BOSC 2015 Schedule

It is our hope to have all the posters and talk slides available on the BOSC F1000 Research Channel, with links to the talk videos. Note some speakers have already made their talks available separately on other services like SlideShare and FigShare, which is fine. Links to any slides, posters and videos will be added to this listing as well.

The full program including abstracts is available here. The PDF of this schedule (without abstracts) is available here.

Sponsors

We are grateful to Google for their generous support for videorecording BOSC 2015, and we thank Curoverse (the team behind the open source platform Arvados) as a returning sponsor and welcome Bina as our newest sponsor.

Pre-BOSC: Codefest 2015

See Codefest 2015 for details.

BOSC Day 1 (Friday, 10 July, 2015)

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 2015)
9:15-10:15	Keynote: Bioinformatics: Still a scary world for biologists (slides)	Holly Bik
10:15-10:45	Coffee Break
10:45-12:30	Session: Data Science	Chair: Rob Davey
10:45- 11:02	Apollo: Scalable & collaborative curation for improved comparative genomics	Mónica Muñoz-Torres [P1]
11:02-11:19	GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised learning of gene expression data	Kévin Rue-Albrecht (poster P2)
11:19-11:36	Arvados: A Free Software Platform for Big Data Science	Peter Amstutz
11:36-11:53	Bringing Hadoop into Bioinformatics with Cloudgene and CloudMan	Sebastian Schoenherr
11:53-12:10	Segway: semi-automated genome annotation	Michael Hoffman [P3]
12:10-12:15	QualiMap 2.0: quality control of high throughput sequencing data	Konstantin Okonechnikov [P4]
12:15-12:20	A Genomics Virtual Laboratory	Andrew Lonie [P5]
12:20-12:25	BioSolr: Building better search for bioinformatics	Tony Burdett [P6]
12:25-12:30	Prioritization of structural variants based on known biological information	Brad Chapman
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: Peter Cock
14:00-14:17	Portable workflow and tool descriptions with the CWL	Michael R. Crusoe [P7]
14:17-14:34	From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences (slides)	Alejandra Gonzalez-Beltran
14:34-14:51	Demystifying the Interoperability of Disparate Genomic Resources	Daniel Blankenberg
14:51-15:08	Increasing the utility of Galaxy workflows	John Chilton
15:10-15:15	Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers	Damion Dooley
15:15-15:20	Evolution of the Galaxy tool ecosystem - happier developers, happier users	Martin Čech [P8]
15:20-15:25	Bionode - Modular and universal bioinformatics (slides)	Bruno Vieira [P9]
15:25-15:30	The EDAM Ontology (poster)	Hervé Ménager [P10]
15:30-16:00	Coffee Break
16:00-17:00	Panel: Open Source, Open Door: increasing diversity in the bioinformatics open source community	Moderator: Mónica Muñoz-Torres Panelists: Holly Bik, Michael R. Crusoe, Aleksandra Pawlik, Jason Williams
17:00-17:10	Open Bioinformatics Foundation (OBF) Update	Hilmar Lapp (President, OBF)
17:10-17:15	Announcements	Nomi Harris
17:15-18:30	BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 1)	Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
17:15-18:30	BOFs: Feel free to organize one!
19:00-	Pay-your-own-way BOSC dinner at Kennedy's (FULL)	RSVP (limited space --you must RSVP to attend)

BOSC Day 2 (Saturday, 11 July, 2015)

Time	Title	Speaker / Chair
9:00-9:05	Announcements	Peter Cock and Nomi Harris
9:05-9:15	Codefest 2015 Report	Brad Chapman (Codefest 2015 Organizer)
9:15-10:15	Keynote: Big Data in Biology	Ewan Birney
10:15-10:45	Coffee Break
10:45-12:30	Session: Open Science and Reproducibility	Chair: Mónica Muñoz-Torres
10:45-11:02	A curriculum for teaching Reproducible Computational Science bootcamps	Hilmar Lapp
11:02-11:19	Research shared: www.researchobject.org (slides)	Norman Morrison [P11]
11:19-11:36	Nextflow: a tool for deploying reproducible computational pipelines (slides)	Paolo Di Tommaso [P12]
11:36-11:53	Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science (slides)	John Fonner [P13]
11:55-12:00	The 500 builds of 300 applications in the HeLmod repository will at least get you started on a full suite of scientific applications	Aaron Kitzmiller
12:00-12:05	Bioboxes: Standardised bioinformatics tools using Docker containers.	Peter Belmann [P14]
12:05-12:10	The perfect fit for reproducible interactive research: Galaxy, Docker, IPython	Björn Grüning
12:10-12:15	COPO: Bridging the Gap from Data to Publication in Plant Science (poster)	Robert Davey [P15]
12:15-12:20	ELIXIR UK building on Data and Software Carpentry to address the challenges in computational training for life scientists	Aleksandra Pawlik [P16]
12:20-12:25	Parallel recipes: towards a common coordination language for scientific workflow management systems	Yves Vandriessche [P17]
12:25-12:30	openSNP - personal genomics and the public domain (slides, poster)	Bastian Greshake [P18]
12:30-13:30	Lunch
13:00-14:00	Poster Session and BOFs (overlapping with lunch)
14:00-14:40	Session: Translational Bioinformatics	Chair: Brad Chapman
14:00-14:17	CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer	Malachi Griffith [P19]
14:17-14:34	From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep & Omics Pipe	Tobias Meissner [P20]
14:35-14:40	Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute	Ishwar Chandramouliswaran [P21]
14:40-15:30	Session: Bioinformatics Open Source Project Updates	Chair: Nomi Harris
14:40-14:57	Biopython Project Update 2015	João Rodrigues
14:57-15:14	Biogems: Challenges in distributed software development in bioinformatics (slides)	George Githinji and Pjotr Prins
15:14-15:31	Apache Taverna: Sustaining research software at the Apache Software Foundation (slideshare)	Stian Soiland-Reyes [P22]
15:30-16:00	Coffee Break
16:00-16:30	Session: Visualization	Chair: Karsten Hokamp
16:00-16:17	Simple, Shareable, Online RNA Secondary Structure Diagrams (slides, slides)	Peter Kerpedjiev
16:17-16:22	BioJS 2.0: an open source standard for biological visualization	Guy Yachdav [P23]
16:22-16:27	Visualising Open PHACTS linked data with widgets	Ian Dunlop [P24]
16:30-17:00	Session: Late-Breaking Lightning Talks	Chair: Hilmar Lapp
16:30-16:35	Biospectra-by-sequencing genetic analysis platform	Aurelie Laugraud [P25]
16:35-16:40	PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities	Shareef Dabdoub
16:40-16:45	Otter/ZMap/SeqTools: A productive alternative to web browser genome visualisation	Gemma Guest [P26]
16:45-16:50	BioaRchive: enabling reproducibility of Bioconductor package versions	Nitesh Turaga [P27]
16:50-16:55	Developing an Arvados BWA-GATK pipeline (slides)	Pjotr Prins [P28]
16:55-17:00	Out of the box cloud solution for Next-Generation Sequencing analysis	Freerk van Dijk [P29]
17:00-17:10	Concluding Remarks	Nomi Harris and Peter Cock
17:15-18:30	BOF/Unconference: Building successful open-source bioinformatics developer communities (Part 2)	Aidan Budd, Dave Clements, Manuel Corpas, Natasha Wood
17:10-18:10	BOFs: Feel free to organize one!
19:00	Pay-your-own-way dinner at the Workshop Gastropub. RSVP here if you want to join us.

Posters

If the speaker also has a talk, the poster link will be above (posters 1 to 29). This table lists poster-only presentations.

Poster	Title	Presenter
P30	Aequatus: Visualising complex similarity relationships among species	Anil Thanki
P31	MOLGENIS Workbench for Systems Medicine	K. Joeri van der Velde
P32	SPINGO: a rapid species-classifier for microbial amplicon sequences	Feargal Ryan
P33	ANNOgesic - A computational pipeline for RNA-Seq based transcriptome annotations of bacteria	Sung-Huan Yu
P34	BioXSD — a data model for sequences, alignments, features, measured and inferred values	Matúš Kalaš
P35	MGkit: A Metagenomic Framework For The Study Of Microbial Communities	Francesco Rubino
P36	From scaffold to submission in a day: a new software pipeline for rapid genome annotation and analysis	Sascha Steinbiss

BOSC 2015 Organizing Committee

Nomi Harris and Peter Cock (Co-Chairs)

Brad Chapman, Rob Davey, Chris Fields, Sarah Hird, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres

BOSC 2015 Program Committee

Nomi Harris, Brad Chapman, Peter Cock, Karsten Hokamp, Raoul Bonnal, Chris Fields, Karen Cranston, Jens Lichtenberg, Eric Talevich, Frank Nothaft, Michael Heuer, Mónica Muñoz-Torres, Francesco Strozzi, Hans-Rudolf Hotz, Timothy Booth, Tiago Antão, George Githinji, Manuel Corpas, Thomas Down, Sarah Hird, Scott Markel, Rob Davey, Spencer Bliven, Michael Reich, Lorena Pantano, Björn Grüning, Hilmar Lapp, Daniel Blankenberg, Amye Kenall, Hervé Menager

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 2016, please email email bosc@open-bio.org