C4RR Agenda

Check the list of talks, lightning talks and demos. All video recording are on YouTube.

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, video)

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

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

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

  • 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, video)

  • 12:30-13:30: Lunch

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

  • 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, video)

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

  • 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, video)

  • 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, video)

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

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

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

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

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

  • 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. (video)

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

  • 12:00-12:50: Lunch

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

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

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

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

  • 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, video)

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

  • 16:00-16:10: Closing Session