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Difference between revisions of "BOSC 2015 Schedule"

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'''Bioinformatics Open Source Conference (BOSC) 2015'''
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__NOTOC__
 +
[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2015]]
  
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[[Image:media/image1.png]]A Special Interest Group (SIG) meeting at ISMB/ECCB 2015
+
This page has links to all the publicly available talk slides, videos and posters. Most of the slides and posters are on our [http://f1000research.com/channels/BOSC BOSC F1000 Research Channel] (others are on SlideShare and FigShare), while the videos are on the [https://www.youtube.com/playlist?list=PLir-OOQiOhXbENjAIFF-JZ0WodnysPqfh BOSC 2015 YouTube playlist].
  
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Dublin, Ireland
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The full program including abstracts is available [http://www.open-bio.org/bosc2015/BOSC2015-program-with-abstracts.pdf here]. The PDF of this schedule (without abstracts) is available [http://www.open-bio.org/w/images/2/2c/BOSC2015-schedule.pdf here].
  
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July 10-11, 2015
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== Sponsors ==
  
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''http://www.open-bio.org/wiki/BOSC_2015''
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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 welcome [http://bina.com/ Bina] as our newest sponsor.
 +
{|
 +
|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]]
 +
|-
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| [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]]
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|rowspan="2"| [[File:Gigascience-07.png‎|200px|left|GigaScience|link=http://www.gigasciencejournal.com/]]
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|rowspan="2"| [[File:Bina_logo.png‎|200px|left|Bina|link=http://www.bina.com/]]
 +
|}
  
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BOSC is organized by the Open Bioinformatics Foundation (OBF, www.open-bio.org). The OBF is a non-profit group that promotes the practice and philosophy of Open Source software development and Open Science in the biological research community.
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== Pre-BOSC: Codefest 2015  ==
  
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{|
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See [[Codefest 2015]] for details, report given at the start of BOSC day two ([http://f1000research.com/slides/4-493 slides], [http://youtu.be/Mt5lUSPzg18 video]).
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!
 
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![[Image:media/image2.png]]
 
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![[Image:media/image3.png]][[Image:media/image4.png]]
 
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![[Image:media/image5.png]]
 
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|}
 
  
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'''Schedule for Day 1 (Friday, 10 July, 2015)'''
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== BOSC Day 1 (Friday, 10 July, 2015) ==
  
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{|
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{| border="1" cellspacing="0" cellpadding="7"
 +
|- style="background:#D8F781"
 
!'''Time'''
 
!'''Time'''
 
!'''Title'''
 
!'''Title'''
−
!'''Speaker / Chair'''
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!'''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|7:30-9:00
 
|7:30-9:00
Line 32: Line 39:
 
|'''Introduction and Welcome'''
 
|'''Introduction and Welcome'''
 
|Nomi Harris and Peter Cock (Co-Chairs, BOSC 2015)
 
|Nomi Harris and Peter Cock (Co-Chairs, BOSC 2015)
−
|-
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|- style="background:#EFFBFB"
 
|9:15-10:15
 
|9:15-10:15
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|'''Keynote:''' '''Bioinformatics: Still a scary world for biologists'''
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|'''Keynote:''' '''Bioinformatics: Still a scary world for biologists''' ([http://figshare.com/articles/Bioinformatics_Still_a_scary_world_for_biologists/1478786 slides], [http://youtu.be/dfCU4hZK2JA video])
 
|Holly Bik
 
|Holly Bik
−
|-
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|- style="background:#FAF4EE"
 
|10:15-10:45
 
|10:15-10:45
 
|'''''Coffee Break'''''
 
|'''''Coffee Break'''''
 
|
 
|
−
|-
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|- style="background:#E6E6E6"
 
|10:45-12:30
 
|10:45-12:30
 
|'''Session: Data Science'''
 
|'''Session: Data Science'''
−
|Chair:
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|Chair: Rob Davey
 
|-
 
|-
 
|10:45- 11:02
 
|10:45- 11:02
−
|Apollo: Scalable & collaborative curation for improved comparative genomics
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|Apollo: Scalable & collaborative curation for improved comparative genomics ([http://youtu.be/R1HQskEw_p4 video])
−
|Mónica Muñoz-Torres
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|Mónica Muñoz-Torres [P1]
 
|-
 
|-
 
|11:02-11:19
 
|11:02-11:19
−
|GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised clustering of gene expression data
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|GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data ([http://f1000research.com/slides/4-248 slides], [http://f1000research.com/posters/4-247 poster], [http://youtu.be/Ih8I-WbdvTg video])
−
|Kévin Rue-Albrecht
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|Kévin Rue-Albrecht [P2]
 
|-
 
|-
 
|11:19-11:36
 
|11:19-11:36
−
|Arvados: A Free Software Platform for Big Data Science
+
|Arvados: A Free Software Platform for Big Data Science ([http://f1000research.com/slides/4-364 slides], [http://youtu.be/NjvjTpdn_so video])
 
|Peter Amstutz
 
|Peter Amstutz
 
|-
 
|-
 
|11:36-11:53
 
|11:36-11:53
−
|Bringing Hadoop into Bioinformatics with Cloudgene and CloudMan
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|Bringing Hadoop into Bioinformatics with Cloudgene and CloudMan ([http://f1000research.com/slides/4-300 slides], [http://youtu.be/Eu4AHr3Rg98 video])
 
|Sebastian Schoenherr
 
|Sebastian Schoenherr
 
|-
 
|-
 
|11:53-12:10
 
|11:53-12:10
−
|Segway: semi-automated genome annotation
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|Segway: semi-automated genome annotation ([http://youtu.be/-GOML8D9iWk video])
−
|Michael Hoffman
+
|Michael Hoffman [P3]
 
|-
 
|-
 
|12:10-12:15
 
|12:10-12:15
−
|QualiMap 2.0: quality control of high throughput sequencing data
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|QualiMap 2.0: quality control of high throughput sequencing data ([http://f1000research.com/slides/4-378 slides], [http://youtu.be/UR_9npHP_yM video], [http://f1000research.com/posters/4-431 poster])
−
|Konstantin Okonechnikov
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|Konstantin Okonechnikov [P4]
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
−
|A Genomics Virtual Laboratory
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|A Genomics Virtual Laboratory ([http://f1000research.com/slides/4-374 slides], [http://youtu.be/ktotH6a_sSo video])
−
|Andrew Lonie
+
|Andrew Lonie [P5]
 
|-
 
|-
 
|12:20-12:25
 
|12:20-12:25
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|BioSolr: Building better search for bioinformatics
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|BioSolr: Building better search for bioinformatics ([http://f1000research.com/slides/4-492 slides], [http://youtu.be/hl3NFE0-UUo video], [http://f1000research.com/posters/4-491 poster])
−
|Tony Burdett
+
|Tony Burdett [P6]
 
|-
 
|-
 
|12:25-12:30
 
|12:25-12:30
−
|Prioritization of structural variants based on known biological information
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|Prioritization of structural variants based on known biological information ([http://f1000research.com/slides/4-280 slides], [http://youtu.be/JZnF_6UnajY video])
 
|Brad Chapman
 
|Brad Chapman
−
|-
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|- style="background:#F7F8E0"
 
|12:30-13:30
 
|12:30-13:30
 
|'''''Lunch'''''
 
|'''''Lunch'''''
Line 86: Line 93:
 
|-
 
|-
 
|13:00-14:00
 
|13:00-14:00
−
|'''Poster Session and Birds of a Feather''' (overlapping with lunch)
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|'''Poster Session and [https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# Birds of a Feather sessions]''' (overlapping with lunch)
 
|
 
|
−
|-
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|- style="background:#E6E6E6"
 
|14:00-15:30
 
|14:00-15:30
 
|'''Session: Standards and Interoperability'''
 
|'''Session: Standards and Interoperability'''
−
|Chair:
+
|Chair: Peter Cock
 
|-
 
|-
 
|14:00-14:17
 
|14:00-14:17
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|Portable workflow and tool descriptions with the CWL
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|Portable workflow and tool descriptions with the CWL (Common Workflow Language) ([http://f1000research.com/slides/4-278 slides], [http://youtu.be/sF4DJVUcjnU video])
−
|Michael R. Crusoe
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|Michael R. Crusoe [<del>P7</del>]
 
|-
 
|-
 
|14:17-14:34
 
|14:17-14:34
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|From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences
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|From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences ([http://f1000research.com/slides/5-220 slides], [http://www.slideshare.net/agbeltran/from-peerreviewed-to-peerreproduced-a-role-for-research-objects-in-scholarly-publishing-in-the-life-sciences alt. slides], [http://youtu.be/brZQZrneuD0 video])
 
|Alejandra Gonzalez-Beltran
 
|Alejandra Gonzalez-Beltran
 
|-
 
|-
 
|14:34-14:51
 
|14:34-14:51
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|Demystifying the Interoperability of Disparate Genomic Resources
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|Demystifying the Interoperability of Disparate Genomic Resources ([http://f1000research.com/slides/4-372 slides], [http://youtu.be/PbVqVlNtFOo video])
 
|Daniel Blankenberg
 
|Daniel Blankenberg
 
|-
 
|-
 
|14:51-15:08
 
|14:51-15:08
−
|Increasing the utility of Galaxy workflows
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|Increasing the utility of Galaxy workflows ([http://f1000research.com/slides/4-399 slides], [http://youtu.be/4ETL81P6p_g video])
 
|John Chilton
 
|John Chilton
 
|-
 
|-
 
|15:10-15:15
 
|15:10-15:15
−
|Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers
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|Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers ([http://f1000research.com/slides/4-496 slides], [http://youtu.be/d4hh2OtpX5E video])
 
|Damion Dooley
 
|Damion Dooley
 
|-
 
|-
 
|15:15-15:20
 
|15:15-15:20
−
|Evolution of the Galaxy tool ecosystem - happier developers, happier users
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|Evolution of the Galaxy tool ecosystem - happier developers, happier users ([http://f1000research.com/slides/4-521 slides], [http://youtu.be/APYzQWg0nrs video])
−
|Martin Čech
+
|Martin Čech [P8]
 
|-
 
|-
 
|15:20-15:25
 
|15:20-15:25
−
|Bionode - Modular and universal bioinformatics
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|Bionode - Modular and universal bioinformatics ([http://f1000research.com/slides/4-288 slides], [http://youtu.be/_CNlpNxkP-k video])
−
|Bruno Vieira
+
|Bruno Vieira [<del>P9</del>]
 
|-
 
|-
 
|15:25-15:30
 
|15:25-15:30
−
|The EDAM Ontology
+
|The EDAM Ontology ([http://f1000research.com/slides/4-359 slides], [http://youtu.be/gsRWyfaYTPE video], [http://f1000research.com/posters/4-227 poster])
−
|Hervé Ménager
+
|Hervé Ménager [P10]
−
|-
+
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
 
|'''''Coffee Break'''''
 
|'''''Coffee Break'''''
 
|
 
|
−
|-
+
|- style="background:#EFFBFB"
 
|16:00-17:00
 
|16:00-17:00
−
|'''Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community'''
+
|'''[[BOSC_2015_Panel|Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community]]'''
 
|'''''Moderator''''': Mónica Muñoz-Torres
 
|'''''Moderator''''': Mónica Muñoz-Torres
  
−
'''''Panelists''''': Holly Bik, Michael Crusoe, Aleksandra Pawlik, Jason Williams
+
'''''Panelists''''': Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams
 
|-
 
|-
 
|17:00-17:10
 
|17:00-17:10
−
|Open Bioinformatics Foundation (OBF) Update
+
|Open Bioinformatics Foundation (OBF) Update ([http://obf.github.io/obf-docs/OBF-Address-BOSC2015/ slides])
 
|Hilmar Lapp (President, OBF)
 
|Hilmar Lapp (President, OBF)
 
|-
 
|-
Line 144: Line 151:
 
|-
 
|-
 
|17:15-18:30
 
|17:15-18:30
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|BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 1)
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|BOF/Unconference: [http://www.hub-hub.de/wiki/index.php?title=BOSC2015Unconf Building successful open-source bioinformatics developer communities] (Part 1; introduction [http://youtu.be/u5O1eG0GDnE video])
 
|Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
 
|Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
 
|-
 
|-
 
|17:15-18:30
 
|17:15-18:30
−
|'''BOFs'''
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|'''[https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# BOFs]''': Feel free to organize one!
 
|
 
|
 
|-
 
|-
 
|19:00-
 
|19:00-
−
|Pay-your-own-way BOSC dinner, Kennedy’s [link]
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|Pay-your-own-way BOSC dinner at Kennedy's (FULL)
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|RSVP at [[bit.ly/BOSC2015-dinner|bit.ly/BOSC2015-dinner ]] (limited space --you must RSVP to attend)
+
|[http://doodle.com/mcqehfpytzutwzum RSVP] (limited space --you must RSVP to attend)
 
|}
 
|}
  
−
'''Schedule for Day 2 (Saturday, 11 July, 2015)'''
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== BOSC Day 2 (Saturday, 11 July, 2015) ==
  
−
{|
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{| border="1" cellspacing="0" cellpadding="7"
 +
|- style="background:#D8F781"
 
!'''Time'''
 
!'''Time'''
 
!'''Title'''
 
!'''Title'''
−
!'''Speaker or'''
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!'''Speaker / Chair'''
−
 
 
−
'''Session Chair'''
 
 
|-
 
|-
 
|9:00-9:05
 
|9:00-9:05
Line 170: Line 176:
 
|-
 
|-
 
|9:05-9:15
 
|9:05-9:15
−
|Codefest 2015 Report
+
|Codefest 2015 Report ([http://f1000research.com/slides/4-493 slides], [http://youtu.be/Mt5lUSPzg18 video])
 
|Brad Chapman (Codefest 2015 Organizer)
 
|Brad Chapman (Codefest 2015 Organizer)
−
|-
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|- style="background:#EFFBFB"
 
|9:15-10:15
 
|9:15-10:15
−
|'''Keynote:''' '''Big Data in Biology'''
+
|'''Keynote:''' '''Big Data in Biology''' ([http://f1000research.com/slides/4-408 slides], [http://youtu.be/acV5qUcIFdo video])
 
|Ewan Birney
 
|Ewan Birney
−
|-
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|- style="background:#FAF4EE"
 
|10:15-10:45
 
|10:15-10:45
 
|'''''Coffee Break'''''
 
|'''''Coffee Break'''''
 
|
 
|
−
|-
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|- style="background:#E6E6E6"
 
|10:45-12:30
 
|10:45-12:30
 
|'''Session: Open Science''' '''and Reproducibility'''
 
|'''Session: Open Science''' '''and Reproducibility'''
−
|Chair:
+
|Chair: Mónica Muñoz-Torres
 
|-
 
|-
 
|10:45-11:02
 
|10:45-11:02
−
|A curriculum for teaching Reproducible Computational Science bootcamps
+
|A curriculum for teaching Reproducible Computational Science bootcamps ([http://reproducible-science-curriculum.github.io/bosc2015/#/ slides], [http://dx.doi.org/10.5281/zenodo.20765 source], [http://youtu.be/omBx1L5pt4w video])
 
|Hilmar Lapp
 
|Hilmar Lapp
 
|-
 
|-
 
|11:02-11:19
 
|11:02-11:19
−
|Research shared: www.researchobject.org
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|Research shared: www.researchobject.org ([http://www.slideshare.net/NormanMorrison2/researchobject-bosc-2015-v2 slides], [http://youtu.be/D6TzbK7FBBM video])
−
|Norman Morrison
+
|Norman Morrison [<del>P11</del>]
 
|-
 
|-
 
|11:19-11:36
 
|11:19-11:36
−
|Nextflow: a tool for deploying reproducible computational pipelines
+
|Nextflow: a tool for deploying reproducible computational pipelines ([http://speakerdeck.com/pditommaso/nextflow-a-tool-for-deploying-reproducible-computational-pipelines slides], [http://youtu.be/hW3-ziwugnc video], [http://f1000research.com/posters/4-430 poster])
−
|Paolo Di Tommaso
+
|Paolo Di Tommaso [P12]
 
|-
 
|-
 
|11:36-11:53
 
|11:36-11:53
−
|Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science
+
|Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science ([http://github.com/johnfonner/presentations/blob/master/FreeBeerToday-iPlantAgaveDocker.pdf slides], [http://youtu.be/jluojupYKU8 video], [http://f1000research.com/posters/4-454 poster])
−
|John Fonner
+
|John Fonner [P13]
 
|-
 
|-
−
|11:55
+
|11:55-12:00
−
|The 500 builds of 300 applications in the HeLmod repository will at least get you started on a full suite of scientific applications
+
|The 500 builds of 300 applications in the HeLmod repository will at least get you started on a full suite of scientific applications ([http://f1000research.com/slides/4-366 slides], [http://youtu.be/_WOfKzS1HtA video])
 
|Aaron Kitzmiller
 
|Aaron Kitzmiller
 
|-
 
|-
−
|12:00
+
|12:00-12:05
−
|Bioboxes: Standardised bioinformatics tools using Docker containers.
+
|Bioboxes: Standardised bioinformatics tools using Docker containers. ([http://f1000research.com/slides/4-404 slides], [http://f1000research.com/posters/4-405 poster])
−
|Peter Belmann
+
|Peter Belmann [P14]
 
|-
 
|-
−
|12:05
+
|12:05-12:10
−
|The perfect fit for reproducible interactive research: Galaxy, Docker, IPython
+
|The perfect fit for reproducible interactive research: Galaxy, Docker, IPython ([http://youtu.be/S2DKQRcHY4s video])
 
|Björn Grüning
 
|Björn Grüning
 
|-
 
|-
−
|12:10
+
|12:10-12:15
−
|COPO: Bridging the Gap from Data to Publication in Plant Science
+
|COPO: Bridging the Gap from Data to Publication in Plant Science ([http://f1000research.com/slides/4-360 slides], [http://youtu.be/4YzTta6vgX8 video], [http://figshare.com/articles/Poster_Presented_at_BOSC_2015/1483428 poster])
−
|Robert Davey
+
|Robert Davey [P15]
 
|-
 
|-
−
|12:15
+
|12:15-12:20
−
|ELIXIR UK building on Data and Software Carpentry to address the challenges in computational training for life scientists
+
|ELIXIR UK building on Data and Software Carpentry to address the challenges in computational training for life scientists ([http://f1000research.com/slides/4-593 slides], [http://youtu.be/eleqMgHvUwM video])
−
|Aleksandra Pawlik
+
|Aleksandra Pawlik [P16]
 
|-
 
|-
−
|12:20
+
|12:20-12:25
−
|Parallel recipes: towards a common coordination language for scientific workflow management systems
+
|Parallel recipes: towards a common coordination language for scientific workflow management systems ([http://f1000research.com/slides/4-333 slides], [http://youtu.be/WJ0uPlrgP2M video])
−
|Yves Vandriessche
+
|Yves Vandriessche [P17]
−
|-
 
−
|12:25
 
−
|openSNP - personal genomics and the public domain
 
−
|Bastian Greshake
 
 
|-
 
|-
 +
|12:25-12:30
 +
|openSNP - personal genomics and the public domain ([http://figshare.com/articles/openSNP_BOSC15_Slides/1480397 slides], [http://youtu.be/HJwHGMdtIkk video], [http://f1000research.com/posters/4-284 poster], [http://figshare.com/articles/openSNP_BOSC15_Poster/1466880 poster])
 +
|Bastian Greshake [P18]
 +
|- style="background:#F7F8E0"
 
|12:30-13:30
 
|12:30-13:30
 
|'''''Lunch'''''
 
|'''''Lunch'''''
Line 234: Line 240:
 
|-
 
|-
 
|13:00-14:00
 
|13:00-14:00
−
|'''Poster Session and BOFs (overlapping with lunch)'''
+
|'''Poster Session and [https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# BOFs] (overlapping with lunch)'''
 
|
 
|
−
|-
+
|- style="background:#E6E6E6"
 
|14:00-14:40
 
|14:00-14:40
 
|'''Session: Translational Bioinformatics'''
 
|'''Session: Translational Bioinformatics'''
Line 242: Line 248:
 
|-
 
|-
 
|14:00-14:17
 
|14:00-14:17
−
|CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer
+
|CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer ([http://f1000research.com/slides/4-277 slides], [http://youtu.be/-d6mjtzwwrA video], [http://f1000research.com/posters/4-276 poster])
−
|Malachi Griffith
+
|Malachi Griffith [P19]
 
|-
 
|-
 
|14:17-14:34
 
|14:17-14:34
−
|From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep &amp; Omics Pipe
+
|From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep &amp; Omics Pipe ([http://youtu.be/K8vBlEa6JmU video], [http://f1000research.com/posters/4-275 poster])
−
|Tobias Meissner
+
|Tobias Meissner [P20]
 
|-
 
|-
 
|14:35-14:40
 
|14:35-14:40
−
|Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute
+
|Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute ([http://f1000research.com/slides/4-498 slides], [http://youtu.be/TuBCuIrsLu0 video], [http://f1000research.com/posters/4-444 poster])
−
|Ishwar Chandramouliswaran
+
|Ishwar Chandramouliswaran [P21]
−
|-
+
|- style="background:#E6E6E6"
 
|14:40-15:30
 
|14:40-15:30
 
|'''Session: Bioinformatics Open Source Project Updates'''
 
|'''Session: Bioinformatics Open Source Project Updates'''
−
|Chair:
+
|Chair: Nomi Harris
 
|-
 
|-
 
|14:40-14:57
 
|14:40-14:57
−
|Biopython Project Update 2015
+
|Biopython Project Update 2015 ([http://f1000research.com/slides/4-279 slides], [http://youtu.be/s5HDZHTxxIg video])
 
|João Rodrigues
 
|João Rodrigues
 
|-
 
|-
 
|14:57-15:14
 
|14:57-15:14
−
|The biogems community: Challenges in distributed software development in bioinformatics
+
|Biogems: Challenges in distributed software development in bioinformatics ([http://f1000research.com/slides/4-282 slides], [http://youtu.be/z1aHjhi2eHI video])
−
|George Githinji
+
|George Githinji and Pjotr Prins 
 
|-
 
|-
 
|15:14-15:31
 
|15:14-15:31
−
|Apache Taverna: Sustaining research software at the Apache Software Foundation
+
|Apache Taverna: Sustaining research software at the Apache Software Foundation ([http://www.slideshare.net/soilandreyes/20150711-bosc2015apachetaverna slides], [http://youtu.be/y-ct1k3AXCM video])
−
|Stian Soiland-Reyes
+
|Stian Soiland-Reyes [<del>P22</del>]
−
|-
+
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
 
|'''''Coffee Break'''''
 
|'''''Coffee Break'''''
 
|
 
|
−
|-
+
|- style="background:#E6E6E6"
 
|16:00-16:30
 
|16:00-16:30
 
|'''Session: Visualization'''
 
|'''Session: Visualization'''
−
|Chair:
+
|Chair: Karsten Hokamp
 
|-
 
|-
 
|16:00-16:17
 
|16:00-16:17
−
|Simple, Shareable, Online RNA Secondary Structure Diagrams
+
|Simple, Shareable, Online RNA Secondary Structure Diagrams ([http://f1000research.com/slides/4-286 slides], [http://www.tbi.univie.ac.at/~pkerp/bosc-2015/ slides])
−
|Stefan Hammer
+
|Peter Kerpedjiev
 
|-
 
|-
 
|16:17-16:22
 
|16:17-16:22
−
|BioJS 2.0: an open source standard for biological visualization
+
|BioJS 2.0: an open source standard for biological visualization ([http://f1000research.com/slides/4-379 slides], [http://youtu.be/VNMu7xetnI4 video])
−
|Guy Yachdav
+
|Guy Yachdav [P23]
 
|-
 
|-
 
|16:22-16:27
 
|16:22-16:27
−
|Visualising Open PHACTS linked data with widgets
+
|Visualising Open PHACTS linked data with widgets ([http://f1000research.com/slides/4-363 slides], [http://youtu.be/PUngTgUOT_Y video])
−
|Ian Dunlop
+
|Ian Dunlop [P24]
−
|-
+
|- style="background:#E6E6E6"
 
|16:30-17:00
 
|16:30-17:00
 
|'''Session: Late-Breaking Lightning Talks'''
 
|'''Session: Late-Breaking Lightning Talks'''
−
|
+
|Chair: Hilmar Lapp
 
|-
 
|-
−
|16:30
+
|16:30-16:35
−
|Biospectra-by-sequencing genetic analysis platform
+
|Biospectra-by-sequencing genetic analysis platform ([http://f1000research.com/slides/4-464 slides], [http://youtu.be/CgsdMizr1N8 video], [http://f1000research.com/posters/4-463 poster])
−
|Aurelie Laugraud
+
|Aurelie Laugraud [P25]
 
|-
 
|-
−
|16:35
+
|16:35-16:40
−
|
+
|PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities ([http://f1000research.com/slides/4-558 slides], [http://youtu.be/tlCnPw-XCIU video])
−
|
+
|Shareef Dabdoub
 
|-
 
|-
−
|16:40
+
|16:40-16:45
−
|
+
|Otter/ZMap/SeqTools: A productive alternative to web browser genome visualisation
−
|
+
|Gemma Guest [P26]
 
|-
 
|-
−
|16:45
+
|16:45-16:50
−
|
+
|BioaRchive: enabling reproducibility of Bioconductor package versions ([http://f1000research.com/slides/4-369 slides], [http://youtu.be/SVSLcl0JVhI video], [http://f1000research.com/posters/4-370 poster])
−
|
+
|Nitesh Turaga [P27]
 
|-
 
|-
−
|16:50
+
|16:50-16:55
−
|
+
|Developing an Arvados BWA-GATK pipeline ([http://f1000research.com/slides/4-283 slides], [http://youtu.be/DjxZmQNpuTc video], [http://f1000research.com/posters/4-281 poster])
−
|
+
|Pjotr Prins [P28]
 
|-
 
|-
−
|16:55
+
|16:55-17:00
−
|
+
|Out of the box cloud solution for Next-Generation Sequencing analysis ([http://f1000research.com/slides/4-357 slides], [http://youtu.be/5gq9GOCxHfA video])
−
|
+
|Freerk van Dijk [P29]
 
|-
 
|-
 
|17:00-17:10
 
|17:00-17:10
Line 322: Line 328:
 
|-
 
|-
 
|17:15-18:30
 
|17:15-18:30
−
|BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 2)
+
|BOF/Unconference: [http://www.hub-hub.de/wiki/index.php?title=BOSC2015Unconf Building successful open-source bioinformatics developer communities] (Part 2)
 
|Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
 
|Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
 
|-
 
|-
 
|17:10-18:10
 
|17:10-18:10
−
|'''BOFs'''
+
|'''[https://docs.google.com/document/d/1yaSjWEZzwiAk6jUiKVk_pbmru1uCJuGbgITIyI3kmfI/edit# BOFs]''': Feel free to organize one!
 +
|
 +
|-
 +
|19:00
 +
| Pay-your-own-way dinner at the Workshop Gastropub. RSVP [http://doodle.com/v2p89ytinbb9d9xa here] if you want to join us.
 
|
 
|
 
|}
 
|}
  
−
''Any last-minute schedule updates will be posted at''
+
=== Posters ===
  
−
''http://www.open-bio.org/wiki/BOSC_2015_Schedule''
+
If the speaker also has a talk, the poster link will be above (posters 1 to 29). This table lists poster-only presentations.
  
−
'''BOSC 2015 Organizing Committee:'''
+
{| border="1" cellspacing="0" cellpadding="7"
 +
|- style="background:#D8F781"
 +
! Poster
 +
! Title
 +
! Presenter
 +
|-
 +
| P30
 +
| [http://f1000research.com/posters/4-186 Aequatus: Visualising complex similarity relationships among species]
 +
| Anil Thanki
 +
|-
 +
| P31
 +
| MOLGENIS Workbench for Systems Medicine
 +
| K. Joeri van der Velde
 +
|-
 +
| P32
 +
| SPINGO: a rapid species-classifier for microbial amplicon sequences
 +
| Feargal Ryan
 +
|-
 +
| P33
 +
| ANNOgesic - A computational pipeline for RNA-Seq based transcriptome annotations of bacteria
 +
| Sung-Huan Yu
 +
|-
 +
| P34
 +
| [http://f1000research.com/posters/4-425 BioXSD — a data model for sequences, alignments, features, measured and inferred values]
 +
| Matúš Kalaš
 +
|-
 +
| P35
 +
| [http://dx.doi.org/10.6084/m9.figshare.1269288 MGkit: A Metagenomic Framework For The Study Of Microbial Communities]
 +
| Francesco Rubino
 +
|-
 +
| P36
 +
| From scaffold to submission in a day: a new software pipeline for rapid genome annotation and analysis
 +
| Sascha Steinbiss
 +
|-
 +
|}
 +
 
 +
<br>
 +
 
 +
== BOSC 2015 Organizing Committee ==
  
 
'''Nomi Harris''' and '''Peter Cock''' (Co-Chairs)
 
'''Nomi Harris''' and '''Peter Cock''' (Co-Chairs)
Line 340: Line 388:
 
Brad Chapman, Rob Davey, Chris Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres
 
Brad Chapman, Rob Davey, Chris Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres
  
−
'''BOSC 2015 Program Committee:''' Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Mónica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antão, 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
+
== BOSC 2015 Program Committee ==
 +
 
 +
Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Mónica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antão, 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
  
 
BOSC is a community effort—we thank all those who made it possible, including the organizing committee, the program committee, the session chairs, our sponsors, and the ISMB SIG chair, Steven Leard.
 
BOSC is a community effort—we thank all those who made it possible, including the organizing committee, the program committee, the session chairs, our sponsors, and the ISMB SIG chair, Steven Leard.
  
−
If you are interested in helping to organize BOSC 2016, please email bosc@open-bio.org.
+
If you are interested in helping to organize BOSC 2016, please email email bosc@open-bio.org
 +
 
 +
== Return to [[BOSC 2015]] main page ==
 +
 
 +
[[Category:BOSC]] [[Category:Conferences]]
 +
[[Category:BOSC Conferences]]

Latest revision as of 18:17, 11 July 2016

BOSC logo

This page has links to all the publicly available talk slides, videos and posters. Most of the slides and posters are on our BOSC F1000 Research Channel (others are on SlideShare and FigShare), while the videos are on the BOSC 2015 YouTube playlist.

The full program including abstracts is available here. The PDF of this schedule (without abstracts) is available here.

Sponsors

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 welcome Bina as our newest sponsor.

Google
             
Curoverse logo
Arvados logo
GigaScience
Bina

Pre-BOSC: Codefest 2015

See Codefest 2015 for details, report given at the start of BOSC day two (slides, video).

BOSC Day 1 (Friday, 10 July, 2015)

Time Title Speaker [Poster] / Chair
7:30-9:00 Registration
9:00-9:15 Introduction and Welcome Nomi Harris and Peter Cock (Co-Chairs, BOSC 2015)
9:15-10:15 Keynote: Bioinformatics: Still a scary world for biologists (slides, video) Holly Bik
10:15-10:45 Coffee Break
10:45-12:30 Session: Data Science Chair: Rob Davey
10:45- 11:02 Apollo: Scalable & collaborative curation for improved comparative genomics (video) Mónica Muñoz-Torres [P1]
11:02-11:19 GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data (slides, poster, video) Kévin Rue-Albrecht [P2]
11:19-11:36 Arvados: A Free Software Platform for Big Data Science (slides, video) Peter Amstutz
11:36-11:53 Bringing Hadoop into Bioinformatics with Cloudgene and CloudMan (slides, video) Sebastian Schoenherr
11:53-12:10 Segway: semi-automated genome annotation (video) Michael Hoffman [P3]
12:10-12:15 QualiMap 2.0: quality control of high throughput sequencing data (slides, video, poster) Konstantin Okonechnikov [P4]
12:15-12:20 A Genomics Virtual Laboratory (slides, video) Andrew Lonie [P5]
12:20-12:25 BioSolr: Building better search for bioinformatics (slides, video, poster) Tony Burdett [P6]
12:25-12:30 Prioritization of structural variants based on known biological information (slides, video) Brad Chapman
12:30-13:30 Lunch
13:00-14:00 Poster Session and Birds of a Feather sessions (overlapping with lunch)
14:00-15:30 Session: Standards and Interoperability Chair: Peter Cock
14:00-14:17 Portable workflow and tool descriptions with the CWL (Common Workflow Language) (slides, video) Michael R. Crusoe [P7]
14:17-14:34 From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences (slides, alt. slides, video) Alejandra Gonzalez-Beltran
14:34-14:51 Demystifying the Interoperability of Disparate Genomic Resources (slides, video) Daniel Blankenberg
14:51-15:08 Increasing the utility of Galaxy workflows (slides, video) John Chilton
15:10-15:15 Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers (slides, video) Damion Dooley
15:15-15:20 Evolution of the Galaxy tool ecosystem - happier developers, happier users (slides, video) Martin Čech [P8]
15:20-15:25 Bionode - Modular and universal bioinformatics (slides, video) Bruno Vieira [P9]
15:25-15:30 The EDAM Ontology (slides, video, poster) Hervé Ménager [P10]
15:30-16:00 Coffee Break
16:00-17:00 Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community Moderator: Mónica Muñoz-Torres

Panelists: Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams

17:00-17:10 Open Bioinformatics Foundation (OBF) Update (slides) Hilmar Lapp (President, OBF)
17:10-17:15 Announcements Nomi Harris
17:15-18:30 BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 1; introduction video) Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
17:15-18:30 BOFs: Feel free to organize one!
19:00- Pay-your-own-way BOSC dinner at Kennedy's (FULL) RSVP (limited space --you must RSVP to attend)

BOSC Day 2 (Saturday, 11 July, 2015)

Time Title Speaker / Chair
9:00-9:05 Announcements Peter Cock and Nomi Harris
9:05-9:15 Codefest 2015 Report (slides, video) Brad Chapman (Codefest 2015 Organizer)
9:15-10:15 Keynote: Big Data in Biology (slides, video) Ewan Birney
10:15-10:45 Coffee Break
10:45-12:30 Session: Open Science and Reproducibility Chair: Mónica Muñoz-Torres
10:45-11:02 A curriculum for teaching Reproducible Computational Science bootcamps (slides, source, video) Hilmar Lapp
11:02-11:19 Research shared: www.researchobject.org (slides, video) Norman Morrison [P11]
11:19-11:36 Nextflow: a tool for deploying reproducible computational pipelines (slides, video, poster) Paolo Di Tommaso [P12]
11:36-11:53 Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science (slides, video, poster) John Fonner [P13]
11:55-12:00 The 500 builds of 300 applications in the HeLmod repository will at least get you started on a full suite of scientific applications (slides, video) Aaron Kitzmiller
12:00-12:05 Bioboxes: Standardised bioinformatics tools using Docker containers. (slides, poster) Peter Belmann [P14]
12:05-12:10 The perfect fit for reproducible interactive research: Galaxy, Docker, IPython (video) Björn Grüning
12:10-12:15 COPO: Bridging the Gap from Data to Publication in Plant Science (slides, video, poster) Robert Davey [P15]
12:15-12:20 ELIXIR UK building on Data and Software Carpentry to address the challenges in computational training for life scientists (slides, video) Aleksandra Pawlik [P16]
12:20-12:25 Parallel recipes: towards a common coordination language for scientific workflow management systems (slides, video) Yves Vandriessche [P17]
12:25-12:30 openSNP - personal genomics and the public domain (slides, video, poster, poster) Bastian Greshake [P18]
12:30-13:30 Lunch
13:00-14:00 Poster Session and BOFs (overlapping with lunch)
14:00-14:40 Session: Translational Bioinformatics Chair: Brad Chapman
14:00-14:17 CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer (slides, video, poster) Malachi Griffith [P19]
14:17-14:34 From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep & Omics Pipe (video, poster) Tobias Meissner [P20]
14:35-14:40 Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute (slides, video, poster) Ishwar Chandramouliswaran [P21]
14:40-15:30 Session: Bioinformatics Open Source Project Updates Chair: Nomi Harris
14:40-14:57 Biopython Project Update 2015 (slides, video) João Rodrigues
14:57-15:14 Biogems: Challenges in distributed software development in bioinformatics (slides, video) George Githinji and Pjotr Prins
15:14-15:31 Apache Taverna: Sustaining research software at the Apache Software Foundation (slides, video) Stian Soiland-Reyes [P22]
15:30-16:00 Coffee Break
16:00-16:30 Session: Visualization Chair: Karsten Hokamp
16:00-16:17 Simple, Shareable, Online RNA Secondary Structure Diagrams (slides, slides) Peter Kerpedjiev
16:17-16:22 BioJS 2.0: an open source standard for biological visualization (slides, video) Guy Yachdav [P23]
16:22-16:27 Visualising Open PHACTS linked data with widgets (slides, video) Ian Dunlop [P24]
16:30-17:00 Session: Late-Breaking Lightning Talks Chair: Hilmar Lapp
16:30-16:35 Biospectra-by-sequencing genetic analysis platform (slides, video, poster) Aurelie Laugraud [P25]
16:35-16:40 PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities (slides, video) Shareef Dabdoub
16:40-16:45 Otter/ZMap/SeqTools: A productive alternative to web browser genome visualisation Gemma Guest [P26]
16:45-16:50 BioaRchive: enabling reproducibility of Bioconductor package versions (slides, video, poster) Nitesh Turaga [P27]
16:50-16:55 Developing an Arvados BWA-GATK pipeline (slides, video, poster) Pjotr Prins [P28]
16:55-17:00 Out of the box cloud solution for Next-Generation Sequencing analysis (slides, video) Freerk van Dijk [P29]
17:00-17:10 Concluding Remarks Nomi Harris and Peter Cock
17:15-18:30 BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 2) Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
17:10-18:10 BOFs: Feel free to organize one!
19:00 Pay-your-own-way dinner at the Workshop Gastropub. RSVP here if you want to join us.

Posters

If the speaker also has a talk, the poster link will be above (posters 1 to 29). This table lists poster-only presentations.

Poster Title Presenter
P30 Aequatus: Visualising complex similarity relationships among species Anil Thanki
P31 MOLGENIS Workbench for Systems Medicine K. Joeri van der Velde
P32 SPINGO: a rapid species-classifier for microbial amplicon sequences Feargal Ryan
P33 ANNOgesic - A computational pipeline for RNA-Seq based transcriptome annotations of bacteria Sung-Huan Yu
P34 BioXSD — a data model for sequences, alignments, features, measured and inferred values Matúš Kalaš
P35 MGkit: A Metagenomic Framework For The Study Of Microbial Communities Francesco Rubino
P36 From scaffold to submission in a day: a new software pipeline for rapid genome annotation and analysis Sascha Steinbiss


BOSC 2015 Organizing Committee

Nomi Harris and Peter Cock (Co-Chairs)

Brad Chapman, Rob Davey, Chris Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres

BOSC 2015 Program Committee

Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Mónica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antão, 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

BOSC is a community effort—we thank all those who made it possible, including the organizing committee, the program committee, the session chairs, our sponsors, and the ISMB SIG chair, Steven Leard.

If you are interested in helping to organize BOSC 2016, please email email bosc@open-bio.org

Return to BOSC 2015 main page

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