BOSC 2016 Schedule

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Revision as of 10:45, 18 July 2016 by Peter (talk | contribs) (BOSC Day 2 (Saturday, July 9, 2016): Codefest report video)

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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 will be on the BOSC 2016 YouTube playlist.

The full program including abstracts is available.


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 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? (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) John Chilton
12:15-12:20 Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics (video) 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) 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 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 (slides) Lorena Pantano Rubino
11:57-12:15 MetaR: simple, high-level languages for data analysis with the R ecosystem (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 (slides) 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 (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 (slides) Christian Brueffer
14:18-14:23 ReportMD: Writing complex scientific reports in R (poster) Peter Humburg [P19]
14:24-14:29 Linuxbrew and Homebrew-Science to Navigate the Software Dependency Labyrinth (slides) Shaun Jackman [P14]
14:30-14:35 SnoVault and encodeD: A novel object-based storage system and applications to ENCODE metadata Benjamin Hitz [P15]
14:35-14:40 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 Union: Dockerizing, Crowdfunding & Opening for Contributors (slides) 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 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 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 (slides) Robin Andeer [P23]
16:24-16:29 Modernization of the Cytoscape ecosystem (slides, poster) Keiichiro Ono [P24]
16:30-16:35 Collaborative Software Development: Lessons from Open Source (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)


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 @ 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

Return to BOSC 2016 main page