BOSC 2016 Schedule

The full program including abstracts is available here.

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) 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) (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	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	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)	(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	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 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	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	Birds of a Feather sessions (BOFs): Feel free to organize one! Sign up here.
19:00	Pay-your-own-way dinner, Marlow's Tavern	(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	Skip the line and balance your work with vQ	Gregory Zynda
P29	Using the Nextflow framework for reproducible in-silico omics analyses across clouds and clusters	Paolo Di Tommaso

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.