Organizers

• Marc Galland, University of Amsterdam.
• Johannes Köster, University of Duisburg-Essen.
• Thomas Cokelaer, Pasteur Institute, Paris.

Key info

When? Friday December 15, 2017. 9:30 to 15.00.

Where? Roeterseiland Campus, room E0.22, Amsterdam

Final program

• 9.30-9.45: Welcome reception
• 9.45-10:00: participant self-intro
• 10.00-10.30: Keynote: The road to reproducibility - Snakemake in 2017 (Johannes Köster, slides)
• 10.30-10.45: coffee break
• 10.45-12: morning session
  • 10.45-11.00: Live-demo - a basic use of a Snakemake pipeline (Marc Galland)
  • 11.00-11.15: Live-demo - Sequanix, a GUI for Snakemake (Thomas Cokelaer)
  • 11.15-11.30: A user perspective (Per Unneberg, SciLifeLab, Sweden)
  • 11.30-12.00: Questions/Answers session (Johannes Köster, Thomas Cokelaer, Marc Galland)
• 12-13: Lunch break
• 13-15: Hackathon: bring your own problem or questions
  • Snakemake tutorial
  • Reproducibility: Snakemake, Bioconda, Github, publication
  • The Snakemake Wrapper Repository
  • The Snakemake Workflows Project
  • The Snakemake Profiles Project
  • Performance: parallelization
  • Sharing workflows and rules
  • Other questions
• 15-17: Drinks and networking at the CREA Café

Scientific committee

• Claire Rioualen, Aix-Marseille University.
• Johannes Köster, University of Duisburg-Essen
• Marc Galland, University of Amsterdam
• Thomas Cokelaer, Pasteur Institute, Paris.

To subscribe

Go to the Eventbrite event page

Where to sleep in the neighbourhood

• Youth hostel
• Amsterdam Tropen Hotel
• Hotel Arena
• Hampshire Hotel - The Manor Amsterdam
• A list of hotels in the Plantage district

Participants

• Arnar Flatberg : arnar.flatberg@ntnu.no
• Endre Bakken Stovner : endrebak85@gmail.com
• Michelle van der Gragt : M.vanderGragt@uva.nl
• Gergana Bounova : g.bounova@nki.nl
• Per Unneberg : per.unneberg@scilifelab.se
• Maria Bernard : maria.bernard@inra.fr
• Tijs Bliek : bliek@uva.nl
• Oliver Stolpe : oliver.stolpe@bihealth.de
• Simon van Heeringen : simon.vanheeringen@gmail.com
• Maryam Ghareghani : mgharegh@mmci.uni-saarland.de
• Changsheng Li : c.li3@uva.nl
• Kai Ding : k.ding@uva.nl
• Rick de Graaf : rick.degraaf@bejo.nl
• Claire Rioualen : rioualenclaire@gmail.com
• Tjitske Los- de Vries : g.t.los@vumc.nl
• Alejandro Abdala : alejandro.abdala@nioz.nl
• Bianca Dößelmann : bianca.doesselmann@uni-hohenheim.de
• Jose Maturana : jlmaturanag@gmail.com
• Mattias de Hollander : m.dehollander@nioo.knaw.nl
• Fatemeh Behjati : fbehjati@mmci.uni-saarland.de
• Azim Dehghani Amirabad : azim.dehghani@gmail.com
• Elise van Bree : E.J.vanBree@uva.nl
• Ineke Knot : i.e.knot@uva.nl
• Nina Haring : N.L.Haring@uva.nl