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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 will take place '''July 8-9, 2016''', in Orlando, Florida, right before ISMB 2016.
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BOSC 2016 was held '''July 8-9, 2016''', in Orlando, Florida, right before ISMB 2016.
  
The '''main abstract call has now closed''' but 'we will reopen the call for late-breaking lightning talks and posters soon'. See [[BOSC_Abstract_Submission]] for requirements.
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'''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]).
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We plan to offer a limited number of [https://news.obf.io/2016/03/01/obf-travel-fellowship-program/ travel fellowships] to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC.
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 +
== Summaries of BOSC 2016 ==
 +
 
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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 The 2016 Bioinformatics Open Source Conference (BOSC) [version 1; referees: not peer reviewed].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:
 +
 
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* 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]
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* GigaScience blog post [http://gigasciencejournal.com/blog/open-bioinformatics-goes-disney/ Open bioinformatics in the house of the mouse] by Scott Edmunds
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* 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)]
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* 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/ismb2016 ISMB conference]. It is sponsored 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.  
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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 talks, posters, panel discussions (see [[BOSC 2015 Schedule|schedule from BOSC 2015]]), and informal discussion groups (see [https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# BOSC 2015 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.
+
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 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).
 
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).
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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.
 +
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{|
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| [[File:Curoverse_logo.png|175px|center|Curoverse logo|link=http://curoverse.com]]
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|-
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| [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]]
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|}
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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 at at bosc@open-bio.org.
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 +
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
 
* April 4, 2016: Deadline for submitting [[BOSC_Abstract_Submission|abstracts]] for full talks
* May 6, 2016: Authors notified
 
 
* June 2, 2016: End of early [https://www.iscb.org/ismb2016-registration registration] discount for ISMB/BOSC  
 
* June 2, 2016: End of early [https://www.iscb.org/ismb2016-registration registration] discount for ISMB/BOSC  
* June 2, 2016: Deadline for submitting abstracts for Late-Breaking Lightning Talks and posters (link will be posted soon)
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* June 2, 2016: Deadline for [[BOSC_Abstract_Submission|submitting abstracts for Late-Breaking Lightning Talks and posters]]
* June 10, 2016: Notification of acceptance for Late-Breaking Lightning Talks and posters
 
 
* [[Codefest 2016]]: July 6-7, 2016, Orlando, FL, USA at [https://familab.org/ FamiLAB]
 
* [[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
 
We plan to offer a limited number of travel fellowships to help offset expenses for some accepted speakers who would not otherwise be able to attend BOSC – please see the for more information. To be considered in time for BOSC, applications to this program are due for the April 15 deadline.
 
  
 
== Registration ==
 
== Registration ==
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* '''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.
* '''Visualization''' -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
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* '''Workflows''' -- focuses on standardized representations and exchange formats for workflows (such as Common Workflow Language) and tools for creating, editing and running workflows.
* '''Translational Bioinformatics''' -- explores 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.
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* '''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.
* '''Bioinformatics Open Source Libraries and Projects''' -- features short talks from new or 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.
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* [[BOSC_2016_Panel|'''Panel: Growing and sustaining open source communities''']]
* '''Panel: Growing and sustaining open source communities'''
 
  
 
== Keynote Speakers ==
 
== Keynote Speakers ==
  
This year's keynote speakers will be Jennifer Gardy (University of British Columbia / British Columbia Centre for Disease Control) and Steven Salzburg (Johns Hopkins University).
+
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]]'''
 
'''[[BOSC_2016_Keynote_Speakers|More information about BOSC 2016 Keynote Speakers]]'''
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* [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 (Equinome Ltd.)
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* 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
 +
 
 +
&lowast; Also reviewed Late-Breaking Lightning Talk abstracts
  
 
== Previous BOSCs ==
 
== Previous BOSCs ==

Latest revision as of 16:32, 28 July 2017


The Bosc Pear

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:

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.

Curoverse logo
Arvados logo

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

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

Members

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

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.