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Revision as of 19:56, 23 May 2015

Bioinformatics Open Source Conference (BOSC) 2015

File:Media/image1.pngA Special Interest Group (SIG) meeting at ISMB/ECCB 2015

Dublin, Ireland

July 10-11, 2015

http://www.open-bio.org/wiki/BOSC_2015

BOSC is organized by the Open Bioinformatics Foundation (OBF, www.open-bio.org). The OBF is a non-profit group that promotes the practice and philosophy of Open Source software development and Open Science in the biological research community.

Curoverse logo.png Google-logo11w.png Arvados.png Gigascience-07.png

Schedule for Day 1 (Friday, 10 July, 2015)

Time Title Speaker / 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 Holly Bik
10:15-10:45 Coffee Break
10:45-12:30 Session: Data Science Chair:
10:45- 11:02 Apollo: Scalable & collaborative curation for improved comparative genomics Mónica Muñoz-Torres
11:02-11:19 GOexpress: A R/Bioconductor package for the identification and visualisation of robust gene ontology signatures through supervised clustering of gene expression data Kévin Rue-Albrecht
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
12:10-12:15 QualiMap 2.0: quality control of high throughput sequencing data Konstantin Okonechnikov
12:15-12:20 A Genomics Virtual Laboratory Andrew Lonie
12:20-12:25 BioSolr: Building better search for bioinformatics Tony Burdett
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 (overlapping with lunch)
14:00-15:30 Session: Standards and Interoperability Chair:
14:00-14:17 Portable workflow and tool descriptions with the CWL Michael R. Crusoe
14:17-14:34 From peer-reviewed to peer-reproduced: a role for research objects in scholarly publishing in the life sciences 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
15:20-15:25 Bionode - Modular and universal bioinformatics Bruno Vieira
15:25-15:30 The EDAM Ontology Hervé Ménager
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 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
19:00- Pay-your-own-way BOSC dinner, Kennedy’s [link] RSVP at bit.ly/BOSC2015-dinner (limited space --you must RSVP to attend)

Schedule for Day 2 (Saturday, 11 July, 2015)

Time Title Speaker or

Session 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:
10:45-11:02 A curriculum for teaching Reproducible Computational Science bootcamps Hilmar Lapp
11:02-11:19 Research shared: www.researchobject.org Norman Morrison
11:19-11:36 Nextflow: a tool for deploying reproducible computational pipelines Paolo Di Tommaso
11:36-11:53 Free beer today: how iPlant + Agave + Docker are changing our assumptions about reproducible science John Fonner
11:55 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 Bioboxes: Standardised bioinformatics tools using Docker containers. Peter Belmann
12:05 The perfect fit for reproducible interactive research: Galaxy, Docker, IPython Björn Grüning
12:10 COPO: Bridging the Gap from Data to Publication in Plant Science Robert Davey
12:15 ELIXIR UK building on Data and Software Carpentry to address the challenges in computational training for life scientists Aleksandra Pawlik
12:20 Parallel recipes: towards a common coordination language for scientific workflow management systems Yves Vandriessche
12:25 openSNP - personal genomics and the public domain Bastian Greshake
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
14:17-14:34 From Fastq To Drug Recommendation - Automated Cancer Report Generation using OncoRep & Omics Pipe Tobias Meissner
14:35-14:40 Cancer Informatics Collaboration and Computation: Two Initiatives of the U.S. National Cancer Institute Ishwar Chandramouliswaran
14:40-15:30 Session: Bioinformatics Open Source Project Updates Chair:
14:40-14:57 Biopython Project Update 2015 João Rodrigues
14:57-15:14 The biogems community: Challenges in distributed software development in bioinformatics George Githinji
15:14-15:31 Apache Taverna: Sustaining research software at the Apache Software Foundation Stian Soiland-Reyes
15:30-16:00 Coffee Break
16:00-16:30 Session: Visualization Chair:
16:00-16:17 Simple, Shareable, Online RNA Secondary Structure Diagrams Stefan Hammer
16:17-16:22 BioJS 2.0: an open source standard for biological visualization Guy Yachdav
16:22-16:27 Visualising Open PHACTS linked data with widgets Ian Dunlop
16:30-17:00 Session: Late-Breaking Lightning Talks
16:30 Biospectra-by-sequencing genetic analysis platform Aurelie Laugraud
16:35
16:40
16:45
16:50
16:55
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

Any last-minute schedule updates will be posted at

http://www.open-bio.org/wiki/BOSC_2015_Schedule

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 bosc@open-bio.org.

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