BOSC 2015 Schedule

From Open Bioinformatics Foundation
Jump to: navigation, search
BOSC logo

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 are on the BOSC 2015 YouTube playlist.

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


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) and Open Access journal GigaScience as returning sponsors, and welcome Bina as our newest sponsor.

Curoverse logo
Arvados logo

Pre-BOSC: Codefest 2015

See Codefest 2015 for details, report given at the start of BOSC day two (slides, video).

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, video) 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 (video) 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 (slides, poster, video) Kévin Rue-Albrecht [P2]
11:19-11:36 Arvados: A Free Software Platform for Big Data Science (slides, video) Peter Amstutz
11:36-11:53 Bringing Hadoop into Bioinformatics with Cloudgene and CloudMan (slides, video) Sebastian Schoenherr
11:53-12:10 Segway: semi-automated genome annotation (video) Michael Hoffman [P3]
12:10-12:15 QualiMap 2.0: quality control of high throughput sequencing data (slides, video, poster) Konstantin Okonechnikov [P4]
12:15-12:20 A Genomics Virtual Laboratory (slides, video) Andrew Lonie [P5]
12:20-12:25 BioSolr: Building better search for bioinformatics (slides, video, poster) Tony Burdett [P6]
12:25-12:30 Prioritization of structural variants based on known biological information (slides, video) 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 (Common Workflow Language) (slides, video) 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, alt. slides, video) Alejandra Gonzalez-Beltran
14:34-14:51 Demystifying the Interoperability of Disparate Genomic Resources (slides, video) Daniel Blankenberg
14:51-15:08 Increasing the utility of Galaxy workflows (slides, video) John Chilton
15:10-15:15 Kipper: A software package for sequence database versioning for Galaxy bioinformatics servers (slides, video) Damion Dooley
15:15-15:20 Evolution of the Galaxy tool ecosystem - happier developers, happier users (slides, video) Martin Čech [P8]
15:20-15:25 Bionode - Modular and universal bioinformatics (slides, video) Bruno Vieira [P9]
15:25-15:30 The EDAM Ontology (slides, video, 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 (slides) 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; introduction video) 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 (slides, video) Brad Chapman (Codefest 2015 Organizer)
9:15-10:15 Keynote: Big Data in Biology (slides, video) 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 (slides, source, video) Hilmar Lapp
11:02-11:19 Research shared: (slides, video) Norman Morrison [P11]
11:19-11:36 Nextflow: a tool for deploying reproducible computational pipelines (slides, video, poster) Paolo Di Tommaso [P12]
11:36-11:53 Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science (slides, video, poster) 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 (slides, video) Aaron Kitzmiller
12:00-12:05 Bioboxes: Standardised bioinformatics tools using Docker containers. (slides, poster) Peter Belmann [P14]
12:05-12:10 The perfect fit for reproducible interactive research: Galaxy, Docker, IPython (video) Björn Grüning
12:10-12:15 COPO: Bridging the Gap from Data to Publication in Plant Science (slides, video, 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 (slides, video) Aleksandra Pawlik [P16]
12:20-12:25 Parallel recipes: towards a common coordination language for scientific workflow management systems (slides, video) Yves Vandriessche [P17]
12:25-12:30 openSNP - personal genomics and the public domain (slides, video, poster, 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 (slides, video, poster) Malachi Griffith [P19]
14:17-14:34 From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep & Omics Pipe (video, poster) Tobias Meissner [P20]
14:35-14:40 Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute (slides, video, poster) Ishwar Chandramouliswaran [P21]
14:40-15:30 Session: Bioinformatics Open Source Project Updates Chair: Nomi Harris
14:40-14:57 Biopython Project Update 2015 (slides, video) João Rodrigues
14:57-15:14 Biogems: Challenges in distributed software development in bioinformatics (slides, video) George Githinji and Pjotr Prins
15:14-15:31 Apache Taverna: Sustaining research software at the Apache Software Foundation (slides, video) 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 (slides, video) Guy Yachdav [P23]
16:22-16:27 Visualising Open PHACTS linked data with widgets (slides, video) 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 (slides, video, poster) Aurelie Laugraud [P25]
16:35-16:40 PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial communities (slides, video) 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 (slides, video, poster) Nitesh Turaga [P27]
16:50-16:55 Developing an Arvados BWA-GATK pipeline (slides, video, poster) Pjotr Prins [P28]
16:55-17:00 Out of the box cloud solution for Next-Generation Sequencing analysis (slides, video) 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.


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

Return to BOSC 2015 main page