C4RR Agenda

Check the list of talks, lightning talks and demos. A PDF copy of the agenda is available here.

Monday 26 June 2017

If you are planning to arrive in Cambridge on 26th June and need a place to dinner, we recommend the Novi.

Tuesday 27 June 2017 - Day 1

  • 10:00-10:40: Registration and Coffee
  • 10:40-10:50: Welcome

  • 10:50-11:10: Docker Containers for Deep Learning Experiments - Paul K. Gerke, Diagnostic Image Analysis Group, Radboudumc Nijmegen (slides)

  • 11:10-11:30: Reproducible high energy physics analyses - Diego Rodríguez, CERN (slides)

  • 11:30-11:50: HPC infrastructure for high energy density physics research - Arturas Venskus, First Light Fusion Limited, Richard King, First Light Fusion Limited

  • 11:50-12:10: Singularity Containers for Reproducible Research - Michael Bauer, University of Michigan / Lawrence Berkeley National Lab

  • 12:10-12:30: Building moving castles: Scaling our analyses from laptops to supercomputers - Matthew Hartley, John Innes Centre, Tjelvar Olsson, John Innes Centre (slides)

  • 12:30-13:30: Lunch

  • 13:30-13:50: Reproducible Analysis for Government - Matthew Upson, Government Digital Service

  • 13:50-14:10 Using Docker and Knitr to create reproducible and extensible publications - David Mawdsley, University of Manchester, Robert Haines, University of Manchester, Caroline Jay, University of Manchester (slides)

  • 14:10-14:20 (Lightning Talk) Using Containers to drive reproducibility best practices in Bioinformatics training - Mark Fernandes (slides)

  • 14:20-14:30 (Lightning talk) Fig2code: create runnable, reproducible figures - Robert Stojnic (slides)

  • 14:30-14:40 (Lightning Talk) Containing infrastructure models for testing and scale - Tom Russell (slides)

  • 14:40-14:50: (Lightning talk) EBI Metagenomics: building shareable and reproducible workflows for metagenomic analysis - Maxim Scheremetjew (slides)

  • 14:50-15:10: Coffee

  • 15:10-15:30: Using Docker to add flexible container support to CyVerse UK - Alice Minotto, Earlham Institute, E. Van Den Bergh, EMBL-EBI, A. Eckes, Earlham Institute, R. P. Davey, Earlham Institute (slides)

  • 15:30-15:50: Beyond the container - configuration management of high throughput workflows in a production environment - Nick James, Eagle Genomics (slides)

  • 15:50-16:10: Reproducibility of Scientific Workflow in the Cloud using Container Virtualization - Rawaa Qasha, Newcastle University (slides)

  • 16:10-16:30: Virtual Container Clusters: building reproducible cluster software environments - Josh Higgins, University of Huddersfield

  • 16:30-16:50: Containers at the Dutch National e-Infrastructure - Jeroen Schot, SURFsara (slides)

  • 16:50-17:10 Using Docker on a Cloud Compute Platform - Chris Richardson, University of Cambridge

  • 17:10-17:20: Wrap up

  • 19:00-22:00: Workshop dinner at The Cambridge Brew House

Wednesday 28 June 2017 - Day 2

  • 09:00-12:00: Demos

    • RosettaHUB, connecting the dots between clouds, containers and research software - Karim Chine, RosettaHUB Ltd.

    • Container adoption & reproducibility - the Training Trojan horse - Mark Fernandes, Quadram Institute Biosciences. (slides)

  • 12:00-12:50: Lunch

  • 12:50-13:40: Sponsored Keynote Talk - Kenji Takeda, Azure for Research, Microsoft (UK)

  • 13:40:14:00: Stencila - Nokome Bentley, Stencila (slides)

  • 13:20-14:40: Applying Containers at The University of Melbourne for HPC, Virtual Laboratories and Training - David Perry, The University of Melbourne

  • 14:40-15:00: A DevOps Approach to Research - Sebastian Pölsterl, Institute of Cancer Research (slides)

  • 14:40-15:00: Coffee

  • 15:00-15:20: oswitch: Docker based “virtual environments” for flexible and reproducible Bioinformatics analyses - Anurag Priyam, Queen Mary University of London (slides)

  • 15:20-15:40: Software “Best Before” Dates: posing questions about containers and digital preservation - James Mooney, The Bodleian Libraries, Oxford; David Gerrard, Cambridge University Library. (slides)

  • 15:40-16:00: Creating executable research compendia to improve reproducibility in the geosciences - Daniel Nüst, Institute for Geoinformatics, University of Münster (slides)

  • 16:00-16:10: Closing Session