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Difference between revisions of "BOSC 2015 Schedule"

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(→‎BOSC Day 1 (Friday, 10 July, 2015): F1000 slides for research objects)
 
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[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2015]]
 
[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2015]]
  
−
It is our hope to have all the posters and talk slides available on the [http://f1000research.com/channels/BOSC BOSC F1000 Research Channel], with links to the talk videos. Note some speakers have already made their talks available separately on other services like SlideShare and FigShare, which is fine. Links to any slides, posters and videos will be added to this listing as well.
+
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].
  
 
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].
 
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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== Sponsors ==
 
== Sponsors ==
  
−
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]) as a returning sponsor and welcome [http://bina.com/ Bina] as our newest sponsor.
+
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:google-logo11w.png‎|205px|left|Google|link=http://www.google.com/]]
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== Pre-BOSC: Codefest 2015  ==
 
== Pre-BOSC: Codefest 2015  ==
  
−
See [[Codefest 2015]] for details.
+
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]).
  
 
== BOSC Day 1 (Friday, 10 July, 2015) ==
 
== BOSC Day 1 (Friday, 10 July, 2015) ==
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|-
 
|-
 
|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 learning of gene expression data ([http://f1000research.com/slides/4-248 slides], [http://f1000research.com/posters/4-247 poster], [https://youtu.be/Ih8I-WbdvTg video])
+
|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 (P2)
+
|Kévin Rue-Albrecht [P2]
 
|-
 
|-
 
|11:19-11:36
 
|11:19-11:36
Line 73: Line 73:
 
|-
 
|-
 
|12:10-12:15
 
|12:10-12:15
−
|QualiMap 2.0: quality control of high throughput sequencing data ([http://youtu.be/UR_9npHP_yM video])
+
|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 [P4]
 
|Konstantin Okonechnikov [P4]
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
−
|A Genomics Virtual Laboratory ([http://youtu.be/ktotH6a_sSo video])
+
|A Genomics Virtual Laboratory ([http://f1000research.com/slides/4-374 slides], [http://youtu.be/ktotH6a_sSo video])
 
|Andrew Lonie [P5]
 
|Andrew Lonie [P5]
 
|-
 
|-
 
|12:20-12:25
 
|12:20-12:25
−
|BioSolr: Building better search for bioinformatics ([http://youtu.be/hl3NFE0-UUo video])
+
|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 [P6]
 
|Tony Burdett [P6]
 
|-
 
|-
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|-
 
|-
 
|14:00-14:17
 
|14:00-14:17
−
|Portable workflow and tool descriptions with the CWL ([http://f1000research.com/slides/4-278 slides], [http://youtu.be/sF4DJVUcjnU video])
+
|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 [P7]
+
|Michael R. Crusoe [<del>P7</del>]
 
|-
 
|-
 
|14:17-14:34
 
|14:17-14:34
−
|From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences ([http://www.slideshare.net/agbeltran/from-peerreviewed-to-peerreproduced-a-role-for-research-objects-in-scholarly-publishing-in-the-life-sciences slides])
+
|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
−
|Demystifying the Interoperability of Disparate Genomic Resources ([http://youtu.be/PbVqVlNtFOo video])
+
|Demystifying the Interoperability of Disparate Genomic Resources ([http://f1000research.com/slides/4-372 slides], [http://youtu.be/PbVqVlNtFOo video])
 
|Daniel Blankenberg
 
|Daniel Blankenberg
 
|-
 
|-
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|-
 
|-
 
|15:10-15:15
 
|15:10-15:15
−
|Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers ([http://youtu.be/d4hh2OtpX5E video])
+
|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 ([http://bit.ly/boscisgreat slides], [http://youtu.be/APYzQWg0nrs video])
+
|Evolution of the Galaxy tool ecosystem - happier developers, happier users ([http://f1000research.com/slides/4-521 slides], [http://youtu.be/APYzQWg0nrs video])
 
|Martin Čech [P8]
 
|Martin Čech [P8]
 
|-
 
|-
 
|15:20-15:25
 
|15:20-15:25
 
|Bionode - Modular and universal bioinformatics ([http://f1000research.com/slides/4-288 slides], [http://youtu.be/_CNlpNxkP-k video])
 
|Bionode - Modular and universal bioinformatics ([http://f1000research.com/slides/4-288 slides], [http://youtu.be/_CNlpNxkP-k video])
−
|Bruno Vieira [P9]
+
|Bruno Vieira [<del>P9</del>]
 
|-
 
|-
 
|15:25-15:30
 
|15:25-15:30
−
|The EDAM Ontology ([http://youtu.be/gsRWyfaYTPE video], [http://f1000research.com/posters/4-227 poster])
+
|The EDAM Ontology ([http://f1000research.com/slides/4-359 slides], [http://youtu.be/gsRWyfaYTPE video], [http://f1000research.com/posters/4-227 poster])
 
|Hervé Ménager [P10]
 
|Hervé Ménager [P10]
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
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|-
 
|-
 
|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)
 
|-
 
|-
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|-
 
|-
 
|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)
 
|- style="background:#EFFBFB"
 
|- 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
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
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|-
 
|-
 
|10:45-11:02
 
|10:45-11:02
−
|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])
+
|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 ([http://www.slideshare.net/NormanMorrison2/researchobject-bosc-2015-v2 slides])
+
|Research shared: www.researchobject.org ([http://www.slideshare.net/NormanMorrison2/researchobject-bosc-2015-v2 slides], [http://youtu.be/D6TzbK7FBBM video])
−
|Norman Morrison [P11]
+
|Norman Morrison [<del>P11</del>]
 
|-
 
|-
 
|11:19-11:36
 
|11:19-11:36
−
|Nextflow: a tool for deploying reproducible computational pipelines ([https://speakerdeck.com/pditommaso/nextflow-a-tool-for-deploying-reproducible-computational-pipelines slides])
+
|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 [P12]
 
|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 ([https://github.com/johnfonner/presentations/blob/master/FreeBeerToday-iPlantAgaveDocker.pdf slides])
+
|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 [P13]
 
|John Fonner [P13]
 
|-
 
|-
 
|11:55-12:00
 
|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
 
|-
 
|-
 
|12:00-12:05
 
|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 [P14]
 
|Peter Belmann [P14]
 
|-
 
|-
 
|12:05-12:10
 
|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
 
|-
 
|-
 
|12:10-12:15
 
|12:10-12:15
−
|COPO: Bridging the Gap from Data to Publication in Plant Science ([http://f1000research.com/slides/4-360 slides], [http://figshare.com/articles/Poster_Presented_at_BOSC_2015/1483428 poster])
+
|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 [P15]
 
|Robert Davey [P15]
 
|-
 
|-
 
|12:15-12:20
 
|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 [P16]
 
|Aleksandra Pawlik [P16]
 
|-
 
|-
 
|12:20-12:25
 
|12:20-12:25
−
|Parallel recipes: towards a common coordination language for scientific workflow management systems ([http://f1000research.com/slides/4-333 slides])
+
|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 [P17]
 
|Yves Vandriessche [P17]
 
|-
 
|-
 
|12:25-12:30
 
|12:25-12:30
−
|openSNP - personal genomics and the public domain ([http://figshare.com/articles/openSNP_BOSC15_Slides/1480397 slides], [http://figshare.com/articles/openSNP_BOSC15_Poster/1466880 poster])
+
|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]
 
|Bastian Greshake [P18]
 
|- style="background:#F7F8E0"
 
|- style="background:#F7F8E0"
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|-
 
|-
 
|14:00-14:17
 
|14:00-14:17
−
|CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer ([http://f1000research.com/slides/4-277 slides], [http://f1000research.com/posters/4-276 poster])
+
|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 [P19]
 
|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 ([http://f1000research.com/posters/4-275 poster])
+
|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 [P20]
 
|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 [P21]
 
|Ishwar Chandramouliswaran [P21]
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
Line 264: Line 264:
 
|-
 
|-
 
|14:40-14:57
 
|14:40-14:57
−
|Biopython Project Update 2015 ([http://f1000research.com/slides/4-279 slides])
+
|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
−
|Biogems: Challenges in distributed software development in bioinformatics ([http://f1000research.com/slides/4-282 slides])
+
|Biogems: Challenges in distributed software development in bioinformatics ([http://f1000research.com/slides/4-282 slides], [http://youtu.be/z1aHjhi2eHI video])
 
|George Githinji and Pjotr Prins   
 
|George Githinji and Pjotr Prins   
 
|-
 
|-
 
|15:14-15:31
 
|15:14-15:31
−
|Apache Taverna: Sustaining research software at the Apache Software Foundation ([http://www.slideshare.net/soilandreyes/20150711-bosc2015apachetaverna slideshare])
+
|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 [P22]
+
|Stian Soiland-Reyes [<del>P22</del>]
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
Line 288: Line 288:
 
|-
 
|-
 
|16:17-16:22
 
|16:17-16:22
−
|BioJS 2.0: an open source standard for biological visualization ([http://f1000research.com/slides/4-379 slides])
+
|BioJS 2.0: an open source standard for biological visualization ([http://f1000research.com/slides/4-379 slides], [http://youtu.be/VNMu7xetnI4 video])
 
|Guy Yachdav [P23]
 
|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 [P24]
 
|Ian Dunlop [P24]
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
Line 300: Line 300:
 
|-
 
|-
 
|16:30-16:35
 
|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 [P25]
 
|Aurelie Laugraud [P25]
 
|-
 
|-
 
|16:35-16:40
 
|16:35-16:40
−
|PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities
+
|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
 
|Shareef Dabdoub
 
|-
 
|-
Line 312: Line 312:
 
|-
 
|-
 
|16:45-16:50
 
|16:45-16:50
−
|BioaRchive: enabling reproducibility of Bioconductor package versions ([http://f1000research.com/slides/4-369 slides], [http://f1000research.com/posters/4-370 poster])
+
|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]
 
|Nitesh Turaga [P27]
 
|-
 
|-
 
|16:50-16:55
 
|16:50-16:55
−
|Developing an Arvados BWA-GATK pipeline ([http://f1000research.com/slides/4-283 slides], [http://f1000research.com/posters/4-281 poster])
+
|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]
 
|Pjotr Prins [P28]
 
|-
 
|-
 
|16:55-17:00
 
|16:55-17:00
−
|Out of the box cloud solution for Next-Generation Sequencing analysis
+
|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]
 
|Freerk van Dijk [P29]
 
|-
 
|-
Line 367: Line 367:
 
|-
 
|-
 
| P34
 
| P34
−
| BioXSD — a data model for sequences, alignments, features, measured and inferred values  
+
| [http://f1000research.com/posters/4-425 BioXSD — a data model for sequences, alignments, features, measured and inferred values]
 
| Matúš Kalaš  
 
| Matúš Kalaš  
 
|-
 
|-

Latest revision as of 22:17, 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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