| Please visit our ***NEW*** OBF/BOSC website: https://www.open-bio.org/ |
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Difference between revisions of "BOSC 2014"
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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> | |
| − | + | ||
| − | + | The 15th Annual Bioinformatics Open Source Conference (BOSC 2014) was held at the Hynes Convention Center in Boston on July 11-12, right before [https://www.iscb.org/ismb2014 ISMB 2014] as one of the official ISMB SIG satellite meetings. Feedback welcome via email bosc@open-bio.org or [https://twitter.com/OBF_BOSC @OBF_BOSC on Twitter]. | |
| − | + | ||
| + | '''[http://www.open-bio.org/wiki/BOSC_2014_Schedule Complete Schedule]''' (with links to posters, slides and videos of the talks) | ||
| + | |||
| + | == Media == | ||
| + | |||
| + | Storify Tweet archives for [https://storify.com/pjacock/bosc-2014-day-one Day One], [https://storify.com/pjacock/bosc-2014-day-two/ Day Two] and [https://storify.com/pjacock/bosc-during-ismb-2014/ during ISMB]. | ||
| + | |||
| + | Brad Chapman's [http://smallchangebio.wordpress.com/2014/07/11/notes-bioinformatics-open-source-conference-2014-day-1-afternoon-visualization-project-updates-and-lightning-talks/ blog posts] | ||
| + | |||
| + | [http://www.open-bio.org/w/images/d/dd/Bosc2014-bioinform.pdf BioInform article about Philip Bourne's keynote talk] (posted with permission) | ||
| + | [http://drjamesmalone.blogspot.co.uk/2014/07/a-paradigm-shift-on-bioinformatics.html James Malone's blog post] | ||
== Important Dates == | == Important Dates == | ||
| − | * | + | * July 9-10, 2014: [[Codefest 2014]], Boston, MA |
| − | |||
* July 11-12, 2014: BOSC 2014, Boston, MA | * July 11-12, 2014: BOSC 2014, Boston, MA | ||
| − | * July 12-16, 2014: ISMB 2014, Boston, MA | + | * July 12-16, 2014: [http://www.iscb.org/ismb2014 ISMB 2014], Boston, MA |
| − | + | * September 18-19, 2014: [http://www.open-bio.org/wiki/EU-Codefest_2014 EU-Codefest 2014], Cambridge, UK | |
== Overview == | == Overview == | ||
| − | The Bioinformatics Open Source Conference (BOSC) is a two-day | + | 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 | + | 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 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 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, [https://twitter.com/OBF_BOSC follow @OBF_BOSC] and use [https://twitter.com/search?q=%23BOSC2014 hash tag #bosc2014]. | 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=%23BOSC2014 hash tag #bosc2014]. | ||
| + | |||
| + | == Registration == | ||
| + | |||
| + | Because BOSC is run as a two-day Special Interest Group (SIG) meeting at the annual ISMB conference, [https://www.iscb.org/ismb2014-registration registration is via ISMB 2014]. You can attend just BOSC, or combine this with attending the full ISMB conference as well. | ||
| + | |||
| + | Note that this year we have [http://news.open-bio.org/news/2014/03/free-student-presenters-bosc-2014/ waived the BOSC registration fee for student presenters of full-length talks]. | ||
| + | |||
| + | If you need a formal invitation letter for your USA VISA application, please contact the ISMB: https://www.iscb.org/ismb2014-registration#visainvitation | ||
| + | |||
| + | == 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:Eagle_logo_2013.jpg|120px|left|Eagle Genomics logo|link=http://www.eaglegenomics.com/]] | ||
| + | |rowspan="2"| | ||
| + | |rowspan="2"| [[File:gigascience-07.png|175px|center|GigaScieece|link=http://www.gigasciencejournal.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"| | ||
| + | |rowspan="2"| [[File:google-logo11w.png|205px|center|Google|link=http://www.google.com/]] | ||
| + | |} | ||
| + | |||
| + | We thank [http://www.eaglegenomics.com/ Eagle Genomics] for sponsoring the BOSC Student Travel Awards again this year, and welcome the open access journal [http://www.gigasciencejournal.com/ GigaScience], and [http://curoverse.com Curoverse] (the team behind the open source platform [http://arvados.org Arvados]) as new sponsors for BOSC 2014. | ||
| + | |||
| + | We are grateful to [http://www.google.com/ Google] for their generous support for videorecording BOSC 2014. | ||
== Session Topics == | == Session Topics == | ||
| − | * 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. | + | * '''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. |
| − | * Software Interoperability -- includes Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together. | + | * '''Software Interoperability''' -- includes Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together. |
| − | * Genome-scale Data and Beyond -- encompasses software and other tools designed for managing, exploring, and analyzing large-scale data to address research questions, such as genome assembly, variant prediction, eQTL analysis, phylogenomics, and epigenetics. | + | * '''Genome-scale Data and Beyond''' -- encompasses software and other tools designed for 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. | + | * '''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 Project Updates -- features 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''' -- features 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. |
| − | * Reproducibility: Rewards and Challenges | + | * '''Panel''': Reproducibility: Rewards and Challenges |
== Keynote Speakers == | == Keynote Speakers == | ||
| − | This year's keynote speakers will be C. Titus Brown (Michigan State University | + | This year's keynote speakers will be Philip Bourne (NIH) and C. Titus Brown (Michigan State University). |
[[BOSC_2014_Keynote_Speakers|More information about BOSC 2014 Keynote Speakers]] | [[BOSC_2014_Keynote_Speakers|More information about BOSC 2014 Keynote Speakers]] | ||
| + | |||
| + | == Submitting Abstracts == | ||
| + | |||
| + | The deadline for submitting abstracts to be considered for full talks was Friday, April 4, 2014. We still have a few spots reserved for last-minute posters--[http://www.open-bio.org/wiki/BOSC_Abstract_Submission submit your abstract here]. | ||
== Organizing Committee == | == Organizing Committee == | ||
| Line 42: | Line 82: | ||
'''Co-Chairs''' | '''Co-Chairs''' | ||
| − | * [http://www.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; James Hutton Institute) | + | * [http://www.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; [http://www.hutton.ac.uk James Hutton Institute]) |
* Nomi L. Harris (Lawrence Berkeley National Laboratory) | * Nomi L. Harris (Lawrence Berkeley National Laboratory) | ||
| Line 54: | Line 94: | ||
* [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] | ||
| Line 61: | Line 101: | ||
* BOSC has been held yearly since 2000. | * BOSC has been held yearly since 2000. | ||
| − | * [[BOSC 2013]] took place in Berlin, Germany, in July 2013. | + | * [[BOSC 2013]] took place in Berlin, Germany, in July 2013. See [https://peerj.com/preprints/83/ Harris et al. (2013) The Bioinformatics Open Source Conference (BOSC) 2013. PeerJ PrePrints 1:e83v1] |
* [[Past BOSC conferences | Information about the first 14 BOSC conferences]] | * [[Past BOSC conferences | Information about the first 14 BOSC conferences]] | ||
== Contact Us == | == Contact Us == | ||
| − | * [ | + | * [https://twitter.com/OBF_BOSC Follow BOSC on Twitter]: @OBF_BOSC, #bosc2014 |
* 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 16:50, 13 April 2017
The 15th Annual Bioinformatics Open Source Conference (BOSC 2014) was held at the Hynes Convention Center in Boston on July 11-12, right before ISMB 2014 as one of the official ISMB SIG satellite meetings. Feedback welcome via email bosc@open-bio.org or @OBF_BOSC on Twitter.
Complete Schedule (with links to posters, slides and videos of the talks)
Media
Storify Tweet archives for Day One, Day Two and during ISMB.
Brad Chapman's blog posts
BioInform article about Philip Bourne's keynote talk (posted with permission)
Important Dates
- July 9-10, 2014: Codefest 2014, Boston, MA
- July 11-12, 2014: BOSC 2014, Boston, MA
- July 12-16, 2014: ISMB 2014, Boston, MA
- September 18-19, 2014: EU-Codefest 2014, Cambridge, UK
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 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 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 #bosc2014.
Registration
Because BOSC is run as a two-day Special Interest Group (SIG) meeting at the annual ISMB conference, registration is via ISMB 2014. You can attend just BOSC, or combine this with attending the full ISMB conference as well.
Note that this year we have waived the BOSC registration fee for student presenters of full-length talks.
If you need a formal invitation letter for your USA VISA application, please contact the ISMB: https://www.iscb.org/ismb2014-registration#visainvitation
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 Eagle Genomics for sponsoring the BOSC Student Travel Awards again this year, and welcome the open access journal GigaScience, and Curoverse (the team behind the open source platform Arvados) as new sponsors for BOSC 2014.
We are grateful to Google for their generous support for videorecording BOSC 2014.
Session Topics
- 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.
- Software Interoperability -- includes Open Source approaches to integrating the latest bioinformatics tools, exploring how we can increase tool connectivity and help communities work better together.
- Genome-scale Data and Beyond -- encompasses software and other tools designed for 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 Project Updates -- features 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: Reproducibility: Rewards and Challenges
Keynote Speakers
This year's keynote speakers will be Philip Bourne (NIH) and C. Titus Brown (Michigan State University).
More information about BOSC 2014 Keynote Speakers
Submitting Abstracts
The deadline for submitting abstracts to be considered for full talks was Friday, April 4, 2014. We still have a few spots reserved for last-minute posters--submit your abstract here.
Organizing Committee
Co-Chairs
- Peter Cock (Biopython developer; James Hutton Institute)
- Nomi L. Harris (Lawrence Berkeley National Laboratory)
Members
- Raoul Jean Pierre Bonnal (Istituto Nazionale Genetica Molecolare (National Institute of Molecular Genetics), Italy)
- Brad Chapman (Biopython developer; Harvard School of Public Health)
- Robert Davey (The Genome Analysis Centre)
- Christopher Fields (National Center for Supercomputing Applications)
- 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 2013 took place in Berlin, Germany, in July 2013. See Harris et al. (2013) The Bioinformatics Open Source Conference (BOSC) 2013. PeerJ PrePrints 1:e83v1
- Information about the first 14 BOSC conferences
Contact Us
- Follow BOSC on Twitter: @OBF_BOSC, #bosc2014
- 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.
