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Difference between revisions of "BOSC 2016 Schedule"

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(Pre-BOSC: Codefest 2016)
 
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[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2016]]
 
[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2016]]
  
The full program including abstracts will be available soon.
+
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-OOQiOhXZoehorqOhcHAUEXQqiVZRS BOSC 2016 YouTube playlist].
 +
 
 +
The [https://www.open-bio.org/w/images/2/24/BOSC2016-program4.pdf full program including abstracts] is available.
  
 
== Sponsors ==
 
== Sponsors ==
Line 15: Line 17:
 
== Pre-BOSC: Codefest 2016  ==
 
== Pre-BOSC: Codefest 2016  ==
  
The Codefest (a pre-BOSC hackathon) takes place July 6-7 in Orlando at FamiLAB. It is FREE and open to all (even if you're not attending BOSC). See [[Codefest 2016]] for details.
+
The Codefest (a pre-BOSC hackathon) took place July 6-7 in Orlando at FamiLAB. It was FREE and open to all (even to those who did not attend BOSC). See [[Codefest 2016]] for details.
  
 
== BOSC Day 1 (Friday, July 8, 2016) ==
 
== BOSC Day 1 (Friday, July 8, 2016) ==
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{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
 
|- style="background:#D8F781"
 
|- style="background:#D8F781"
!'''Time'''
+
! style="width: 6em" |'''Time'''
 
!'''Title'''
 
!'''Title'''
!'''Speaker or Session Chair'''
+
! style="width: 25%" | '''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|7:30-9:00
 
|7:30-9:00
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|- style="background:#EFFBFB"
 
|- style="background:#EFFBFB"
 
|9:15-10:15
 
|9:15-10:15
|'''Keynote''': ''The open-source outbreak: can data prevent the next pandemic?''
+
|'''Keynote''': ''The open-source outbreak: can data prevent the next pandemic?'' ([https://youtu.be/5KfnXZQ4RzQ video], [http://www.slideshare.net/jennifergardy/bosc-2016-the-opensource-outbreak slides])
|Jennifer Gardy
+
|[https://www.open-bio.org/wiki/BOSC_2016_Keynote_Speakers Jennifer Gardy]
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|10:15-10:45
 
|10:15-10:45
Line 46: Line 48:
 
|-
 
|-
 
|10:45-11:03
 
|10:45-11:03
|GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes
+
|GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes ([https://youtu.be/EpHn_WhXlI8 video], [http://f1000research.com/slides/5-1633 slides], [http://f1000research.com/posters/5-1634 poster])
|Ted Liefeld [1]
+
|Ted Liefeld [P1]
 
|-
 
|-
 
|11:03-11:21
 
|11:03-11:21
|This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language
+
|This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language ([https://youtu.be/__8qUDZGeLc video], [http://f1000research.com/slides/5-1622 slides])
|Michael R. Crusoe [2]
+
|Michael R. Crusoe [P2]
 
|-
 
|-
 
|11:21-11:39
 
|11:21-11:39
|CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language
+
|CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language ([https://youtu.be/zrOfNqPnZCk video], [http://f1000research.com/slides/5-1617 slides], [http://f1000research.com/posters/5-1615 poster])
|Dan Leehr [3]
+
|Dan Leehr [P3]
 
|-
 
|-
 
|11:39-11:57
 
|11:39-11:57
|Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil
+
|Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil ([https://youtu.be/COKqH4FqvxI video], [http://f1000research.com/slides/5-1624 slides])
 
|Peter Amstutz
 
|Peter Amstutz
 
|-
 
|-
|11:57-12:02
+
|11:57-12:15
|Planemo – A Scientific Workflow SDK
+
|Planemo – A Scientific Workflow SDK ([https://youtu.be/kVa-oWxWDww video], [http://f1000research.com/slides/5-1742 slides])
 
|John Chilton
 
|John Chilton
 
|-
 
|-
|12:03-12:08
+
|12:15-12:20
|Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics
+
|Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics ([https://youtu.be/VtGyidSuMd8 video], [http://f1000research.com/slides/5-1887 slides])
 
|Daniel Blankenberg
 
|Daniel Blankenberg
 
|-
 
|-
|12:09-12:14
+
|12:21-12:26
|NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
+
|NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts ([https://youtu.be/Sf-MVuug3sQ video], [https://prezi.com/qbn8ys1oa5fm/nextflowworkbench-bosc-2016/ slides], [http://f1000research.com/posters/5-1651 poster])
|Fabien Campagne [4]
+
|Fabien Campagne [P4]
 
|-
 
|-
|12:15-12:20
+
|12:26-12:30
|Promoting platform interoperability with portable bcbio workflows
 
|Brad Chapman
 
|-
 
|12:20-12:25
 
 
|Questions for lightning talk speakers in this session
 
|Questions for lightning talk speakers in this session
 
|
 
|
Line 86: Line 84:
 
|-
 
|-
 
|13:00-14:00
 
|13:00-14:00
|'''Poster Session and Birds of a Feather sessions''' (overlapping with lunch)
+
|'''Poster Session and [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ Birds of a Feather] sessions''' (overlapping with lunch)
 +
(Feel free to [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ organize a BoF]!)
 
|
 
|
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
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|-
 
|-
 
|14:00-14:18
 
|14:00-14:18
|Enhancements to MISO: An open-source community-driven LIMS
+
|Enhancements to MISO: An open-source community-driven LIMS ([https://youtu.be/znrRsPip5D0 video], [http://f1000research.com/slides/5-1608 slides])
 
|Andre Masella
 
|Andre Masella
 
|-
 
|-
 
|14:18-14:36
 
|14:18-14:36
|Biothings APIs: high-performance bioentity-centric web services
+
|Biothings APIs: high-performance bioentity-centric web services ([https://youtu.be/296cGIZ6Ps8 video], [http://www.slideshare.net/ChunleiWu/biothings-apis-highperformance-bioentitycentric-web-services slides], [http://f1000research.com/posters/5-1954 poster])
|Chunlei Wu [5]
+
|Chunlei Wu [P5]
 
|-
 
|-
 
|14:36-14:54
 
|14:36-14:54
|The Noctua Modeling Tool
+
|The Noctua Modeling Tool ([https://youtu.be/W9_udk6Oz2E video], [http://f1000research.com/slides/5-1678 slides], [http://f1000research.com/posters/5-1677 poster])
|Seth Carbon [6]
+
|Seth Carbon [P6]
 
|-
 
|-
 
|14:54-15:12
 
|14:54-15:12
|Processing phenotype data using Phenopackets-API and PXFTools
+
|Processing phenotype data using Phenopackets-API and PXFTools ([https://youtu.be/8UreKE1eGNY video], [http://f1000research.com/slides/5-1649 slides])
 
|Chris Mungall
 
|Chris Mungall
 
|-
 
|-
 
|15:12-15:17
 
|15:12-15:17
|The EDAM Ontology
+
|Promoting platform interoperability with portable bcbio workflows ([https://youtu.be/kMoAWjHhOVc video], [http://f1000research.com/slides/5-1639 slides])
|Jon Ison [7]
+
|Brad Chapman
 
|-
 
|-
 
|15:18-15:23
 
|15:18-15:23
|Towards traceable, scriptable, and efficient data distribution for next-generation genomics
+
|Towards traceable, scriptable, and efficient data distribution for next-generation genomics ([https://youtu.be/yRR8qhRJqt8 video], [http://f1000research.com/slides/5-1623 slides], [http://f1000research.com/posters/5-1625 poster])
|John Bradley [8]
+
|John Bradley [P8]
 +
|-
 +
|15:24-15:29
 +
|Questions for lightning talks in this session
 +
|
 
|-
 
|-
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
Line 126: Line 129:
 
|'''''Moderator''''': Mónica Muñoz-Torres
 
|'''''Moderator''''': Mónica Muñoz-Torres
  
'''''Panelists''''':  Abigail Cabunoc Mayes, Bastian Greshake, <br>Jamie Whitacre, John Chilton, Natasha Wood
+
'''''Panelists''''':  Abigail Cabunoc Mayes, Bastian Greshake, Jamie Whitacre, John Chilton, Natasha Wood
 
|-
 
|-
 
|17:00-17:10
 
|17:00-17:10
 
|Open Bioinformatics Foundation (OBF) Update
 
|Open Bioinformatics Foundation (OBF) Update
|
+
|Hilmar Lapp
 
|-
 
|-
 
|17:10-17:15
 
|17:10-17:15
Line 137: Line 140:
 
|-
 
|-
 
|17:15-18:30
 
|17:15-18:30
|'''Bird of a Feather sessions (BOFs)''': Feel free to organize one! Sign up [here].
+
|'''Birds of a Feather sessions (BOFs)''': Feel free to organize one! Sign up [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ here].
 
|
 
|
 
|-
 
|-
 
|19:00
 
|19:00
| Pay-your-own-way dinner at Paradiso 37 (at Disney Springs shopping center)
+
| Pay-your-own-way dinner at Paradiso 37 (at Disney Springs shopping center)--*NOW FULL*
|
+
| (Limited space--you must RSVP to attend)
 
|}
 
|}
  
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{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
 
|- style="background:#D8F781"
 
|- style="background:#D8F781"
!'''Time'''
+
! style="width: 6em" | '''Time'''
 
!'''Title'''
 
!'''Title'''
!'''Speaker or Session Chair'''
+
!'''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|9:00-9:05
 
|9:00-9:05
Line 158: Line 161:
 
|-
 
|-
 
|9:05-9:15
 
|9:05-9:15
|[[Codefest_2016|Codefest 2016]] Report  
+
|[[Codefest_2016|Codefest 2016]] Report ([https://youtu.be/-1cthBe-Xcg video], [http://f1000research.com/slides/5-1640 slides])
 
|Brad Chapman (Codefest Organizer)
 
|Brad Chapman (Codefest Organizer)
 
|- style="background:#EFFBFB"
 
|- style="background:#EFFBFB"
 
|9:15-10:15
 
|9:15-10:15
|'''Keynote''': ''Open source, open access, and open data: why science moves faster in an open world''
+
|'''Keynote''': ''Open source, open access, and open data: why science moves faster in an open world'' ([https://youtu.be/TYmpxLHy_UM video], [http://f1000research.com/slides/5-1701 slides])
|Steven Salzberg
+
|[https://www.open-bio.org/wiki/BOSC_2016_Keynote_Speakers Steven Salzberg]
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|10:15-10:45
 
|10:15-10:45
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|-
 
|-
 
|10:45-11:03
 
|10:45-11:03
|Mango: Data Exploration on Large Genomic Datasets
+
|Mango: Data Exploration on Large Genomic Datasets ([https://youtu.be/67og0xCZxZ4 video])
|Alyssa Morrow [9]
+
|Alyssa Morrow [P9]
 
|-
 
|-
 
|11:03-11:21
 
|11:03-11:21
|ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets
+
|ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets ([https://youtu.be/su_oltymp78 video])
 
|Frank Nothaft
 
|Frank Nothaft
 
|-
 
|-
Line 186: Line 189:
 
|-
 
|-
 
|11:39-11:57
 
|11:39-11:57
|Characterization of the small RNA transcriptome using the bcbio-nextgen python framework
+
|Characterization of the small RNA transcriptome using the bcbio-nextgen python framework ([https://youtu.be/hESTyIKuGQY video], [http://f1000research.com/slides/5-1627 slides])
 
|Lorena Pantano Rubino
 
|Lorena Pantano Rubino
 
|-
 
|-
 
|11:57-12:15
 
|11:57-12:15
|MetaR: simple, high-level languages for data analysis with the R ecosystem
+
|MetaR: simple, high-level languages for data analysis with the R ecosystem ([https://youtu.be/bWYhuQCSaqU video], [https://prezi.com/x6nhbkext0ga/metar-bosc-2016/ slides], [http://f1000research.com/posters/5-1652 poster])
|Fabien Campagne [10]
+
|Fabien Campagne [P10]
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
|Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data
+
|Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data ([https://youtu.be/51nuQ3c063Q video], [http://f1000research.com/slides/5-1650 slides], [http://f1000research.com/posters/5-2014 poster])
|Jorge Duitama [11]
+
|Jorge Duitama [P11]
 
|-
 
|-
 
|12:21-12:26
 
|12:21-12:26
|GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale<br>gene regulatory networks
+
|GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks ([https://youtu.be/HP-oMNEi9cU video], [http://f1000research.com/slides/5-1637 slides], [http://f1000research.com/posters/5-1618 poster])
|Kam D. Dahlquist [12]
+
|Kam D. Dahlquist [P12]
 
|- style="background:#F7F8E0"
 
|- style="background:#F7F8E0"
 
|12:30-13:30
 
|12:30-13:30
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|-
 
|-
 
|13:00-14:00
 
|13:00-14:00
|'''Poster Session and BOFs (overlapping with lunch)'''
+
|'''Poster Session and [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ Birds of a Feather] sessions''' (overlapping with lunch)
 +
(Feel free to [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ organize a BoF]!)
 
|
 
|
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
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|-
 
|-
 
|14:00-14:18
 
|14:00-14:18
|Biopython Project Update 2016
+
|Biopython Project Update 2016 ([https://youtu.be/JxOm1Bjyt9M video], [http://f1000research.com/slides/5-1712 slides])
 
|Christian Brueffer
 
|Christian Brueffer
 
|-
 
|-
 
|14:18-14:23
 
|14:18-14:23
|Sequenceserver: a modern graphical user interface for custom BLAST databases
+
|ReportMD: Writing complex scientific reports in R ([https://youtu.be/SFY7KrAB1uA video], [http://f1000research.com/slides/5-1802 slides], [http://f1000research.com/posters/5-1647 poster])
|Anurag Priyam [13]
+
|Peter Humburg [P19]
 
|-
 
|-
 
|14:24-14:29
 
|14:24-14:29
|Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth
+
|Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth ([https://youtu.be/2QlH-3Bm0ns video], [http://sjackman.ca/linuxbrew-slides/#/ slides], [http://f1000research.com/posters/5-1795 poster])
|Shaun Jackman [14]
+
|Shaun Jackman [P14]
 
|-
 
|-
 
|14:30-14:35
 
|14:30-14:35
|SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata
+
|SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata ([https://youtu.be/Y1Dp72hDg0w video])
|Benjamin Hitz [15]
+
|Benjamin Hitz [P15]
 +
|-
 +
| 14:35-14:40
 +
| Questions for lightning talk speakers in Developer Tools and Libraries session
 +
|
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
 
|14:40-15:30
 
|14:40-15:30
Line 234: Line 242:
 
|-
 
|-
 
|14:40-14:58
 
|14:40-14:58
|State of the openSNP.org Union: Dockerizing, Crowdfunding & Opening for Contributors
+
|State of the openSNP.org Union: Dockerizing, Crowdfunding & Opening for Contributors ([https://youtu.be/KsoDPk-wVVE video], [http://f1000research.com/slides/5-1643 slides])
|Bastian Greshake [16]
+
|Bastian Greshake [P16]
 
|-
 
|-
 
|14:58-15:16
 
|14:58-15:16
|The GenePattern Notebook Environment
+
|The GenePattern Notebook Environment ([https://youtu.be/dIhFMceSETU video], [http://f1000research.com/posters/5-1900 poster])
|Michael Reich [17]
+
|Michael Reich [P17]
 
|-
 
|-
 
|15:16-15:21
 
|15:16-15:21
|Reproducibility in computationally intensive workflows with continuous analysis
+
|Reproducibility in computationally intensive workflows with continuous analysis ([https://youtu.be/pXBk0YL-k04 video], [http://f1000research.com/slides/5-1811 slides])
 
|Brett K Beaulieu-Jones
 
|Brett K Beaulieu-Jones
 
|-
 
|-
 
|15:22-15:27
 
|15:22-15:27
|Reproducible Research in the Cloud with the Refinery Platform
+
|Reproducible Research in the Cloud with the Refinery Platform ([https://youtu.be/dX9En3GvtDk video])
|Nils Gehlenborg [18]
+
|Nils Gehlenborg [P18]
 
|-
 
|-
 
|15:28-15:33
 
|15:28-15:33
|ReportMD: Writing complex scientific reports in R
+
| Questions for lightning talk speakers in Open Science and Reproducibility session
|Peter Humburg [19]
+
|
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
Line 262: Line 270:
 
|-
 
|-
 
|16:00-16:05
 
|16:00-16:05
|Apollo Genome Annotation Editor: Latest Updates, Including Galaxy Integration
+
|Apollo Genome Annotation Editor: Latest Updates, Including Galaxy Integration ([https://youtu.be/NNqnAZE1ZOE video])
|Mónica C. Muñoz-Torres [20]
+
|Mónica C. Muñoz-Torres [P20]
 
|-
 
|-
 
|16:06-16:11
 
|16:06-16:11
|An invitation to the bioinformatics community to participate in the HUBzero® open source release
+
|An invitation to the bioinformatics community to participate in the HUBzero® open source release ([https://youtu.be/Xbox7-AEPJ8 video], [http://f1000research.com/posters/5-1800 poster])
|Michael Zentner [21]
+
|Michael Zentner [P21]
 
|-
 
|-
 
|16:12-16:17
 
|16:12-16:17
|PDB on steroids – compressive structural bioinformatics
+
|PDB on steroids – compressive structural bioinformatics ([https://youtu.be/1WEevvFpjQU video], [http://f1000research.com/slides/5-1755 slides], [http://f1000research.com/posters/5-1752 poster])
|Peter Rose [22]
+
|Peter Rose [P22]
 
|-
 
|-
 
|16:18-16:23
 
|16:18-16:23
|Puzzle: VCF/GEMINI interface for genetic disease analysis
+
|Puzzle: VCF/GEMINI interface for genetic disease analysis ([https://youtu.be/JKI_taSh5D8 video], [http://f1000research.com/slides/5-1816 slides])
|Robin Andeer [23]
+
|Robin Andeer [P23]
 
|-
 
|-
 
|16:24-16:29
 
|16:24-16:29
|Modernization of the Cytoscape ecosystem
+
|Modernization of the Cytoscape ecosystem ([https://youtu.be/MKmhDU47BZQ video], [http://f1000research.com/slides/5-1661 slides], [http://f1000research.com/posters/5-1662 poster])
|Keiichiro Ono [24]
+
|Keiichiro Ono [P24]
 
|-
 
|-
 
|16:30-16:35
 
|16:30-16:35
|Collaborative Software Development: Lessons from Open Source
+
|Collaborative Software Development: Lessons from Open Source ([https://youtu.be/1af4M0xK7_4 video], [http://f1000research.com/slides/5-1660 slides])
 
|Abigail Cabunoc Mayes
 
|Abigail Cabunoc Mayes
 
|-
 
|-
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|-
 
|-
 
|17:00-18:30
 
|17:00-18:30
|'''BOFs''': Feel free to organize one!
+
|'''Birds of a Feather sessions (BOFs)''': Feel free to organize one! Sign up [https://docs.google.com/document/d/1zKSzP4_6_ezVw1g4Igy8ZRdFDBJ268uMy_5LKA98Mc0/ here].
 
|
 
|
 
|-
 
|-
 
|19:00
 
|19:00
| Pay-your-own-way dinner (TBA)
+
| Pay-your-own-way dinner, [http://www.marlowstavern.com/menu#/georgiafoodmenu Marlow's Tavern], 9101 International Dr, Orlando
|
+
(Meet in Swan lobby at 6:20 to share rides)
 +
| (Limited space--you must RSVP to attend)
 
|}
 
|}
  
 
== Posters ==
 
== Posters ==
  
If a poster presenter also is giving a talk, the poster link will be in the schedule above. The table below lists poster-only presentations.
+
If a poster presenter also is giving a talk, the poster number will be in the schedule above (in square brackets after the talk title). The table below lists poster-only presentations.
  
 
{| border="1" cellspacing="0" cellpadding="7"
 
{| border="1" cellspacing="0" cellpadding="7"
Line 312: Line 321:
 
! Presenter
 
! Presenter
 
|-
 
|-
| 25
+
| P25
 
| Lightweight sample labeling, barcoding and tracking systems for the academic laboratory
 
| Lightweight sample labeling, barcoding and tracking systems for the academic laboratory
 
| Dimitra Sarantopoulou
 
| Dimitra Sarantopoulou
 
|-
 
|-
| 26
+
| P26
| Kronos: a workflow assembler for genome analytics and informatics
+
| [http://f1000research.com/posters/5-1912 Kronos: a workflow assembler for genome analytics and informatics]
 
| Jafar Taghiyar
 
| Jafar Taghiyar
 
|-
 
|-
| 27
+
| P27
| PhyPipe: an automated pipeline for phylogenetic reconstruction from multilocus sequences
+
| [http://f1000research.com/posters/5-1609 PhyPipe: an automated pipeline for phylogenetic reconstruction from multilocus sequences]
 
| Javier Correa Alvarez
 
| Javier Correa Alvarez
 
|-
 
|-
| 28
+
| P28
| Skip the line and balance your work with vQ
+
| BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data [walk-in]
| Gregory Zynda
+
| Andrey Kartashov
 +
|-
 +
| P29
 +
| Using the Nextflow framework for reproducible in-silico omics analyses across clouds and clusters
 +
| Paolo Di Tommaso
 
|-
 
|-
 
|}
 
|}
 +
 +
'''We have a few spots for walk-in posters!''' Contact bosc @ open-bio.org if you'd like to present one.
  
 
== BOSC 2016 Organizing Committee ==
 
== BOSC 2016 Organizing Committee ==
Line 340: Line 355:
 
Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova*, George Githinji, Christopher Fields, Hilmar Lapp*, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko*, Kai Blin*, Spencer Bliven*, Brad Chapman*, Michael Crusoe, Bastian Greshake*, Hans-Rudolf Hotz*, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues*, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock*, Björn Grüning, Karsten Hokamp*, Amye Kenall, John Chilton, Konrad Förstner*, Jens Lichtenberg, Monica C Munoz-Torres
 
Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova*, George Githinji, Christopher Fields, Hilmar Lapp*, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko*, Kai Blin*, Spencer Bliven*, Brad Chapman*, Michael Crusoe, Bastian Greshake*, Hans-Rudolf Hotz*, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues*, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock*, Björn Grüning, Karsten Hokamp*, Amye Kenall, John Chilton, Konrad Förstner*, Jens Lichtenberg, Monica C Munoz-Torres
  
* Also reviewed Late-Breaking Lightning Talk abstracts
+
&lowast; Also reviewed Late-Breaking Lightning Talk abstracts
  
 
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.

Latest revision as of 23:02, 20 May 2017

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 2016 YouTube playlist.

The full program including abstracts is available.

Sponsors

We are grateful to Curoverse (the team behind the open source platform Arvados) as returning sponsors for BOSC 2016,

Curoverse logo
Arvados logo

Pre-BOSC: Codefest 2016

The Codefest (a pre-BOSC hackathon) took place July 6-7 in Orlando at FamiLAB. It was FREE and open to all (even to those who did not attend BOSC). See Codefest 2016 for details.

BOSC Day 1 (Friday, July 8, 2016)

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 2016)
9:15-10:15 Keynote: The open-source outbreak: can data prevent the next pandemic? (video, slides) Jennifer Gardy
10:15-10:45 Coffee Break
10:45-12:30 Session: Workflows Chair: Brad Chapman
10:45-11:03 GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes (video, slides, poster) Ted Liefeld [P1]
11:03-11:21 This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language (video, slides) Michael R. Crusoe [P2]
11:21-11:39 CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language (video, slides, poster) Dan Leehr [P3]
11:39-11:57 Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil (video, slides) Peter Amstutz
11:57-12:15 Planemo – A Scientific Workflow SDK (video, slides) John Chilton
12:15-12:20 Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics (video, slides) Daniel Blankenberg
12:21-12:26 NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts (video, slides, poster) Fabien Campagne [P4]
12:26-12:30 Questions for lightning talk speakers in this session
12:30-13:30 Lunch
13:00-14:00 Poster Session and Birds of a Feather sessions (overlapping with lunch)

(Feel free to organize a BoF!)

14:00-15:30 Session: Standards and Interoperability Chair: Hilmar Lapp
14:00-14:18 Enhancements to MISO: An open-source community-driven LIMS (video, slides) Andre Masella
14:18-14:36 Biothings APIs: high-performance bioentity-centric web services (video, slides, poster) Chunlei Wu [P5]
14:36-14:54 The Noctua Modeling Tool (video, slides, poster) Seth Carbon [P6]
14:54-15:12 Processing phenotype data using Phenopackets-API and PXFTools (video, slides) Chris Mungall
15:12-15:17 Promoting platform interoperability with portable bcbio workflows (video, slides) Brad Chapman
15:18-15:23 Towards traceable, scriptable, and efficient data distribution for next-generation genomics (video, slides, poster) John Bradley [P8]
15:24-15:29 Questions for lightning talks in this session
15:30-16:00 Coffee Break
16:00-17:00 Panel: Growing and sustaining open source communities Moderator: Mónica Muñoz-Torres

Panelists: Abigail Cabunoc Mayes, Bastian Greshake, Jamie Whitacre, John Chilton, Natasha Wood

17:00-17:10 Open Bioinformatics Foundation (OBF) Update Hilmar Lapp
17:10-17:15 Announcements Nomi Harris
17:15-18:30 Birds of a Feather sessions (BOFs): Feel free to organize one! Sign up here.
19:00 Pay-your-own-way dinner at Paradiso 37 (at Disney Springs shopping center)--*NOW FULL* (Limited space--you must RSVP to attend)

BOSC Day 2 (Saturday, July 9, 2016)

Time Title Speaker [Poster] / Chair
9:00-9:05 Announcements Peter Cock and Nomi Harris
9:05-9:15 Codefest 2016 Report (video, slides) Brad Chapman (Codefest Organizer)
9:15-10:15 Keynote: Open source, open access, and open data: why science moves faster in an open world (video, slides) Steven Salzberg
10:15-10:45 Coffee Break
10:45-12:30 Session: Data Science Chair: Heather Wiencko
10:45-11:03 Mango: Data Exploration on Large Genomic Datasets (video) Alyssa Morrow [P9]
11:03-11:21 ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets (video) Frank Nothaft
11:21-11:39 SUPERSMART - A Self-Updating platform for Estimating Rates of Speciation and Migration, Ages, and
Relationships of Taxa
Hannes Hettling
11:39-11:57 Characterization of the small RNA transcriptome using the bcbio-nextgen python framework (video, slides) Lorena Pantano Rubino
11:57-12:15 MetaR: simple, high-level languages for data analysis with the R ecosystem (video, slides, poster) Fabien Campagne [P10]
12:15-12:20 Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data (video, slides, poster) Jorge Duitama [P11]
12:21-12:26 GRNmap and GRNsight: open source software for dynamical systems modeling and visualization of medium-scale gene regulatory networks (video, slides, poster) Kam D. Dahlquist [P12]
12:30-13:30 Lunch
13:00-14:00 Poster Session and Birds of a Feather sessions (overlapping with lunch)

(Feel free to organize a BoF!)

14:00-14:40 Session: Developer tools and libraries Chair: Chris Fields
14:00-14:18 Biopython Project Update 2016 (video, slides) Christian Brueffer
14:18-14:23 ReportMD: Writing complex scientific reports in R (video, slides, poster) Peter Humburg [P19]
14:24-14:29 Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth (video, slides, poster) Shaun Jackman [P14]
14:30-14:35 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata (video) Benjamin Hitz [P15]
14:35-14:40 Questions for lightning talk speakers in Developer Tools and Libraries session
14:40-15:30 Session: Open Science and Reproducibility Chair: Peter Cock
14:40-14:58 State of the openSNP.org Union: Dockerizing, Crowdfunding & Opening for Contributors (video, slides) Bastian Greshake [P16]
14:58-15:16 The GenePattern Notebook Environment (video, poster) Michael Reich [P17]
15:16-15:21 Reproducibility in computationally intensive workflows with continuous analysis (video, slides) Brett K Beaulieu-Jones
15:22-15:27 Reproducible Research in the Cloud with the Refinery Platform (video) Nils Gehlenborg [P18]
15:28-15:33 Questions for lightning talk speakers in Open Science and Reproducibility session
15:30-16:00 Coffee Break
16:00-17:00 Session: Late-Breaking Lightning Talks Chair: Karsten Hokamp
16:00-16:05 Apollo Genome Annotation Editor: Latest Updates, Including Galaxy Integration (video) Mónica C. Muñoz-Torres [P20]
16:06-16:11 An invitation to the bioinformatics community to participate in the HUBzero® open source release (video, poster) Michael Zentner [P21]
16:12-16:17 PDB on steroids – compressive structural bioinformatics (video, slides, poster) Peter Rose [P22]
16:18-16:23 Puzzle: VCF/GEMINI interface for genetic disease analysis (video, slides) Robin Andeer [P23]
16:24-16:29 Modernization of the Cytoscape ecosystem (video, slides, poster) Keiichiro Ono [P24]
16:30-16:35 Collaborative Software Development: Lessons from Open Source (video, slides) Abigail Cabunoc Mayes
16:35-16:40 Questions for lightning talk presenters
16:40-16:50 Concluding remarks Nomi Harris and Peter Cock
17:00-18:30 Birds of a Feather sessions (BOFs): Feel free to organize one! Sign up here.
19:00 Pay-your-own-way dinner, Marlow's Tavern, 9101 International Dr, Orlando

(Meet in Swan lobby at 6:20 to share rides)

(Limited space--you must RSVP to attend)

Posters

If a poster presenter also is giving a talk, the poster number will be in the schedule above (in square brackets after the talk title). The table below lists poster-only presentations.

Poster Title Presenter
P25 Lightweight sample labeling, barcoding and tracking systems for the academic laboratory Dimitra Sarantopoulou
P26 Kronos: a workflow assembler for genome analytics and informatics Jafar Taghiyar
P27 PhyPipe: an automated pipeline for phylogenetic reconstruction from multilocus sequences Javier Correa Alvarez
P28 BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data [walk-in] Andrey Kartashov
P29 Using the Nextflow framework for reproducible in-silico omics analyses across clouds and clusters Paolo Di Tommaso

We have a few spots for walk-in posters! Contact bosc @ open-bio.org if you'd like to present one.

BOSC 2016 Organizing Committee

Nomi Harris and Peter Cock (Co-Chairs)

Brad Chapman, Chris Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather Wiencko

BOSC 2016 Program Committee

Nomi Harris, Michael Heuer, Karen Cranston, Gianluca Della Vedova*, George Githinji, Christopher Fields, Hilmar Lapp*, Scott Markel, Frank Nothaft, Lorena Pantano, Michael Reich, Morgan Taschuk, Heather Wiencko*, Kai Blin*, Spencer Bliven*, Brad Chapman*, Michael Crusoe, Bastian Greshake*, Hans-Rudolf Hotz*, Herve Menager, Fiona Nielsen, Konstantin Okonechnikov, João Rodrigues*, Eric Talevich, Jason Williams, Melissa Wilson Sayres, Peter Cock*, Björn Grüning, Karsten Hokamp*, Amye Kenall, John Chilton, Konrad Förstner*, Jens Lichtenberg, Monica C Munoz-Torres

∗ Also reviewed Late-Breaking Lightning Talk abstracts

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 2017, please email bosc@open-bio.org.

Return to BOSC 2016 main page