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Difference between revisions of "BOSC 2016"
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<div style="float:left; maxwidth: 180px; margin-left:25px; margin-right:15px; background-color: #FFFFFF">[[Image:Pear.png|left|The Bosc Pear]]</div> | <div style="float:left; maxwidth: 180px; margin-left:25px; margin-right:15px; background-color: #FFFFFF">[[Image:Pear.png|left|The Bosc Pear]]</div> | ||
| − | + | BOSC 2016 was held '''July 8-9, 2016''', in Orlando, Florida, right before ISMB 2016. | |
| − | BOSC 2016 | + | '''Check out the complete [[BOSC_2016_Schedule|schedule]]''', including self-organizing [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/edit#heading=h.m64zx0e3odcv BOFs], and follow us on Twitter ([https://twitter.com/OBF_BOSC @OBF_BOSC] and hashtag [https://twitter.com/search?f=tweets&vertical=default&q=%23bosc2016&src=savs #BOSC2016]). |
| + | |||
| + | |||
| + | == Summaries of BOSC 2016 == | ||
| + | |||
| + | The [https://f1000research.com/articles/5-2464/v1 BOSC 2016 report] was published in F1000 research in October 2016: | ||
| + | * Harris NL, Cock PJA, Chapman B et al. The 2016 Bioinformatics Open Source Conference (BOSC) [version 1; referees: not peer reviewed]. F1000Research 2016, 5(ISCB Comm J):2464 | ||
| + | (doi: [http://dx.doi.org/10.12688/f1000research.9663.1 10.12688/f1000research.9663.1]) | ||
| + | |||
| + | In addition, there were thousands of tweets about BOSC 2016 by participants, and a number of blog posts, including: | ||
| + | |||
| + | * Peter Cock's Storify of BOSC tweets: [https://storify.com/pjacock/bosc-2016-day-one part one], [https://storify.com/pjacock/bosc-2016-day-two part two] | ||
| + | * Heather Wiencko's [https://storify.com/HLWiencko/bosc2016-panel Storify of the BOSC panel tweets] | ||
| + | * GigaScience blog post [http://gigasciencejournal.com/blog/open-bioinformatics-goes-disney/ Open bioinformatics in the house of the mouse] by Scott Edmunds | ||
| + | * Brad Chapman's excellent summaries: [https://smallchangebio.wordpress.com/2016/07/08/bosc2016_day1a/ Day 1 (morning)], [https://smallchangebio.wordpress.com/2016/07/08/bosc2016day1b/ Day 1 (afternoon)], [https://smallchangebio.wordpress.com/2016/07/09/bosc2016day2a/ Day 2 (morning)], [https://smallchangebio.wordpress.com/2016/07/09/bosc2016day2b/ Day 2 (afternoon)] | ||
| + | * Robin Andeer's [http://www.robinandeer.com/blog/2016/07/12/bosc-2016/ Codefest and BOSC 2016 blog post] | ||
== Overview == | == Overview == | ||
| − | The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual [http://www.iscb.org/ | + | The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual [http://www.iscb.org/ismb2016 ISMB conference]. It is organized by the [[Main_Page|Open Bioinformatics Foundation (OBF)]], a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. |
| − | Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC was held in 2000, there were already many 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 being developed, 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 bioinformatics and open science software, 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 | + | Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC was held in 2000, there were already many 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 being developed, 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 bioinformatics and open science software, 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 (see the [[BOSC 2016 Schedule]]), and informal discussion groups (see [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/edit# BOSC 2016 Birds-of-a-Feather notes]) 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. |
| − | We also organize a two-day community development session prior to the conference ([[Codefest | + | We also organize a two-day community development session prior to the conference ([[Codefest 2016]]). This is an opportunity for anyone interested in open science, biology and programming to meet, discuss and work collaboratively. Everyone is welcome to attend Codefest (whether or not you attend BOSC). |
| − | 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=% | + | 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=%23BOSC2016 hash tag #bosc2016]. |
== Sponsors == | == Sponsors == | ||
BOSC is organised by the [[Main_Page|Open Bioinformatics Foundation]], a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. | BOSC is organised by the [[Main_Page|Open Bioinformatics Foundation]], a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. | ||
| + | |||
| + | {| | ||
| + | | [[File:Curoverse_logo.png|175px|center|Curoverse logo|link=http://curoverse.com]] | ||
| + | |- | ||
| + | | [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]] | ||
| + | |} | ||
| + | |||
| + | We thank [http://curoverse.com Curoverse] (the team behind the open source platform [http://arvados.org Arvados]) as returning sponsors. | ||
We gratefully accept sponsorships from relevant private companies. These sponsorships enable us to offer free registration to some BOSC speakers to lower the financial barrier of their attendance. | We gratefully accept sponsorships from relevant private companies. These sponsorships enable us to offer free registration to some BOSC speakers to lower the financial barrier of their attendance. | ||
| − | If you would like to be a sponsor of BOSC, please contact us | + | |
| + | If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org. | ||
== Important Dates == | == Important Dates == | ||
| + | * April 4, 2016: Deadline for submitting [[BOSC_Abstract_Submission|abstracts]] for full talks | ||
| + | * June 2, 2016: End of early [https://www.iscb.org/ismb2016-registration registration] discount for ISMB/BOSC | ||
| + | * June 2, 2016: Deadline for [[BOSC_Abstract_Submission|submitting abstracts for Late-Breaking Lightning Talks and posters]] | ||
| + | * [[Codefest 2016]]: July 6-7, 2016, Orlando, FL, USA at [https://familab.org/ FamiLAB] | ||
* BOSC 2016: July 8-9, 2016, Orlando, FL, USA | * BOSC 2016: July 8-9, 2016, Orlando, FL, USA | ||
* [https://www.iscb.org/ismb2016 ISMB 2016]: July 8-12,, 2016, Orlando, FL, USA | * [https://www.iscb.org/ismb2016 ISMB 2016]: July 8-12,, 2016, Orlando, FL, USA | ||
| Line 38: | Line 66: | ||
* '''Standards and Interoperability''' -- includes standards such as ontologies, formats, etc, as well as Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together. | * '''Standards and Interoperability''' -- includes standards such as ontologies, formats, etc, as well as Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together. | ||
* '''Data Science''' -- encompasses software and approaches to managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics. | * '''Data Science''' -- encompasses software and approaches to managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics. | ||
| − | * ''' | + | * '''Workflows''' -- focuses on standardized representations and exchange formats for workflows (such as Common Workflow Language) and tools for creating, editing and running workflows. |
| − | * ''' | + | * '''Developer Tools and Libraries''' -- includes Bio* libraries such as Biopython, and tools to help developers install or maintain analysis packages, configure web-based services, store and exchange metadata, etc. |
| − | * ''' | + | * [[BOSC_2016_Panel|'''Panel: Growing and sustaining open source communities''']] |
| + | |||
| + | == Keynote Speakers == | ||
| + | |||
| + | This year's keynote speakers will be Jennifer Gardy (University of British Columbia / British Columbia Centre for Disease Control) and Steven Salzberg (Johns Hopkins University). | ||
| + | |||
| + | '''[[BOSC_2016_Keynote_Speakers|More information about BOSC 2016 Keynote Speakers]]''' | ||
== Organizing Committee == | == Organizing Committee == | ||
| Line 52: | Line 86: | ||
* [http://bcbio.wordpress.com Brad Chapman] ([http://biopython.org Biopython developer]; [http://compbio.sph.harvard.edu/chb/ Harvard School of Public Health]) | * [http://bcbio.wordpress.com Brad Chapman] ([http://biopython.org Biopython developer]; [http://compbio.sph.harvard.edu/chb/ Harvard School of Public Health]) | ||
| − | |||
* Christopher Fields (National Center for Supercomputing Applications) | * Christopher Fields (National Center for Supercomputing Applications) | ||
* Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland) | * Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland) | ||
* [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp] (Center for Genomic and Computational Biology (GCB), Duke University) | * [http://www.bioperl.org/wiki/Hilmar_Lapp Hilmar Lapp] (Center for Genomic and Computational Biology (GCB), Duke University) | ||
* [http://berkeleybop.org/person/monica-munoz-torres Mónica Muñoz-Torres] (Berkeley Bioinformatics Open Source Projects) | * [http://berkeleybop.org/person/monica-munoz-torres Mónica Muñoz-Torres] (Berkeley Bioinformatics Open Source Projects) | ||
| + | * Heather Wiencko (PlusVital) | ||
| + | |||
| + | == Review Committee == | ||
| + | |||
| + | Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova*, George Githinji, Christopher Fields, Hilmar Lapp*, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko*, Kai Blin*, Spencer Bliven*, Brad Chapman*, Michael Crusoe, Bastian Greshake*, Hans-Rudolf Hotz*, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues*, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock*, Björn Grüning, Karsten Hokamp*, Amye Kenall, John Chilton, Konrad Förstner*, Jens Lichtenberg, Monica C Munoz-Torres | ||
| + | |||
| + | ∗ Also reviewed Late-Breaking Lightning Talk abstracts | ||
== Previous BOSCs == | == Previous BOSCs == | ||
* BOSC has been held yearly since 2000. | * BOSC has been held yearly since 2000. | ||
| − | * [BOSC 2015] took place July 10-11 in Dublin, Ireland. | + | * [[BOSC 2015]] took place July 10-11 in Dublin, Ireland. |
| + | ** Check out the complete [[BOSC_2015_Schedule|schedule]] with links to slides, posters and videos - mostly on our [http://f1000research.com/channels/BOSC F1000 Research BOSC Channel], with the videos on the [https://www.youtube.com/playlist?list=PLir-OOQiOhXbENjAIFF-JZ0WodnysPqfh BOSC YouTube]. | ||
| + | ** Read the [http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004691 BOSC 2015 Summary Report in PLOS Computational Biology]. | ||
* [[Past BOSC conferences | Information about the first 15 BOSC conferences]] | * [[Past BOSC conferences | Information about the first 15 BOSC conferences]] | ||
Latest revision as of 21:32, 28 July 2017
BOSC 2016 was held July 8-9, 2016, in Orlando, Florida, right before ISMB 2016.
Check out the complete schedule, including self-organizing BOFs, and follow us on Twitter (@OBF_BOSC and hashtag #BOSC2016).
Summaries of BOSC 2016
The BOSC 2016 report was published in F1000 research in October 2016:
- Harris NL, Cock PJA, Chapman B et al. The 2016 Bioinformatics Open Source Conference (BOSC) [version 1; referees: not peer reviewed]. F1000Research 2016, 5(ISCB Comm J):2464
(doi: 10.12688/f1000research.9663.1)
In addition, there were thousands of tweets about BOSC 2016 by participants, and a number of blog posts, including:
- Peter Cock's Storify of BOSC tweets: part one, part two
- Heather Wiencko's Storify of the BOSC panel tweets
- GigaScience blog post Open bioinformatics in the house of the mouse by Scott Edmunds
- Brad Chapman's excellent summaries: Day 1 (morning), Day 1 (afternoon), Day 2 (morning), Day 2 (afternoon)
- Robin Andeer's Codefest and BOSC 2016 blog post
Overview
The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. It is organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.
Open Source software has flourished in the bioinformatics community for well over a decade. When the first BOSC was held in 2000, there were already many 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 being developed, 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 bioinformatics and open science software, 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 (see the BOSC 2016 Schedule), and informal discussion groups (see BOSC 2016 Birds-of-a-Feather notes) 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.
We also organize a two-day community development session prior to the conference (Codefest 2016). This is an opportunity for anyone interested in open science, biology and programming to meet, discuss and work collaboratively. Everyone is welcome to attend Codefest (whether or not you attend BOSC).
Please spread the word about BOSC--all are welcome. On Twitter, follow @OBF_BOSC and use hash tag #bosc2016.
Sponsors
BOSC is organised by the Open Bioinformatics Foundation, a non-profit, volunteer-run group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community.
 |
 |
We thank Curoverse (the team behind the open source platform Arvados) as returning sponsors.
We gratefully accept sponsorships from relevant private companies. These sponsorships enable us to offer free registration to some BOSC speakers to lower the financial barrier of their attendance.
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
Important Dates
- April 4, 2016: Deadline for submitting abstracts for full talks
- June 2, 2016: End of early registration discount for ISMB/BOSC
- June 2, 2016: Deadline for submitting abstracts for Late-Breaking Lightning Talks and posters
- Codefest 2016: July 6-7, 2016, Orlando, FL, USA at FamiLAB
- BOSC 2016: July 8-9, 2016, Orlando, FL, USA
- ISMB 2016: July 8-12,, 2016, Orlando, FL, USA
Registration
Because BOSC is run as a two-day Special Interest Group (SIG) meeting at the annual ISMB conference, registration is via ISMB 2016. You can register for BOSC (which allows you to drop in on other SIGs as well), or register to attend the full ISMB/ECCB conference plus BOSC.
Session Topics
We welcome submissions relating to all aspects of bioinformatics and open science software, including (but not limited to):
- Open Science and Reproducible Research -- covers 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.
- Standards and Interoperability -- includes standards such as ontologies, formats, etc, as well as Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together.
- Data Science -- encompasses software and approaches to managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics.
- Workflows -- focuses on standardized representations and exchange formats for workflows (such as Common Workflow Language) and tools for creating, editing and running workflows.
- Developer Tools and Libraries -- includes Bio* libraries such as Biopython, and tools to help developers install or maintain analysis packages, configure web-based services, store and exchange metadata, etc.
- Panel: Growing and sustaining open source communities
Keynote Speakers
This year's keynote speakers will be Jennifer Gardy (University of British Columbia / British Columbia Centre for Disease Control) and Steven Salzberg (Johns Hopkins University).
More information about BOSC 2016 Keynote Speakers
Organizing Committee
Co-Chairs
- Peter Cock (Biopython developer; James Hutton Institute)
- Nomi L. Harris (Lawrence Berkeley National Laboratory)
Members
- Brad Chapman (Biopython developer; Harvard School of Public Health)
- Christopher Fields (National Center for Supercomputing Applications)
- Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
- Hilmar Lapp (Center for Genomic and Computational Biology (GCB), Duke University)
- Mónica Muñoz-Torres (Berkeley Bioinformatics Open Source Projects)
- Heather Wiencko (PlusVital)
Review Committee
Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova*, George Githinji, Christopher Fields, Hilmar Lapp*, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko*, Kai Blin*, Spencer Bliven*, Brad Chapman*, Michael Crusoe, Bastian Greshake*, Hans-Rudolf Hotz*, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues*, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock*, Björn Grüning, Karsten Hokamp*, Amye Kenall, John Chilton, Konrad Förstner*, Jens Lichtenberg, Monica C Munoz-Torres
∗ Also reviewed Late-Breaking Lightning Talk abstracts
Previous BOSCs
- BOSC has been held yearly since 2000.
- BOSC 2015 took place July 10-11 in Dublin, Ireland.
- Check out the complete schedule with links to slides, posters and videos - mostly on our F1000 Research BOSC Channel, with the videos on the BOSC YouTube.
- Read the BOSC 2015 Summary Report in PLOS Computational Biology.
- Information about the first 15 BOSC conferences
Contact Us
- Follow BOSC on Twitter: @OBF_BOSC, #bosc2016
- 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.
ISMB Code of Conduct
In March 2015, ISMB published a Code of Conduct that applies to SIGs (including BOSC) as well as the main ISMB/ECCB meeting.
