EOSC-Nordic portals workshop

2 Jun 2022, 08:30 → 3 Jun 2022, 16:00 Europe/Copenhagen

Zoom

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

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)

Friday, 3 June

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)