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EOSC-Nordic portals workshop

Europe/Copenhagen
Zoom

Zoom

Abdulrahman Azab Mohamed (University of Oslo), Anne Fouilloux (UiO), Kessy Abarenkov (UT)
Description

Galaxy is an open-source platform for FAIR data analysis that enables users to:

  • Use tools from various domains (that can be plugged into workflows) through its graphical web interface;
  • Run code in interactive environments (RStudio, Jupyter...) along with other tools or workflows;
  • Manage data by sharing and publishing results, workflows, and visualizations
  • Ensure reproducibility by capturing the necessary information to repeat and understand data analyses.
  • You will also learn about Research Objects and the Research Object Hub for making Open Science in practice a reality.


PlutoF is a Data management and Publishing Platform. In PlutoF, you can manage your full data lifecycle. From Data Management Plan to the publishing and archiving your datasets in machine readable format.

This is a training workshop on the usage and implementations of Galaxy and PlutoF tools

  • Thursday, 2 June
    • Welcome & logistics
    • PlutoF

      Contributors: Kessy Abarenkov, Urmas Kõljalg, Sergei Põlme, Allan Zirk

      Introduction to data management in PlutoF - 50m (Kessy Abarenkov)

      Third-party annotations in PlutoF - 20m (Kessy Abarenkov)

      Introduction to SH/TH paradigms - 30m (Urmas Kõljalg)

      PlutoF analysis module and publishing - 50m (Kessy Abarenkov)

      Lunch

      Hands-on: PlutoF analysis module - massBLASTer SH matching - 45m (Kessy Abarenkov)

      Hands-on: PlutoF analysis module - SH matching analysis - 45m (Kessy Abarenkov)

      FungalTraits database - 45m (Sergei Põlme)

    • Lunch break
    • PlutoF

      Contributors: Kessy Abarenkov, Urmas Kõljalg, Sergei Põlme, Allan Zirk

      Introduction to data management in PlutoF - 50m (Kessy Abarenkov)

      Third-party annotations in PlutoF - 20m (Kessy Abarenkov)

      Introduction to SH/TH paradigms - 30m (Urmas Kõljalg)

      PlutoF analysis module and publishing - 50m (Kessy Abarenkov)

      Lunch

      Hands-on: PlutoF analysis module - massBLASTer SH matching - 45m (Kessy Abarenkov)

      Hands-on: PlutoF analysis module - SH matching analysis - 45m (Kessy Abarenkov)

      FungalTraits database - 45m (Sergei Põlme)

    • Welcome & logistics: Welcome
    • Galaxy

      Contributors (instructors, helpers): Anne Claire Fouilloux, Galaxy-EU team, [Abdulrahman Azab]

      Attendees can choose different training from the Galaxy Training Network for instance:

      • Introduction to Galaxy platform (user point of view)
      • Hands-on: Galaxy 101 for everyone & Extracting Workflows from Histories & Copernicus data in Galaxy
      • The Functionally Assembled Terrestrial Ecosystem Simulator (FATES) in Galaxy
      • Galaxy for tools developers (planemo)
      • Research Object Concepts
      • The RoHub portal for managing Research Objects
      • ROs creation and lifecycle (from the Jupyter notebook and GUI)
    • Lunch break
    • Galaxy

      Contributors (instructors, helpers): Anne Claire Fouilloux, Galaxy-EU team, [Abdulrahman Azab]

      Attendees can choose different training from the Galaxy Training Network for instance:

      • Introduction to Galaxy platform (user point of view)
      • Hands-on: Galaxy 101 for everyone & Extracting Workflows from Histories & Copernicus data in Galaxy
      • The Functionally Assembled Terrestrial Ecosystem Simulator (FATES) in Galaxy
      • Galaxy for tools developers (planemo)
      • Research Object Concepts
      • The RoHub portal for managing Research Objects
      • ROs creation and lifecycle (from the Jupyter notebook and GUI)