| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2015"
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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> | ||
| − | === * * * | + | Thanks to all for a successful meeting! We hope to see you at [[BOSC 2016]] in Orlando, Florida! |
| − | + | ||
| + | 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]. | ||
| + | |||
| + | The full program including abstracts is available [http://www.open-bio.org/bosc2015/BOSC2015-program-with-abstracts.pdf here], and we wrote up a report as [http://dx.doi.org/10.1371/journal.pcbi.1004691 Harris et al (2016)]. | ||
| + | |||
| + | == Summaries of BOSC 2015 by Participants == | ||
| + | There were over 2000 tweets about #BOSC2015, and a number of articles and blog posts, some of which are listed below. | ||
| + | |||
| + | * Uduak Grace Thomas's [http://www.open-bio.org/bosc2015/BOSC-Diversity-GenomeWeb.pdf GenomeWeb article about our diversity efforts] (original available at [https://www.genomeweb.com/informatics/bosc-community-discusses-ways-boost-diversity-participation-bioinformatics GenomeWeb]). | ||
| + | |||
| + | * Brad Chapman's excellent summaries: [https://smallchangebio.wordpress.com/2015/07/10/bosc2015day1a/ Day 1 (morning)], [https://smallchangebio.wordpress.com/2015/07/11/bosc2015day1b/ Day 2 (afternoon)], [https://smallchangebio.wordpress.com/2015/07/11/notes-bioinformatics-open-source-conference-2015-day-2-morning-ewan-birney-open-science-and-reproducibility/ Day 2 (morning)], [https://smallchangebio.wordpress.com/2015/07/11/bosc2015day2b/ Day 2 (afternoon)] | ||
| + | |||
| + | * Peter Cock's Storify of BOSC tweets: [https://storify.com/pjacock/bosc-2015-day-one part one], [https://storify.com/pjacock/bosc-2015-day-two part two] | ||
| + | |||
| + | * [https://storify.com/bmpvieira/dublin-conferences Bruno Vieira's Storify] about Codefest, BOSC, and ISMB/ECCB 2015 | ||
| + | |||
| + | * [http://gigasciencejournal.com/blog/open-bioinformatics-irish-free-software-state/ Scott Edmunds' GigaScience blog post] | ||
| + | |||
| + | * [http://www.flax.co.uk/blog/2015/07/13/biosolr-at-bosc-2015-open-source-search-for-bioinformatics/ Matt Pearce's blog post about BOSC and BioSolr] | ||
| + | |||
| + | * [http://phdops.kblin.org/2015-on-overengineering.html Kai Blin's thoughts on BOSC and why we shouldn't overengineer bioinformatics analyses] | ||
| + | |||
| + | * [http://thedaoofflow.fluxionary.net/2015/07/bosc-2015-wrap-up/ Konrad Förstner's wrap-up] | ||
| + | |||
| + | * [http://okko73313.blogspot.de/2015/07/bosc-2015-amazing-as-always.html Konstantin Okonechnikov's summary ("BOSC 2015: amazing as always")] | ||
| + | |||
| + | *[http://eukaryoticebullience.blogspot.com/2015/07/reflections-on-bosc2015-keynote-and.html Holly Bik's reflections] | ||
| + | |||
| + | If you wrote a BOSC report and would like it to be listed here, please email us at bosc@open-bio.org. | ||
== Overview == | == Overview == | ||
| − | The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual [http://www.iscb.org/ismbeccb2015 ISMB conference]. It is sponsored by the Open Bioinformatics Foundation ( | + | The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual [http://www.iscb.org/ismbeccb2015 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. |
| + | |||
| + | 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 [[BOSC_2015_Schedule|talks, posters, panel discussions]], and [https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# iinformal 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. | ||
| − | + | We also organize a two-day community development session prior to the conference ([[Codefest 2015]]). 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=%23BOSC2015 hash tag #bosc2015]. | 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=%23BOSC2015 hash tag #bosc2015]. | ||
| − | == | + | == 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. | ||
| + | |||
| + | {| | ||
| + | |rowspan="2"| [[File:google-logo11w.png|205px|left|Google|link=http://www.google.com/]] | ||
| + | |rowspan="2"| | ||
| − | + | | [[File:Curoverse_logo.png|175px|center|Curoverse logo|link=http://curoverse.com]] | |
| + | |- | ||
| + | | [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]] | ||
| + | |rowspan="2"| [[File:Gigascience-07.png|200px|left|GigaScience|link=http://www.gigasciencejournal.com/]] | ||
| + | |rowspan="2"| [[File:Bina_logo.png|200px|left|Bina|link=http://www.bina.com/]] | ||
| + | |} | ||
| − | We | + | We are grateful to [http://www.google.com/ Google] for their generous support for videorecording BOSC 2015, and we thank [http://curoverse.com Curoverse] (the team behind the open source platform [http://arvados.org Arvados]) and Open Access journal [http://www.gigasciencejournal.com/ GigaScience] as returning sponsors, and [http://bina.com/ Bina] as our newest sponsor. |
| − | If you | + | If you would like to be a sponsor of BOSC, please contact us at at bosc@open-bio.org. |
== Important Dates == | == Important Dates == | ||
| − | + | * [[Codefest 2015]]: July 8-9, 2015, Dublin (Trinity College) | |
| − | |||
| − | |||
| − | |||
| − | * [[Codefest 2015]]: July 8-9, 2015, Dublin | ||
* '''BOSC 2015: July 10-11, 2015, Dublin''' | * '''BOSC 2015: July 10-11, 2015, Dublin''' | ||
* ISMB/ECCB 2015: July 10-14, 2015, Dublin | * ISMB/ECCB 2015: July 10-14, 2015, Dublin | ||
| + | |||
| + | == Registration == | ||
| + | |||
| + | Because BOSC is run as a two-day Special Interest Group (SIG) meeting at the annual ISMB conference, [https://www.iscb.org/ismbeccb2015-registration registration is via ISMB/ECCB 2015]. 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. | ||
| + | |||
| + | If you need a formal invitation letter for your Ireland VISA application, please [https://www.iscb.org/ismbeccb2015-registration#visainvitation contact the ISMB]. | ||
== Session Topics == | == Session Topics == | ||
| Line 39: | Line 82: | ||
* '''Visualization''' -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation. | * '''Visualization''' -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation. | ||
* '''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. | * '''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. | ||
| − | * '''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 | + | * '''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. |
| − | * '''Panel | + | * '''[[BOSC_2015_Panel|Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community.]]''' ''Chair'': Monica Munoz-Torres. ''Panelists'': Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams. |
| + | |||
| + | [[Image:EwanBirney2.jpg|120px|right|Ewan Birney]] | ||
== Keynote Speakers == | == Keynote Speakers == | ||
| + | [[Image:HollyBik.png|100px|left|Holly Bik]] | ||
| + | |||
This year's keynote speakers will be Holly Bik (University of Birmingham) and Ewan Birney (EMBL-EBI). | This year's keynote speakers will be Holly Bik (University of Birmingham) and Ewan Birney (EMBL-EBI). | ||
| − | [[BOSC_2015_Keynote_Speakers|More information about BOSC 2015 Keynote Speakers]] | + | '''[[BOSC_2015_Keynote_Speakers|More information about BOSC 2015 Keynote Speakers]]''' |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
== Organizing Committee == | == Organizing Committee == | ||
| Line 65: | Line 107: | ||
'''Members''' | '''Members''' | ||
| − | |||
* [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]) | ||
* [http://www.tgac.ac.uk/bioinformatics/sequencing-informatics/robert-davey/ Robert Davey] (The Genome Analysis Centre) | * [http://www.tgac.ac.uk/bioinformatics/sequencing-informatics/robert-davey/ Robert Davey] (The Genome Analysis Centre) | ||
* 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] ( | + | * [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 | + | * [http://berkeleybop.org/person/monica-munoz-torres Mónica Muñoz-Torres] (Berkeley Bioinformatics Open Source Projects) |
| − | '''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] | ||
| + | |||
| + | == Review Committee == | ||
| + | |||
| + | Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Monica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antao, George Githinji, Manuel Corpas, Thomas Down, Sarah Hird, Scott Markel, Rob Davey, Spencer Bliven, Michael Reich, Lorena Pantano, Björn Grüning, Hilmar Lapp, Daniel Blankenberg, Amye Kenall, Hervé Menager. | ||
== Survey about BOSC 2015 location == | == Survey about BOSC 2015 location == | ||
| − | We have asked you, and you have spoken! 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and—most importantly—what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) just after the Galaxy Community Conference, rather than as an ISMB SIG. Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority prefer BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin on 10-11 July, 2015, right before ISMB 2015. | + | We have asked you, and you have spoken! ([http://news.open-bio.org/news/2014/09/bosc-2015-will-be-in-dublin/ blog post]) 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and—most importantly—what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) just after the Galaxy Community Conference, rather than as an ISMB SIG. Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority prefer BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin on 10-11 July, 2015, right before ISMB 2015. |
Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and we welcome suggestions of people to invite.) You can reach us at bosc@open-bio.org. | Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and we welcome suggestions of people to invite.) You can reach us at bosc@open-bio.org. | ||
Latest revision as of 12:45, 18 April 2017
Thanks to all for a successful meeting! We hope to see you at BOSC 2016 in Orlando, Florida!
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.
The full program including abstracts is available here, and we wrote up a report as Harris et al (2016).
Summaries of BOSC 2015 by Participants
There were over 2000 tweets about #BOSC2015, and a number of articles and blog posts, some of which are listed below.
- Uduak Grace Thomas's GenomeWeb article about our diversity efforts (original available at GenomeWeb).
- Brad Chapman's excellent summaries: Day 1 (morning), Day 2 (afternoon), Day 2 (morning), Day 2 (afternoon)
- Bruno Vieira's Storify about Codefest, BOSC, and ISMB/ECCB 2015
If you wrote a BOSC report and would like it to be listed here, please email us at bosc@open-bio.org.
Overview
The Bioinformatics Open Source Conference (BOSC) is run as a two-day meeting before the annual ISMB conference. 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 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, and iinformal 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.
We also organize a two-day community development session prior to the conference (Codefest 2015). 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 #bosc2015.
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 are grateful to Google for their generous support for videorecording BOSC 2015, and we thank Curoverse (the team behind the open source platform Arvados) and Open Access journal GigaScience as returning sponsors, and Bina as our newest sponsor.
If you would like to be a sponsor of BOSC, please contact us at at bosc@open-bio.org.
Important Dates
- Codefest 2015: July 8-9, 2015, Dublin (Trinity College)
- BOSC 2015: July 10-11, 2015, Dublin
- ISMB/ECCB 2015: July 10-14, 2015, Dublin
Registration
Because BOSC is run as a two-day Special Interest Group (SIG) meeting at the annual ISMB conference, registration is via ISMB/ECCB 2015. 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.
If you need a formal invitation letter for your Ireland VISA application, please contact the ISMB.
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.
- Visualization -- focuses on approaches for interactive as well as static visual representations of biomedical data, ranging from exploration to explanation.
- 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.
- 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.
- Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community. Chair: Monica Munoz-Torres. Panelists: Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams.
Keynote Speakers
This year's keynote speakers will be Holly Bik (University of Birmingham) and Ewan Birney (EMBL-EBI).
More information about BOSC 2015 Keynote Speakers
Organizing Committee
Co-Chairs
- Peter Cock (Biopython developer; James Hutton Institute)
- Nomi L. Harris (Lawrence Berkeley National Laboratory)
Outreach Coordinator
- Sarah Hird (University of California, Davis)
Members
- Brad Chapman (Biopython developer; Harvard School of Public Health)
- Robert Davey (The Genome Analysis Centre)
- 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)
Ex Officio (Members of the OBF Board)
Review Committee
Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Monica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antao, George Githinji, Manuel Corpas, Thomas Down, Sarah Hird, Scott Markel, Rob Davey, Spencer Bliven, Michael Reich, Lorena Pantano, Björn Grüning, Hilmar Lapp, Daniel Blankenberg, Amye Kenall, Hervé Menager.
Survey about BOSC 2015 location
We have asked you, and you have spoken! (blog post) 59 past and/or future BOSC attendees participated in our survey, answering questions about what they liked at BOSC 2014, what changes they’d like to see, and—most importantly—what they thought about the proposal to possibly hold BOSC 2015 in Norwich (UK) just after the Galaxy Community Conference, rather than as an ISMB SIG. Although some survey participants indicated that they would be more likely to attend BOSC 2015 if it were co-located with GCC, the majority prefer BOSC to remain an ISMB SIG, so we will hold BOSC 2015 in Dublin on 10-11 July, 2015, right before ISMB 2015.
Although the survey is now closed, we are always happy to hear your suggestions for BOSC 2015. (We are particularly interested in increasing diversity at BOSC, and we welcome suggestions of people to invite.) You can reach us at bosc@open-bio.org.
Previous BOSCs
- BOSC has been held yearly since 2000.
- BOSC 2014 took place in Boston, MA, July 11-12, 2014.
- Information about the first 14 BOSC conferences
Contact Us
- Follow BOSC on Twitter: @OBF_BOSC, #bosc2015
- 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.
