Difference between revisions of "BOSC 2016 Schedule"

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(Accidentally gave a lightning talk 6 min instead of 5)
(Curoverse sponsors BOSC 2016)
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The full program including abstracts will be available soon.
The full program including abstracts will be available soon.
== 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  ==

Revision as of 11:31, 15 June 2016

BOSC logo

The full program including abstracts will be available soon.


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 or Session 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
11:03-11:21 This is Why We Can Have Nice Things: Getting to 1.0 of the Common Workflow Language Michael R. Crusoe
11:21-11:39 CWL in Practice: Experiences, challenges, and results from adopting Common Workflow Language Dan Leehr
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
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
14:36-14:54 The Noctua Modeling Tool Seth Carbon
14:54-15:12 Processing phenotype data using Phenopackets-API and PXFTools Chris Mungall
15:12-15:17 The EDAM Ontology Jon Ison
15:18-15:23 Towards traceable, scriptable, and efficient data distribution for next-generation genomics John Bradley
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 BOFs: Feel free to organize one!
19:00 Pay-your-own-way dinner (TBA)

BOSC Day 2 (Saturday, July 9, 2016)

Time Title Speaker or Session 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
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
12:15-12:20 Development of NGSEP as an open-source comprehensive solution for analysis of high throughput sequencing data Jorge Duitama
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
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
14:24-14:29 Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth Shaun Jackman
14:30-14:35 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata Benjamin Hitz
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
14:58-15:16 The GenePattern Notebook Environment Michael Reich
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
15:28-15:33 ReportMD: Writing complex scientific reports in R Peter Humburg
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
16:06-16:11 MoCA : A Tool for Motif Conservation Analysis Saket Choudhary
16:12-16:17 PDB on steroids – compressive structural bioinformatics Peter Rose
16:18-16:23 Puzzle: VCF/GEMINI interface for genetic disease analysis Robin Andeer
16:24-16:29 Modernization of the Cytoscape ecosystem Keiichiro Ono
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)


If a poster presenter also is giving a talk, the poster link will be above. The table below lists poster-only presentations.

Poster Title Presenter

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

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