neylon of the Public Library of Science.
More information about BOSC 2013 Keynote Speakers
Session Topics
The conference schedule is available here as HTML and here as a PDF file, including Birds of a Feather (BoF) meetings.
- Open Science and Reproducible Research -- New this year, this session encompasses the theory and practice of open science, including open notebook science, open data, transparent and reproducible workflows, and shared standards for reviewing and publishing research papers.
- Cloud and Parallel Computing -- This session focuses on approaches that use cloud and other massively parallel infrastructures for processing and analyzing large and heterogeneous biological data. We are particularly interested in solutions demonstrating how to build new or extend existing software, resources and workflows to perform at scale for "Big Data" problems.
- Genome-scale Data Management -- This session encompasses software and other tools designed for managing, exploring, and analyzing genome-level data to address research questions, including but not limited to genome assembly, variant prediction, eQTL analysis, and phylogenomic methods.
- Visualization -- Current data acquisition technologies are moving us more and more towards a "data first, hypothesis later" paradigm for scientific research. As a result, data visualization and visual analytics are of increasing importance. This session focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
- Software Interoperability -- This session covers Open Source approaches to integrating the latest bioinformatics tools. Building flexible, reproducible workflows with connected tools is essential to modern bioinformatics. The goal of this session is to investigate how we can increase tool connectivity and help communities work better together.
- 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 large scale population and family sequencing data, bioinformatics methodologies for clinical research, and tools for discovering clinically useful associations in human databases. We especially welcome work that bridges the gap between research and patients, making analysis tools available and understandable for non-scientists.
- 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 abstracts for this session.
- Panel: Strategies for funding and maintaining open source software
Submitting Abstracts
The deadline for abstract submissions for talks was April 12, 2013. Late poster abstracts were accepted until June 7. We have reserved a few spaces for walk-in posters, which must meet the BOSC requirements of open source and recognized license. The ISMB staff specify that posters should not exceed the following dimensions: 0.95 m wide x 1.30 m high.
Sponsor
We thank Eagle Genomics, Ltd. for helping to sponsor three Student Travel Awards at BOSC 2013. Each student winner will receive $250 towards travel expenses. In addition, the Open Bioinformatics Foundation will grant these three students free admission to the conference.
BOSC 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)
- Christopher Fields (National Center for Supercomputing Applications)
- Jeremy Goecks (Emory University)
- Hans-Rudolf Hotz (Friedrich Miescher Institute for Biomedical Research)
- Hilmar Lapp (National Evolutionary Synthesis Center)
Ex Officio (Members of the OBF Board)
Previous BOSCs
- BOSC has been held yearly since 2000.
- BOSC 2012 took place in Long Beach, California, in July 2012.
- Information about the first 13 BOSC conferences
Contact Us
- Follow BOSC on Twitter: @OBF_BOSC, #bosc2013
- 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, or would like to volunteer to help out, please contact the organizers at bosc@open-bio.org.
