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Difference between revisions of "BOSC 2016 Schedule"

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(BOSC Day 2 (Saturday, July 9, 2016))
(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 ==
 +
 
 +
We are grateful to [http://curoverse.com Curoverse] (the team behind the open source platform [http://arvados.org Arvados]) as returning sponsors for BOSC 2016,
 +
{|
 +
| [[File:Curoverse_logo.png|175px|center|Curoverse logo|link=http://curoverse.com]]
 +
|-
 +
| [[File: Arvados.png|150px|center|Arvados logo|link=http://arvados.org]]
 +
|}
  
 
== Pre-BOSC: Codefest 2016  ==
 
== Pre-BOSC: Codefest 2016  ==
  
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 [Poster] / 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
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|10:45-12:30
 
|10:45-12:30
 
|'''Session: Workflows'''
 
|'''Session: Workflows'''
|Chair: TBA
+
|Chair: Brad Chapman
 
|-
 
|-
|10:45- 11:02
+
|10:45-11:03
|
+
|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 [P1]
 
|-
 
|-
|11:02-11:19
+
|11:03-11:21
|
+
|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 [P2]
 
|-
 
|-
|11:19-11:36
+
|11:21-11:39
|
+
|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 [P3]
 
|-
 
|-
|11:36-11:53
+
|11:39-11:57
|
+
|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
 
|-
 
|-
|11:53-12:10
+
|11:57-12:15
|
+
|Planemo – A Scientific Workflow SDK ([https://youtu.be/kVa-oWxWDww video], [http://f1000research.com/slides/5-1742 slides])
|
+
|John Chilton
|-
 
|12:10-12:15
 
|
 
|
 
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
|
+
|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
 
|-
 
|-
|12:20-12:25
+
|12:21-12:26
|
+
|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 [P4]
 
|-
 
|-
|12:25-12:30
+
|12:26-12:30
|
+
|Questions for lightning talk speakers in this session
 
|
 
|
 
|- style="background:#F7F8E0"
 
|- style="background:#F7F8E0"
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|-
 
|-
 
|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"
 
|14:00-15:30
 
|14:00-15:30
 
|'''Session: Standards and Interoperability'''
 
|'''Session: Standards and Interoperability'''
|Chair:  
+
|Chair: Hilmar Lapp
 
|-
 
|-
|14:00-14:17
+
|14:00-14:18
|
+
|Enhancements to MISO: An open-source community-driven LIMS ([https://youtu.be/znrRsPip5D0 video], [http://f1000research.com/slides/5-1608 slides])
|
+
|Andre Masella
 
|-
 
|-
|14:17-14:34
+
|14:18-14:36
|
+
|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 [P5]
 
|-
 
|-
|14:34-14:51
+
|14:36-14:54
|
+
|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 [P6]
 
|-
 
|-
|14:51-15:08
+
|14:54-15:12
|
+
|Processing phenotype data using Phenopackets-API and PXFTools ([https://youtu.be/8UreKE1eGNY video], [http://f1000research.com/slides/5-1649 slides])
|
+
|Chris Mungall
 
|-
 
|-
|15:10-15:15
+
|15:12-15:17
|
+
|Promoting platform interoperability with portable bcbio workflows ([https://youtu.be/kMoAWjHhOVc video], [http://f1000research.com/slides/5-1639 slides])
|
+
|Brad Chapman
 
|-
 
|-
|15:15-15:20
+
|15:18-15:23
|
+
|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 [P8]
 
|-
 
|-
|15:20-15:25
+
|15:24-15:29
|
+
|Questions for lightning talks in this session
 
|
 
|
 
|-
 
|-
|15:25-15:30
 
|
 
|
 
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
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|- style="background:#EFFBFB"
 
|- style="background:#EFFBFB"
 
|16:00-17:00
 
|16:00-17:00
|Panel: Growing and sustaining open source communities
+
|[[BOSC_2016_Panel|Panel: Growing and sustaining open source communities]]
 
|'''''Moderator''''': Mónica Muñoz-Torres
 
|'''''Moderator''''': Mónica Muñoz-Torres
  
'''''Panelists''''':  John Chilton, Bastian Greshake, Abigail Cabunoc Mayes, Jamie Whitacre, 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 (or do Sat. morning?)
+
|Open Bioinformatics Foundation (OBF) Update
|
+
|Hilmar Lapp
 
|-
 
|-
 
|17:10-17:15
 
|17:10-17:15
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|-
 
|-
 
|17:15-18:30
 
|17:15-18:30
|'''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 BOSC dinner (TBA)
+
| 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 / Chair'''
+
!'''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|9:00-9:05
 
|9:00-9:05
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|-
 
|-
 
|9:05-9:15
 
|9:05-9:15
|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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|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
 
|10:45-12:30
 
|10:45-12:30
|Session: ''''Data Science''''
+
|'''Session: Data Science'''
|
+
| Chair: Heather Wiencko
 
|-
 
|-
|10:45-11:02
+
|10:45-11:03
|
+
|Mango: Data Exploration on Large Genomic Datasets ([https://youtu.be/67og0xCZxZ4 video])
|
+
|Alyssa Morrow [P9]
 
|-
 
|-
|11:02-11:19
+
|11:03-11:21
|
+
|ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets ([https://youtu.be/su_oltymp78 video])
|
+
|Frank Nothaft
 
|-
 
|-
|11:19-11:36
+
|11:21-11:39
|
+
|SUPERSMART - A Self-Updating platform for Estimating Rates of Speciation and Migration, Ages, and<br>Relationships of Taxa
|
+
|Hannes Hettling
|-
 
|11:36-11:53
 
|
 
|
 
 
|-
 
|-
|11:55-12:00
+
|11:39-11:57
|
+
|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
 
|-
 
|-
|12:00-12:05
+
|11:57-12:15
|
+
|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 [P10]
|-
 
|12:05-12:10
 
|
 
|
 
|-
 
|12:10-12:15
 
|
 
|
 
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
|
+
|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 [P11]
 
|-
 
|-
|12:20-12:25
+
|12:21-12:26
|
+
|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 [P12]
|-
 
|12:25-12:30
 
|
 
|
 
 
|- 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"
 
|14:00-14:40
 
|14:00-14:40
|'''Session: Developer tools and libraries''
+
|'''Session: Developer tools and libraries'''
 
|Chair: Chris Fields
 
|Chair: Chris Fields
 
|-
 
|-
|14:00-14:17
+
|14:00-14:18
|
+
|Biopython Project Update 2016 ([https://youtu.be/JxOm1Bjyt9M video], [http://f1000research.com/slides/5-1712 slides])
|
+
|Christian Brueffer
 +
|-
 +
|14:18-14:23
 +
|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])
 +
|Peter Humburg [P19]
 +
|-
 +
|14:24-14:29
 +
|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 [P14]
 
|-
 
|-
|14:17-14:34
+
|14:30-14:35
|
+
|SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata ([https://youtu.be/Y1Dp72hDg0w video])
|
+
|Benjamin Hitz [P15]
 
|-
 
|-
|14:35-14:40
+
| 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
|'''Session: Open Science and Reproducibility''
+
|'''Session: Open Science and Reproducibility'''
|Chair:  
+
|Chair: Peter Cock
 
|-
 
|-
|14:40-14:57
+
|14:40-14:58
|
+
|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 [P16]
 +
|-
 +
|14:58-15:16
 +
|The GenePattern Notebook Environment ([https://youtu.be/dIhFMceSETU video], [http://f1000research.com/posters/5-1900 poster])
 +
|Michael Reich [P17]
 +
|-
 +
|15:16-15:21
 +
|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
 
|-
 
|-
|14:57-15:14
+
|15:22-15:27
|
+
|Reproducible Research in the Cloud with the Refinery Platform ([https://youtu.be/dX9En3GvtDk video])
|
+
|Nils Gehlenborg [P18]
 
|-
 
|-
|15:14-15:31
+
|15:28-15:33
|
+
| Questions for lightning talk speakers in Open Science and Reproducibility session
 
|
 
|
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
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|
 
|
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
|16:00-16:30
+
|16:00-17:00
 
|'''Session: Late-Breaking Lightning Talks'''
 
|'''Session: Late-Breaking Lightning Talks'''
|
+
| Chair: Karsten Hokamp
 +
|-
 +
|16:00-16:05
 +
|Apollo Genome Annotation Editor: Latest Updates, Including Galaxy Integration ([https://youtu.be/NNqnAZE1ZOE video])
 +
|Mónica C. Muñoz-Torres [P20]
 +
|-
 +
|16:06-16:11
 +
|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 [P21]
 
|-
 
|-
|16:00-16:17
+
|16:12-16:17
|
+
|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 [P22]
 
|-
 
|-
|16:17-16:22
+
|16:18-16:23
|
+
|Puzzle: VCF/GEMINI interface for genetic disease analysis ([https://youtu.be/JKI_taSh5D8 video], [http://f1000research.com/slides/5-1816 slides])
|
+
|Robin Andeer [P23]
 
|-
 
|-
|16:22-16:27
+
|16:24-16:29
|
+
|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 [P24]
|- style="background:#E6E6E6"
 
|16:30-17:00
 
|'''Session: Late-Breaking Lightning Talks'''
 
|
 
 
|-
 
|-
 
|16:30-16:35
 
|16:30-16:35
|
+
|Collaborative Software Development: Lessons from Open Source ([https://youtu.be/1af4M0xK7_4 video], [http://f1000research.com/slides/5-1660 slides])
|
+
|Abigail Cabunoc Mayes
 
|-
 
|-
 
|16:35-16:40
 
|16:35-16:40
|
+
|Questions for lightning talk presenters
|
 
|-
 
|16:40-16:45
 
|
 
|
 
|-
 
|16:45-16:50
 
|
 
|
 
|-
 
|16:50-16:55
 
|
 
 
|
 
|
 
|-
 
|-
|16:55-17:00
+
|16:40-16:50
 
|Concluding remarks
 
|Concluding remarks
 
|Nomi Harris and Peter Cock
 
|Nomi Harris and Peter Cock
 
|-
 
|-
 
|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 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 321: Line 321:
 
! Presenter
 
! Presenter
 
|-
 
|-
| P30
+
| P25
|  
+
| Lightweight sample labeling, barcoding and tracking systems for the academic laboratory
|  
+
| Dimitra Sarantopoulou
 +
|-
 +
| P26
 +
| [http://f1000research.com/posters/5-1912 Kronos: a workflow assembler for genome analytics and informatics]
 +
| Jafar Taghiyar
 +
|-
 +
| P27
 +
| [http://f1000research.com/posters/5-1609 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 ==
 
== BOSC 2016 Organizing Committee ==
Line 335: Line 353:
 
== BOSC 2016 Program Committee ==  
 
== 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
+
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
 +
 
 +
&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.
  
If you are interested in helping to organize BOSC 2017, please email bosc@open-bio.org
+
If you are interested in helping to organize BOSC 2017, please email bosc@open-bio.org.
  
 
== Return to [[BOSC 2016]] main page ==
 
== Return to [[BOSC 2016]] main page ==

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