BOSC 2014 Schedule

You can download the full program with abstracts (PDF), however this wiki page is considered the definitive schedule and will be updated with any last minute changes.

This year we have allocated all the talks an equal slot, 15 minutes plus 3 minutes for questions (making 18 minutes), except for the project update session where this is reduced to 10 minutes plus 2 minutes for questions (making 12 minutes in all). Lightning talks are 5 minutes only (no questions), and are intended for a brief introduction with the expectation that people who are interested in the topic will find the speaker during a break or poster session to talk with them.

We aim to record all the talks and the video links will be posted here, along with links to slides where available.

Pre-BOSC Codefest: July 9-10, 2014

See Codefest 2014 for details.

BOSC Day 1: Friday, 11 July 2014

Time	Topic	Speaker [Poster], Moderator, or notes
7:30-9:00	Registration	Early arrival is recommended as there are usually long lines
9:00-9:15	Introduction and Welcome	Nomi Harris and/or Peter Cock (Chairs, BOSC 2014)
9:15-10:15	Keynote: A History of Bioinformatics (in the Year 2039) (video, slideshare, notes)	C. Titus Brown
10:15-10:45	Coffee Break
10:45-12:30	Session: Genome-scale Data and Beyond	Chair: Chris Fields
10:45-11:03	[Genome-Scale] ADAM: Fast, Scalable Genomic Analysis (video)	Frank Austin Nothaft [P1]
11:03-11:21	[Genome-Scale] A Framework for Benchmarking RNA-seq Pipelines (video)	Rory Kirchner
11:21-11:39	[Genome-Scale] New Frontiers of Genome Assembly with SPAdes 3.1	Andrey Prjibelski [P2]
11:39-11:57	[Genome-Scale] SigSeeker: An Ensemble for Analysis of Epigenetic Data (video)	Jens Lichtenberg [P3]
11:57-12:15	[Genome-Scale] Galaxy as an Extensible Job Execution Platform	John Chilton
12:15-12:30	Open Bioinformatics Foundation (OBF) update	Hilmar Lapp (OBF President)
12:30-13:30	Lunch	(and poster session)
13:00-14:00	Poster Session and Birds of a Feather (overlapping with lunch)	Suggest a BOF topic here!
14:00-15:30	Session: Visualization	Chair: Rob Davey
14:00-14:18	[Visualization] WormGUIDES: an Interactive Informatic Developmental Atlas at Subcellular Resolution	Anthony Santella [P4]
14:18-14:36	[Visualization] BioJS: an Open Source Standard for Biological Visualisation	Manuel Corpas [P5]
14:36-14:54	[Visualization] Biodalliance: a Fast, Extensible Genome Browser	Thomas Down
14:54-15:12	[Visualization] TGAC Browser: Visualisation Solutions for Big Data in the Genomic Era (video)	Anil S. Thanki [P6]
15:12-15:30	[Visualization] Explore, Analyze, and Share Genomic Data Using Integrated Genome Browser	Ann Loraine
15:30-16:00	Coffee Break
16:00-17:00	Session: Bioinformatics Open Source Project Updates	Chair: Peter Cock
16:00-16:12	[Updates] BioMart 0.9 – Introducing Tools for Data Analysis and Visualisation (video)	Arek Kasprzyk
16:12-16:24	[Updates] Biocaml: The OCaml Bioinformatics Library (video)	Ashish Agarwal
16:24-16:36	[Updates] BioRuby and Distributed Development	Pjotr Prins
16:36-16:48	[Updates] Biopython Project Update (video)	Wibowo Arindrarto
16:48-17:00	[Updates] Shared Bioinformatics Databases Within Unipro UGENE	Ivan Protsyuk [P7]
17:00-17:30	Session: Lightning Talks	Chair: Peter Cock
17:00-17:05	[Lightning] Fostering the Next Generation of Data-driven Open Science with R (video)	Karthik Ram
17:07-17:12	[Lightning] Tripal: an Open Source Toolkit for Building Genomic and Genetic Data Websites and Databases	Margaret Staton
17:14-17:19	[Lightning] PLUTo: Phyloinformatic Literature Unlocking Tools (video)	Ross Mounce
17:21-17:26	[Lightning] A Publication Model that Aligns with the Key Open Source Software Principles (video)	Michael L. Markie [P8]
17:27-17:30	Announcements	Nomi Harris and/or Peter Cock
17:30-18:30	BOFs	Suggest a BOF topic here!
19:00	Pay-your-own-way Friday BOSC dinner (FULL) The Asgard Irish Pub and Restaurant, 350 Massachusetts Avenue, Cambridge, MA (1.2 miles north of the convention center).	Only those who have already RSVPed will be admitted.

BOSC Day 2: Saturday, 12 July 2014

Time	Topic	Speaker or Moderator
8:55-9:00	Announcements	Peter Cock and/or Nomi Harris (Chairs, BOSC 2014)
9:00-9:15	Codefest 2014 Report (video)	Brad Chapman
9:15-10:15	Keynote: Biomedical Research as an Open Digital Enterprise (slidesshare)	Philip Bourne
10:15-10:45	Coffee Break
10:45-12:30	Session: Software Interoperability	Chair: Raoul Bonnal
10:45-11:03	[Interoperability] Pathview: an R/Bioconductor Package for Pathway-based Data Integration and Visualization	Weijun Luo [P9]
11:03-11:21	[Interoperability] Use of Semantically Annotated Resources in the Mobyle2 Web Framework	Hervé Ménager
11:21-11:39	[Interoperability] Towards Ubiquitous OWL Computing: Simplifying Programmatic Authoring of and Querying with OWL Axioms	Hilmar Lapp
11:39-11:57	[Interoperability] Integrating Taverna Player into Scratchpads	Robert Haines [P10]
11:57-12:15	[Interoperability] Small Tools for Bioinformatics	Pjotr Prins
12:30-13:30	Lunch	(and poster session)
13:00-14:00	Poster Session and Birds of a Feather (overlapping with lunch)	Suggest a BOF topic here!
14:00-15:30	Session: Open Science and Reproducible Research	Chair: Hilmar Lapp
14:00-14:18	[Open Science] SEEK for Science: A Data Management Platform which Supports Open and Reproducible Science	Carole Goble [P11]
14:18-14:36	[Open Science] Arvados: Achieving Computational Reproducibility and Data Provenance in Large-Scale Genomic Analyses	Brett Smith
14:36-14:54	[Open Science] Enhancing the Galaxy Experience through Community Involvement	Daniel Blankenberg
14:54-15:12	[Open Science] Supporting Dynamic Community Developed Biological Pipelines	Brad Chapman
15:12-15:30	[Open Science] Open as a Strategy for Durability, Reproducibility and Scalability	Jonathan Rees
15:30-16:00	Coffee Break
16:00-17:00	Panel: Reproducibility: Rewards and Challenges	Moderator: Brad Chapman; Panelists: Phil Bourne, Titus Brown, Varsha Khodiyar, Kaitlin Thaney
17:00-17:10	Presentation of Student Travel Awards & Concluding Remarks	Nomi Harris (Co-Chair, BOSC 2014)
17:10-18:00	BOFs	Suggest a BOF topic here!
19:00	Pay-your-own-way BOSC Saturday dinner: Summer Shack, 50 Dalton St., Boston	Dinner now FULL. If you RSVPed yes but can't attend, please edit your RSVP

Note: the ISMB reception starts at 17:30...

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Posters

If the speaker also gave a talk, any poster link will be above (posters 1 to 11). This table lists poster-only presentations.

Poster	Title	Presenter
P12	Advantages and challenges of using the Galaxy API within an integrated data analysis and visualization platform	Ilya Sytchev
P13	Connecting computational steps for NGS, and beyond.	Laurent Gautier
P14	Updates to MISO, the open-source NGS LIMS project	Xingdong Bian
P15	Running Taverna Workflows within IPython Notebook	Alan Williams / Aleksandra Pawlik (TBC)
P16	Reconstruction of ancestral genomes in presence of gene gain and loss	Shuai Jiang
P17	Withdrawn	Withdrawn
P18	GEPETTO Update: An Open Source Framework for Gene Prioritization	Hoan Nguyen
P19	NeoPipe: An Open Source Framework for Protein sequence analysis	Hoan Nguyen
P20	MyGene.info updates: scalable gene-centric web services with user contributions	Chunlei Wu
P21	Aiding the journey from data to publication in the plant sciences	Robert Davey
P22	Bio2RDF mobile: an app for biological semantic web databases	Maxime Déraspe
P24	BioBuilds: A Model for Long Term Sustainability of Open Source Bioinformatics	Chris Mueller
P25	GigaGalaxy: A GigaSolution for reproducible and sustainable genomic data publication and analysis	Scott Edmunds
...	...	...

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We thank Eagle Genomics for sponsoring the BOSC Student Travel Awards again this year, and welcome the open access journal GigaScience, and Curoverse (the team behind the open source platform Arvados) as new sponsors for BOSC 2014.

We are grateful to Google for their generous support for videorecording BOSC 2014.

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