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Difference between revisions of "BOSC 2016 Schedule"

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(→‎BOSC 2016 Program Committee)
(Poster numbers as P1 not just 1)
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!'''Time'''
 
!'''Time'''
 
!'''Title'''
 
!'''Title'''
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!'''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|7:30-9:00
 
|7:30-9:00
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|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
−
|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
−
|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
−
|Dan Leehr [3]
+
|Dan Leehr [P3]
 
|-
 
|-
 
|11:39-11:57
 
|11:39-11:57
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|12:09-12:14
 
|12:09-12:14
 
|NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
 
|NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts
−
|Fabien Campagne [4]
+
|Fabien Campagne [P4]
 
|-
 
|-
 
|12:15-12:20
 
|12:15-12:20
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|14:18-14:36
 
|14:18-14:36
 
|Biothings APIs: high-performance bioentity-centric web services
 
|Biothings APIs: high-performance bioentity-centric web services
−
|Chunlei Wu [5]
+
|Chunlei Wu [P5]
 
|-
 
|-
 
|14:36-14:54
 
|14:36-14:54
 
|The Noctua Modeling Tool
 
|The Noctua Modeling Tool
−
|Seth Carbon [6]
+
|Seth Carbon [P6]
 
|-
 
|-
 
|14:54-15:12
 
|14:54-15:12
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|15:12-15:17
 
|15:12-15:17
 
|The EDAM Ontology
 
|The EDAM Ontology
−
|Jon Ison [7]
+
|Jon Ison [P7]
 
|-
 
|-
 
|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
−
|John Bradley [8]
+
|John Bradley [P8]
 
|-
 
|-
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
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!'''Time'''
 
!'''Time'''
 
!'''Title'''
 
!'''Title'''
−
!'''Speaker or Session Chair'''
+
!'''Speaker [Poster] / Chair'''
 
|-
 
|-
 
|9:00-9:05
 
|9:00-9:05
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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
−
|Alyssa Morrow [9]
+
|Alyssa Morrow [P9]
 
|-
 
|-
 
|11:03-11:21
 
|11:03-11:21
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|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
−
|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
−
|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<br>gene regulatory networks
−
|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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|14:18-14:23
 
|14:18-14:23
 
|Sequenceserver: a modern graphical user interface for custom BLAST databases
 
|Sequenceserver: a modern graphical user interface for custom BLAST databases
−
|Anurag Priyam [13]
+
|Anurag Priyam [P13]
 
|-
 
|-
 
|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
−
|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
−
|Benjamin Hitz [15]
+
|Benjamin Hitz [P15]
 
|- style="background:#E6E6E6"
 
|- style="background:#E6E6E6"
 
|14:40-15:30
 
|14:40-15:30
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|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
−
|Bastian Greshake [16]
+
|Bastian Greshake [P16]
 
|-
 
|-
 
|14:58-15:16
 
|14:58-15:16
 
|The GenePattern Notebook Environment
 
|The GenePattern Notebook Environment
−
|Michael Reich [17]
+
|Michael Reich [P17]
 
|-
 
|-
 
|15:16-15:21
 
|15:16-15:21
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|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
−
|Nils Gehlenborg [18]
+
|Nils Gehlenborg [P18]
 
|-
 
|-
 
|15:28-15:33
 
|15:28-15:33
 
|ReportMD: Writing complex scientific reports in R
 
|ReportMD: Writing complex scientific reports in R
−
|Peter Humburg [19]
+
|Peter Humburg [P19]
 
|- style="background:#FAF4EE"
 
|- style="background:#FAF4EE"
 
|15:30-16:00
 
|15:30-16:00
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|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
−
|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
−
|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
−
|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
−
|Robin Andeer [23]
+
|Robin Andeer [P23]
 
|-
 
|-
 
|16:24-16:29
 
|16:24-16:29
 
|Modernization of the Cytoscape ecosystem
 
|Modernization of the Cytoscape ecosystem
−
|Keiichiro Ono [24]
+
|Keiichiro Ono [P24]
 
|-
 
|-
 
|16:30-16:35
 
|16:30-16:35
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! 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
 
| 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
 
| 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
 
| Skip the line and balance your work with vQ
 
| Gregory Zynda
 
| Gregory Zynda

Revision as of 14:10, 20 June 2016

BOSC logo

The full program including abstracts will be available soon.

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) 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.

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? 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 Ted Liefeld [P1]
11:03-11:21 This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language Michael R. Crusoe [P2]
11:21-11:39 CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language Dan Leehr [P3]
11:39-11:57 Using the Common Workflow Language (CWL) to run portable workflows with Arvados and Toil Peter Amstutz
11:57-12:02 Planemo – A Scientific Workflow SDK John Chilton
12:03-12:08 Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics Daniel Blankenberg
12:09-12:14 NextflowWorkbench: Reproducible and Reusable Workflows for Beginners and Experts Fabien Campagne [P4]
12:15-12:20 Promoting platform interoperability with portable bcbio workflows Brad Chapman
12:20-12:25 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)
14:00-15:30 Session: Standards and Interoperability Chair: Hilmar Lapp
14:00-14:18 Enhancements to MISO: An open-source community-driven LIMS Andre Masella
14:18-14:36 Biothings APIs: high-performance bioentity-centric web services Chunlei Wu [P5]
14:36-14:54 The Noctua Modeling Tool Seth Carbon [P6]
14:54-15:12 Processing phenotype data using Phenopackets-API and PXFTools Chris Mungall
15:12-15:17 The EDAM Ontology Jon Ison [P7]
15:18-15:23 Towards traceable, scriptable, and efficient data distribution for next-generation genomics John Bradley [P8]
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
17:10-17:15 Announcements Nomi Harris
17:15-18:30 Bird 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)

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 Brad Chapman (Codefest Organizer)
9:15-10:15 Keynote: Open source, open access, and open data: why science moves faster in an open world 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 Alyssa Morrow [P9]
11:03-11:21 ADAM Enables Distributed Analyses Across Large Scale Genomic Datasets 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 Lorena Pantano Rubino
11:57-12:15 MetaR: simple, high-level languages for data analysis with the R ecosystem Fabien Campagne [P10]
12:15-12:20 Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data 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 		Kam D. Dahlquist [P12]
12:30-13:30 Lunch
13:00-14:00 Poster Session and BOFs (overlapping with lunch)
14:00-14:40 Session: Developer tools and libraries Chair: Chris Fields
14:00-14:18 Biopython Project Update 2016 Christian Brueffer
14:18-14:23 Sequenceserver: a modern graphical user interface for custom BLAST databases Anurag Priyam [P13]
14:24-14:29 Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth Shaun Jackman [P14]
14:30-14:35 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata Benjamin Hitz [P15]
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 Bastian Greshake [P16]
14:58-15:16 The GenePattern Notebook Environment Michael Reich [P17]
15:16-15:21 Reproducibility in computationally intensive workflows with continuous analysis Brett K Beaulieu-Jones
15:22-15:27 Reproducible Research in the Cloud with the Refinery Platform Nils Gehlenborg [P18]
15:28-15:33 ReportMD: Writing complex scientific reports in R Peter Humburg [P19]
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 Mónica C. Muñoz-Torres [P20]
16:06-16:11 An invitation to the bioinformatics community to participate in the HUBzero® open source release Michael Zentner [P21]
16:12-16:17 PDB on steroids – compressive structural bioinformatics Peter Rose [P22]
16:18-16:23 Puzzle: VCF/GEMINI interface for genetic disease analysis Robin Andeer [P23]
16:24-16:29 Modernization of the Cytoscape ecosystem Keiichiro Ono [P24]
16:30-16:35 Collaborative Software Development: Lessons from Open Source 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 BOFs: Feel free to organize one!
19:00 Pay-your-own-way dinner (TBA)

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.

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 Skip the line and balance your work with vQ Gregory Zynda

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

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