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Difference between revisions of "BOSC 2017"

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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>
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The 18th Annual Bioinformatics Open Source Conference (BOSC 2017) was held '''July 22-23, 2017 in Prague''' as part of the  [https://www.iscb.org/ismbeccb2017 ISMB/ECCB meeting].
  
<div style="float:left; maxwidth: 180px; margin-left:25px; margin-right:15px; background-color: #FFFFFF">[[Image:Pear.png|left|The Bosc Pear]]</div>
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=== Check out the [[BOSC 2017 Schedule]], including [https://docs.google.com/document/d/1pCkjxooRxHhh3mcqxy7h083mUxt2Ldh1N0kJRwNdjx8/edit self-organizing Birds-of-a-feather groups (BOFs)!] ===
  
BOSC 2017 will be held July 24-25, 2017 in Prague as part of the new combined [https://www.iscb.org/ismbeccb2017 ISMB/EECB/COSI meeting] to be held July 21-25, 2017.
+
For 2018, we are trying something different and holding [[BOSC 2018]] along with the Galaxy Community Conference in a new unified event ([https://gccbosc2018.sched.com/ GCC BOSC 2018]), which will take place in Portland, Oregon, June 25-30.  
  
 
== Overview ==
 
== Overview ==
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The Bioinformatics Open Source Conference (BOSC) is organized by the [https://www.open-bio.org/wiki/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. Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.
 
The Bioinformatics Open Source Conference (BOSC) is organized by the [https://www.open-bio.org/wiki/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. Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.
  
We also organize Codefest, a two-day community development session, just before or after BOSC ([[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 [[Codefest]], a two-day community development session, usually just before or after BOSC. 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 2017]] (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=%23BOSC2017 hash tag #bosc2017].
 
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=%23BOSC2017 hash tag #bosc2017].
 +
 +
== Summaries of BOSC 2017 ==
 +
 +
There were lots of [https://twitter.com/search?f=tweets&vertical=default&q=%23BOSC2017 tweets about #BOSC2017] by participants, and a number of blog posts, including:
 +
 +
* Peter Cock's Storify of BOSC tweets: [https://storify.com/pjacock/bosc-2017-day-one Day 1], [https://storify.com/pjacock/bosc-2017-day-two Day 2]
 +
* [https://twitter.com/yoyehudi @yoyehudi]'s writeups. republished by PLOS Comp Biol Field Reports: [https://medium.com/plos-comp-biol-field-reports-2016/bosc-2017-day-1-fbe73f01de2e Day 1], [https://medium.com/plos-comp-biol-field-reports-2016/bosc-2017-day-2-part-1-bosc2017-ismbeccb-9d4d8fda000c Day 2 (Part 1)], [https://medium.com/plos-comp-biol-field-reports-2016/bosc-2017-day-2-part-2-bosc2017-ismbeccb-af4bf4a63a84 Day 2 (Part 2)], [https://medium.com/@yoyehudi/bosc-2017-day-2-part-3-keynote-bosc2017-ismbeccb-5a1598be50c4 Day 2 (part 3)]
 +
* Brad Chapman's summaries (on GitHub, so if you disagree with him, you can submit pull requests): [https://github.com/chapmanb/bcbb/blob/master/posts/conferences/bosc2017_day1a.md Day 1 (morning)], [https://github.com/chapmanb/bcbb/blob/master/posts/conferences/bosc2017_day1b.md Day 1 (afternoon)], [https://github.com/chapmanb/bcbb/blob/master/posts/conferences/bosc2017_day2a.md Day 2 (morning)]
 +
* Recap by Jonathan Sobel (of [http://www.genome.beer/ BeerDeCoded] fame): [https://jonathansobel1.wordpress.com/2017/07/27/bosc-session-of-the-eccbismb-2017/ Jonathan's report]. (Jonathan received an [https://github.com/OBF/obf-docs/blob/master/Travel_fellowships.md OBF Travel Fellowship])
 +
* Robin Andeer's [http://www.robinandeer.com/blog/2017/07/24/Codefest-and-BOSC-2017/ Codefest and BOSC 2017 blog post]
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* Bérénice Batut's [https://www.flickr.com/photos/134305289@N03/35287392054/in/album-72157684042963763/ photos]
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* Neil Saunders' [https://nsaunders.wordpress.com/2017/07/25/twitter-coverage-of-the-bioinformatics-open-source-conference-2017/ BOSC2017 Twitter analysis] and [https://nsaunders.wordpress.com/2017/08/02/twitter-coverage-of-the-ismbeccb-conference-2017/ ISMB/ECCB 2017 Twitter analysis]
  
 
== Important Dates ==
 
== Important Dates ==
* March 1, 2017: [[BOSC_Abstract_Submission|Abstract]] submission portal opens
+
 
* April 13, 2017: Deadline for submitting [[BOSC_Abstract_Submission|abstracts]] for full talks (there will be a later deadline for late-breaking lightning talks and posters)
+
* April 13, 2017: Deadline for [[BOSC_Abstract_Submission|submitting abstracts]] for full talks
* July 21-25: Combined [https://www.iscb.org/ismbeccb2017 ISMB/EECB/COSI meeting]
+
* June 5, 2017: Deadline for submitting abstracts for late-breaking lightning talks and/or late posters (no walk-in posters accepted this year)
* July 24-25, 2017: BOSC 2017, Prague
+
* July 20-21, 2017: [[Codefest 2017]], [https://brmlab.cz/ Brmlab, Prague]  (a non-profit, community-run hackerspace)
* July 26-27, 2017: Codefest 2017, Prague (place TBD)
+
* July 21-25: Combined [https://www.iscb.org/ismbeccb2017 ISMB/ECCB meeting]
 +
* '''July 22-23, 2017: BOSC 2017, Prague'''
  
 
== Session Topics ==
 
== Session Topics ==
We welcome submissions relating to all aspects of bioinformatics and open science software, including (but not limited to):
+
BOSC covers all aspects of bioinformatics and open science software, including (but not limited to):
 
* Open Science and Reproducible Research
 
* Open Science and Reproducible Research
 
* Open Biomedical Data
 
* Open Biomedical Data
* Open Publishing
+
* Citizen/Participatory Science
* Growing and Diversifying Open Source Communities
 
 
* Standards and Interoperability
 
* Standards and Interoperability
 
* Data Science
 
* Data Science
 
* Workflows
 
* Workflows
 
* Visualization
 
* Visualization
* Translational Bioinformatics
+
* Medical and Translational Bioinformatics
 
* Developer Tools and Libraries
 
* Developer Tools and Libraries
 
* Bioinformatics Open Source Project Progress Reports
 
* Bioinformatics Open Source Project Progress Reports
 +
* [[BOSC_2017_Panel|PANEL: Open Data--Standards, Opportunities and Challenges]]
 +
 +
== Keynote Speakers ==
 +
 +
This year's keynote speakers will be Nick Loman (University of Birmingham), a vocal proponent of open genomic data in healthcare who heads the Zibra project, and Madeleine Ball (Open Humans), who is dedicated to opening human health data.
 +
 +
'''[[BOSC_2017_Keynote_Speakers|More information about BOSC 2017 Keynote Speakers]]'''
 +
 +
== Registration ==
 +
 +
To attend BOSC 2017, you need to register for [https://www.iscb.org/ismbeccb2017-registration ISMB/ECCB 2017]. You can register for the full meeting (July 21-25) or just the first two full days (July 22-23).
 +
 +
In the past, BOSC has taken place the two days before ISMB as a Special Interest Group (SIG). This year, ISMB is trying a new structure: the SIGs (now called Communities of Special Interest, or COSIs) are integrated into the main ISMB meeting. BOSC will take place the first two full days of ISMB (July 22-23). BOSC attendees can register for the full ISMB/ECCB meeting (July 21-25) or for just two days (there is no single-day registration option this year). Note that the pricing structure is designed to encourage participants to join ISCB, as this saves you money overall.
 +
 +
If you choose the July 22-23 option, this includes the opening ISMB reception and keynote the evening of July 21. As in past years, you will be able to move freely between all of the COSIs that take place during the days for which you register.
  
 
== 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.
sors.
 
  
We gratefully accept sponsorships from relevant private companies. These sponsorships enable us to offer free registration to some BOSC speakers to help increase diversity at our meeting.
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<center>
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{|
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| [[File:Thehyve-logo-small.png|200px|center|The Hyve logo|link=http://thehyve.nl/]]
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| &nbsp;&nbsp;&nbsp;
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| [[File:MSLLogo_small.png|220px|center|Mozilla Science Lab logo|link=https://science.mozilla.org/]]
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| &nbsp;&nbsp;&nbsp;
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| [[File:Repositive_logo_long.png|220px|center|Repositive Limited logo|link=https://repositive.io/]]
 +
|}
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{|
 +
| &nbsp;&nbsp;&nbsp;
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| [[File:Gigascience-07.png‎|200px|center|GigaScience|link=http://www.gigasciencejournal.com/]]
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| &nbsp;&nbsp;&nbsp;
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| [[File:SB_logo_navy.png‎|220px|center|Seven Bridges|link=https://www.sevenbridges.com/]]
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| &nbsp;&nbsp;&nbsp;
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| [[File:eLife.png‎|200px|center|eLife|link=https://elifesciences.org/labs]]
 +
|}
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</center>
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 +
We are grateful to and welcome [http://thehyve.nl/ The Hyve] (open source solutions for bioinformatics), [https://science.mozilla.org/ Mozilla Science Lab] (a community of researchers, developers, and librarians making research open and accessible), [https://repositive.io/ Repositive Limited] (connecting the genomics community with the data they need), [https://www.sevenbridges.com/ Seven Bridges] (the Biomedical Data Analysis Platform) and [https://elifesciences.org/labs eLife] (cutting-edge technology for cutting-edge research) as new sponsors for BOSC 2017, and [http://gigasciencejournal.com GigaScience] (an open access, open data, open peer-review journal) as a returning sponsor.
  
 
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
 
If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.
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'''Chair'''
 
'''Chair'''
 
 
* Nomi L. Harris (Lawrence Berkeley National Laboratory)
 
* Nomi L. Harris (Lawrence Berkeley National Laboratory)
  
'''Members'''
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'''Co-Chair'''
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* Heather Wiencko ([https://www.hostedgraphite.com Hosted Graphite], Dublin Ireland)
  
 +
'''Organizing Committee Members'''
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* Karsten Hokamp (Smurfit Institute of Genetics, Trinity College Dublin, Ireland)
 
* [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.scri.ac.uk/staff/petercock Peter Cock] ([http://biopython.org Biopython developer]; [http://www.hutton.ac.uk 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])
 
* Christopher Fields (National Center for Supercomputing Applications)
 
* Christopher Fields (National Center for Supercomputing Applications)
 
* Bastian Greshake (OpenSNP)
 
* Bastian Greshake (OpenSNP)
* 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/people/monica-munoz-torres/ Mónica Muñoz-Torres]  ([http://berkeleybop.org/ Berkeley Bioinformatics Open Source Projects])
* Heather Wiencko (PlusVital)
+
 
 +
== Review Committee ==
 +
 
 +
Kai Blin*, Christian Brueffer*, Scott Cain*, Jacqueline Campbell, Brad Chapman*, John Chilton, Peter Cock*, Karen Cranston, Anamaria Crisan, Michael Crusoe, Philip Ewels, Christopher Fields*, Konrad Förstner*, George Githinji, Bastian Greshake*, Björn Grüning, Nomi Harris*, Michael Heuer*, Karsten Hokamp*, Hans-Rudolf Hotz*, Shaun Jackman, Hilmar Lapp, Jessica Maia, Scott Markel*, Hervé Ménager, Monica Munoz-Torres, Frank Nothaft, Konstantin Okonechnikov, Kieran O'Neill*, Lorena Pantano*, Michael Reich, Surya Saha*, Gianluca Della Vedova*, Heather Wiencko*, Jason Williams
 +
 
 +
&lowast; Also reviewed Late-Breaking Lightning Talk abstracts
  
 
== Previous BOSCs ==
 
== Previous BOSCs ==
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* BOSC has been held yearly since 2000.
 
* BOSC has been held yearly since 2000.
 
* [[BOSC 2016]] took place July 8-9, 2016 in Orlando, Florida, right before ISMB 2016.
 
* [[BOSC 2016]] took place July 8-9, 2016 in Orlando, Florida, right before ISMB 2016.
** 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].
+
** Check out the complete [[BOSC_2016_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].
+
** Read the [https://f1000research.com/articles/5-2464/v1 BOSC 2016 Summary Report], also on F1000.
* [[Past BOSC conferences | Information about the first 15 BOSC conferences]]
+
 
 +
* [[Past BOSC conferences | Information about the first 17 BOSC conferences]]
  
 
== Contact Us ==
 
== Contact Us ==
  
 
* [https://twitter.com/OBF_BOSC Follow BOSC on Twitter]: @OBF_BOSC, #bosc2017
 
* [https://twitter.com/OBF_BOSC Follow BOSC on Twitter]: @OBF_BOSC, #bosc2017
* 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 [http://lists.open-bio.org/mailman/listinfo/bosc-announce bosc-announce].  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 20:51, 27 January 2018

The Bosc Pear

The 18th Annual Bioinformatics Open Source Conference (BOSC 2017) was held July 22-23, 2017 in Prague as part of the ISMB/ECCB meeting.

Check out the BOSC 2017 Schedule, including self-organizing Birds-of-a-feather groups (BOFs)!

For 2018, we are trying something different and holding BOSC 2018 along with the Galaxy Community Conference in a new unified event (GCC BOSC 2018), which will take place in Portland, Oregon, June 25-30.

Overview

The Bioinformatics Open Source Conference (BOSC) 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. Since its inception in 2000, BOSC has provided a forum for developers and users to interact and share research results and ideas in open source bioinformatics. BOSC’s broad spectrum of topics includes practical techniques for solving bioinformatics problems; software development practices; standards and ontologies; approaches that promote open science and sharing of data, results and software; and ways to grow open source communities while promoting diversity within them.

We also organize a Codefest, a two-day community development session, usually just before or after BOSC. 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 2017 (whether or not you attend BOSC).

Please spread the word about BOSC--all are welcome. On Twitter, follow @OBF_BOSC and use hash tag #bosc2017.

Summaries of BOSC 2017

There were lots of tweets about #BOSC2017 by participants, and a number of blog posts, including:

Important Dates

  • April 13, 2017: Deadline for submitting abstracts for full talks
  • June 5, 2017: Deadline for submitting abstracts for late-breaking lightning talks and/or late posters (no walk-in posters accepted this year)
  • July 20-21, 2017: Codefest 2017, Brmlab, Prague (a non-profit, community-run hackerspace)
  • July 21-25: Combined ISMB/ECCB meeting
  • July 22-23, 2017: BOSC 2017, Prague

Session Topics

BOSC covers all aspects of bioinformatics and open science software, including (but not limited to):

  • Open Science and Reproducible Research
  • Open Biomedical Data
  • Citizen/Participatory Science
  • Standards and Interoperability
  • Data Science
  • Workflows
  • Visualization
  • Medical and Translational Bioinformatics
  • Developer Tools and Libraries
  • Bioinformatics Open Source Project Progress Reports
  • PANEL: Open Data--Standards, Opportunities and Challenges

Keynote Speakers

This year's keynote speakers will be Nick Loman (University of Birmingham), a vocal proponent of open genomic data in healthcare who heads the Zibra project, and Madeleine Ball (Open Humans), who is dedicated to opening human health data.

More information about BOSC 2017 Keynote Speakers

Registration

To attend BOSC 2017, you need to register for ISMB/ECCB 2017. You can register for the full meeting (July 21-25) or just the first two full days (July 22-23).

In the past, BOSC has taken place the two days before ISMB as a Special Interest Group (SIG). This year, ISMB is trying a new structure: the SIGs (now called Communities of Special Interest, or COSIs) are integrated into the main ISMB meeting. BOSC will take place the first two full days of ISMB (July 22-23). BOSC attendees can register for the full ISMB/ECCB meeting (July 21-25) or for just two days (there is no single-day registration option this year). Note that the pricing structure is designed to encourage participants to join ISCB, as this saves you money overall.

If you choose the July 22-23 option, this includes the opening ISMB reception and keynote the evening of July 21. As in past years, you will be able to move freely between all of the COSIs that take place during the days for which you register.

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.

The Hyve logo
   
Mozilla Science Lab logo
   
Repositive Limited logo
   
GigaScience
   
Seven Bridges
   
eLife

We are grateful to and welcome The Hyve (open source solutions for bioinformatics), Mozilla Science Lab (a community of researchers, developers, and librarians making research open and accessible), Repositive Limited (connecting the genomics community with the data they need), Seven Bridges (the Biomedical Data Analysis Platform) and eLife (cutting-edge technology for cutting-edge research) as new sponsors for BOSC 2017, and GigaScience (an open access, open data, open peer-review journal) as a returning sponsor.

If you would like to be a sponsor of BOSC, please contact us at bosc@open-bio.org.

Organizing Committee

Chair

  • Nomi L. Harris (Lawrence Berkeley National Laboratory)

Co-Chair

Organizing Committee Members

Review Committee

Kai Blin*, Christian Brueffer*, Scott Cain*, Jacqueline Campbell, Brad Chapman*, John Chilton, Peter Cock*, Karen Cranston, Anamaria Crisan, Michael Crusoe, Philip Ewels, Christopher Fields*, Konrad Förstner*, George Githinji, Bastian Greshake*, Björn Grüning, Nomi Harris*, Michael Heuer*, Karsten Hokamp*, Hans-Rudolf Hotz*, Shaun Jackman, Hilmar Lapp, Jessica Maia, Scott Markel*, Hervé Ménager, Monica Munoz-Torres, Frank Nothaft, Konstantin Okonechnikov, Kieran O'Neill*, Lorena Pantano*, Michael Reich, Surya Saha*, Gianluca Della Vedova*, Heather Wiencko*, Jason Williams

∗ Also reviewed Late-Breaking Lightning Talk abstracts

Previous BOSCs

Contact Us

  • Follow BOSC on Twitter: @OBF_BOSC, #bosc2017
  • If you'd like to join the mailing list for BOSC-related announcements, including the call for abstracts and deadline reminders, please subscribe to bosc-announce. 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.