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Difference between revisions of "BOSC 2016 Schedule"
From Open Bioinformatics Foundation
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[[File:Pear.png|120px|right|BOSC logo|link=BOSC_2016]] | [[File:Pear.png|120px|right|BOSC logo|link=BOSC_2016]] | ||
| − | 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 | + | 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. | The [https://www.open-bio.org/w/images/2/24/BOSC2016-program4.pdf full program including abstracts] is available. | ||
| Line 17: | Line 17: | ||
== Pre-BOSC: Codefest 2016 == | == 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 | + | 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) == | ||
| Line 48: | Line 48: | ||
|- | |- | ||
|10:45-11:03 | |10:45-11:03 | ||
| − | |GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes ([http://f1000research.com/slides/5-1633 slides], [http://f1000research.com/posters/5-1634 poster]) | + | |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] | |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 ([http://f1000research.com/slides/5-1622 slides]) | + | |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] | |Michael R. Crusoe [P2] | ||
|- | |- | ||
|11:21-11:39 | |11:21-11:39 | ||
| − | |CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language ([http://f1000research.com/slides/5-1617 slides], [http://f1000research.com/posters/5-1615 poster]) | + | |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] | |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 ([http://f1000research.com/slides/5-1624 slides]) | + | |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 | ||
|- | |- | ||
|11:57-12:15 | |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 | ||
|- | |- | ||
|12:15-12:20 | |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 | ||
|- | |- | ||
|12:21-12:26 | |12:21-12:26 | ||
| − | |NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts ([https://prezi.com/qbn8ys1oa5fm/nextflowworkbench-bosc-2016/ slides], [http://f1000research.com/posters/5-1651 poster]) | + | |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] | |Fabien Campagne [P4] | ||
|- | |- | ||
| Line 93: | Line 93: | ||
|- | |- | ||
|14:00-14:18 | |14:00-14:18 | ||
| − | |Enhancements to MISO: An open-source community-driven LIMS ([http://f1000research.com/slides/5-1608 slides]) | + | |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 ([http://www.slideshare.net/ChunleiWu/biothings-apis-highperformance-bioentitycentric-web-services slides]) | + | |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] | |Chunlei Wu [P5] | ||
|- | |- | ||
|14:36-14:54 | |14:36-14:54 | ||
| − | |The Noctua Modeling Tool ([http://f1000research.com/slides/5-1678 slides], [http://f1000research.com/posters/5-1677 poster]) | + | |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] | |Seth Carbon [P6] | ||
|- | |- | ||
|14:54-15:12 | |14:54-15:12 | ||
| − | |Processing phenotype data using Phenopackets-API and PXFTools ([http://f1000research.com/slides/5-1649 slides]) | + | |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 | ||
| − | |Promoting platform interoperability with portable bcbio workflows ([http://f1000research.com/slides/5-1639 slides]) | + | |Promoting platform interoperability with portable bcbio workflows ([https://youtu.be/kMoAWjHhOVc video], [http://f1000research.com/slides/5-1639 slides]) |
|Brad Chapman | |Brad Chapman | ||
|- | |- | ||
|15:18-15:23 | |15:18-15:23 | ||
| − | |Towards traceable, scriptable, and efficient data distribution for next-generation genomics ([http://f1000research.com/slides/5-1623 slides], [http://f1000research.com/posters/5-1625 poster]) | + | |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] | |John Bradley [P8] | ||
|- | |- | ||
| Line 133: | Line 133: | ||
|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 161: | Line 161: | ||
|- | |- | ||
|9:05-9:15 | |9:05-9:15 | ||
| − | |[[Codefest_2016|Codefest 2016]] Report ([http://f1000research.com/slides/5-1640 slides]) | + | |[[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'' ([https://youtu.be/TYmpxLHy_UM video]) | + | |'''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]) |
|[https://www.open-bio.org/wiki/BOSC_2016_Keynote_Speakers Steven Salzberg] | |[https://www.open-bio.org/wiki/BOSC_2016_Keynote_Speakers Steven Salzberg] | ||
|- style="background:#FAF4EE" | |- style="background:#FAF4EE" | ||
| Line 177: | Line 177: | ||
|- | |- | ||
|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 [P9] | |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 189: | Line 189: | ||
|- | |- | ||
|11:39-11:57 | |11:39-11:57 | ||
| − | |Characterization of the small RNA transcriptome using the bcbio-nextgen python framework ([http://f1000research.com/slides/5-1627 slides]) | + | |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 ([https://prezi.com/x6nhbkext0ga/metar-bosc-2016/ slides], [http://f1000research.com/posters/5-1652 poster]) | + | |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] | |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 ([http://f1000research.com/slides/5-1650 slides]) | + | |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] | |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 gene regulatory networks ([http://f1000research.com/slides/5-1637 slides], [http://f1000research.com/posters/5-1618 poster]) | + | |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] | |Kam D. Dahlquist [P12] | ||
|- style="background:#F7F8E0" | |- style="background:#F7F8E0" | ||
| Line 218: | Line 218: | ||
|- | |- | ||
|14:00-14:18 | |14:00-14:18 | ||
| − | |Biopython Project Update 2016 ([http://f1000research.com/slides/5- | + | |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 | ||
| − | |ReportMD: Writing complex scientific reports in R ([http://f1000research.com/posters/5-1647 poster]) | + | |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] | |Peter Humburg [P19] | ||
|- | |- | ||
|14:24-14:29 | |14:24-14:29 | ||
| − | |Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth ([http://sjackman.ca/linuxbrew-slides/#/ slides]) | + | |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] | |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 [P15] | |Benjamin Hitz [P15] | ||
|- | |- | ||
| Line 242: | Line 242: | ||
|- | |- | ||
|14:40-14:58 | |14:40-14:58 | ||
| − | |State of the openSNP.org Union: Dockerizing, Crowdfunding & Opening for Contributors ([http://f1000research.com/slides/5-1643 slides]) | + | |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] | |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 [P17] | |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 [P18] | |Nils Gehlenborg [P18] | ||
|- | |- | ||
| Line 270: | 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 [P20] | |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 [P21] | |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 [P22] | |Peter Rose [P22] | ||
|- | |- | ||
|16:18-16:23 | |16:18-16:23 | ||
| − | |Puzzle: VCF/GEMINI interface for genetic disease analysis ([https:// | + | |Puzzle: VCF/GEMINI interface for genetic disease analysis ([https://youtu.be/JKI_taSh5D8 video], [http://f1000research.com/slides/5-1816 slides]) |
|Robin Andeer [P23] | |Robin Andeer [P23] | ||
|- | |- | ||
|16:24-16:29 | |16:24-16:29 | ||
| − | |Modernization of the Cytoscape ecosystem ([http://f1000research.com/slides/5-1661 slides], [http://f1000research.com/posters/5-1662 poster]) | + | |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] | |Keiichiro Ono [P24] | ||
|- | |- | ||
|16:30-16:35 | |16:30-16:35 | ||
| − | |Collaborative Software Development: Lessons from Open Source ([http://f1000research.com/slides/5-1660 slides]) | + | |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 | ||
|- | |- | ||
| Line 326: | Line 326: | ||
|- | |- | ||
| P26 | | 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 | ||
|- | |- | ||
Latest revision as of 04:02, 21 May 2017
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,
 |
 |
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.
