Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration

Comment: What is a Learning Pathway?
A graphic depicting a winding path from a start symbol to a trophy, with tutorials along the way
We recommend you follow the tutorials in the order presented on this page. They have been selected to fit together and build up your knowledge step by step. If a lesson has both slides and a tutorial, we recommend you start with the slides, then proceed with the tutorial.

This Learning Pathway collects the results of Intellectual Output 3 in the Gallantries Project

Success Criteria:

Year 1: Introduction to genomics and genome annotation

This will give students a good basic knowledge in the application domain of this IO and give them their first taste of data management [SC3.1,SC3.3,SC3.5]

Lesson Slides Hands-on Recordings
Introduction to Genome Annotation

Year 1: Prokaryotic annotation

This module will cover the background relevant to annotating prokaryotic genomes in Galaxy (one of the two main classes of genomes), and collaborative curation with Apollo, as well as further exploration of annotation from code. [SC1.5, SC3.1-4]

Lesson Slides Hands-on Recordings
Genome annotation with Prokka
Refining Genome Annotations with Apollo (prokaryotes)

Year 2: FAIR Data

This submodule will focus specifically on how learners can make their data more FAIR (findable, accessible, interoperable, and reusable) [SC3.5]

Lesson Slides Hands-on Recordings
FAIR in a nutshell
FAIR Galaxy Training Material
FAIR data management solutions
FAIR Bioimage Metadata
RO-Crate - Introduction
Exporting Workflow Run RO-Crates from Galaxy
RO-Crate in Python
Best practices for workflows in GitHub repositories
Workflow Run RO-Crate Introduction

Year 2: Automatic Annotation

Building on the modules developed in the previous years, this will be further automated giving students the tools required to scale genome annotation regardless of the size of their organism. [SC1.1, SC1.6, SC2.1, SC3.1, SC3.3]

Lesson Slides Hands-on Recordings
Genome annotation with Funannotate

Year 3: Eukaryotic annotation

This module will cover the background relevant to annotating eukaryotic genomes in Galaxy (the second of the two main genome classes), and collaborative curation with Apollo. Additionally students will learn about automating this annotation process using Galaxy and code. [SC1.5, SC2.1, SC3.1-4]

Lesson Slides Hands-on Recordings
Masking repeats with RepeatMasker
Long non-coding RNAs (lncRNAs) annotation with FEELnc
Refining Genome Annotations with Apollo (eukaryotes)

Year 3: Official Gene Set

One of the key tasks in annotation is producing an official gene set (OGS), and ensuring integrity and validation of all of the curated annotations. This will also further familiarise students with public databases and the process for submitting datasets. [SC3.1, SC3.5]

Lesson Slides Hands-on Recordings

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemann


These individuals or organisations provided funding support for the development of this resource