GTN Metadata

Authors:

Overview
Questions:

What metadata is required or possible to set in a Tutorial, Slide, Topic, or FAQ

Objectives:

Know where to find all of the available metadata, so you can reference it later.

Time estimation: 10 minutes

Supporting Materials:

Published: Jun 2, 2022

Last modification: Nov 2, 2023

License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT

purl PURL: https://gxy.io/GTN:T00070

version Revision: 5

Training Materials

A dictionary/map
layout
Free Text

This must be set to tutorial_hands_on

Possible Values:

tutorial_hands_on

Example(s)
layout: "tutorial_hands_on"
title
Free Text

Title of the tutorial (it will appear on the tutorial page and the topic page)

Example(s)
title: Clustering in Machine Learning
title: Breve introducción a Galaxy - en español
title: Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
contributions
A dictionary/map

List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial.

Example(s)
contributions:
    authorship:
        - shiltemann
        - bebatut
    editing:
        - hexylena
        - bebatut
        - natefoo
    testing:
        - bebatut
    infrastructure:
        - natefoo
    translation:
        - shiltemann
    funding:
        - gallantries
List of Items

These entities wrote the bulk of the training material, they may have done the analysis, built the workflow, and wrote the text themselves.

List of Items

These entities edited the text, either for spelling and grammar, flow, GTN-fit, or other similar editing categories

List of Items

These entities provided funding support for the development of this resource

List of Items

These entities managed and provided infrastructure to the GTN or for training purposes

List of Items

These entities tested the tutorial to ensure it works correctly for students, or reported issues with the tutorial.

List of Items

These entities did translation and localisation work on this resource

List of Items

These entities contributed UX or Design improvements to this tutorial or the GTN as a whole
time_estimation
Free Text

An estimation of the time needed to complete the hands-on.

Example(s)
time_estimation: 10M
time_estimation: 1H30M
Required Pattern: Must match the following regular expression
/^(?:([0-9]*)[Hh])*(?:([0-9]*)[Mm])*(?:([0-9.]*)[Ss])*$/
A dictionary/map

A dictionary of abbreviations and their expansions.

Example(s)
abbreviations:
    SQL: Structured Query Language
    API: Application Programming Interface
Free Text

The expansion of the abbreviated term.
List of Items

List of tutorial contributors. Please use contributions instead as it provides more detailed accounting of tutorial history.

Example(s)
contributors:
- hexylena
- shiltemann
Free Text

A copyright attribution string, as required by some licenses.

Example(s)
copyright: © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors
Boolean

true to hide your tutorial from the topic page (optional). This is useful if you need a tutorial for a workshop, but have not finished making it up to GTN standards.

List of Items

A dictionary/map

Any additional variables you want to set on the page
List of Items

list of resources that the reader of the material could follow at the end of the tutorial

Example(s)
follow_up_training:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml
  
- type: external
  title: The Unix Shell
  link: "http://swcarpentry.github.io/shell-novice/"
  
- type: none
  title: "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04."
  
Sequence Value (List of items)
A dictionary/map
type
Free Text

the type of link

Possible Values:

internal

external

none

Example(s)
type: "internal"
type: "external"
type: "none"
Free Text

URL of the external resource

Free Text

Title of the external resource

Free Text

[Internal Only] The name of the topic

List of Items

[Internal Only] List of required tutorials inside that topic
Decimal Number

Currently unused.
Free Text

Link to a gitter channel that is more relevant for the tutorial than the default. E.g. a single cell tutorial could use Galaxy-Training-Network/galaxy-single-cell to link to their specific chat room.

Example(s)
gitter: Galaxy-Training-Network/galaxy-single-cell
gitter: galaxy-genome-annotation/Lobby
Free Text

This must be set to external to link to an external tutorial

Possible Values:

external

Example(s)
hands_on: "external"
Free Text

link to the external tutorial

Example(s)
hands_on_url: https://docs.qiime2.org/jupyterbooks/cancer-microbiome-intervention-tutorial/index.html#
List of Items

List of take-home messages. This information will appear at the end of the tutorial. These should really be a key point, something that should stick in their mind; what you want them to take home from the tutorial.

Example(s)
key_points:
- Pangeo ecosystem enables big data analysis in geosciences
- The MiModD suite of tools bundles most of the functionality required to perform mapping-by-sequencing analyses with Galaxy
- It can drastically simplify management of large numbers of VMs
Free Text

The document language.

Possible Values:

es

en

fr

Example(s)
lang: "es"
lang: "en"
lang: "fr"
Free Text

Here give a feeling of what level the material is at.

Possible Values:

Introductory

Intermediate

Advanced

Example(s)
level: "Introductory"
level: "Intermediate"
level: "Advanced"
Free Text

An SPDX identifier for the alternative license that is used for that particular material. This is only relevant for materials which have been imported from an external source and were originally licensed under another license. For new materials we strongly encourage contributors to not use this key as materials are CC-BY, by default.

Example(s)
license: MIT
license: Apache-2.0
A dictionary/map

Example(s)
notebook:
    language: python
    pyolite: true

notebook:
    language: python
    snippet: topics/climate/tutorials/pangeo-notebook/preamble.md
language
Free Text

Possible Values:

python

bash

r

sql

Example(s)
language: "python"
language: "bash"
language: "r"
language: "sql"
List of Items

A list of packages that must be installed before running this tutorial. This value is not currently used, but might be in the future.

Example(s)
packages:
- tidyverse
Boolean

The GTN has support for JupyterLite and the Pyodide kernel which runs Python in the browser via webassembly/javascript. This comes with some restrictions:

Python only

No filesystem access (so no wget prep steps)

Little to no cell magic

However, it means we can run a lot of our Python training directly in the GTN! And in the future, hopefully, we will be able to embed individual cells of the notebook directly in the Python training, so the user doesn’t even need to switch pages.

Enabling this field will enable pyolite links for this notebook.
Free Text

If you have an alternative preamble for your notebook that students should know before following (e.g. they must load X datasets in their history), it can be listed here.

This text will be shown in the GTN tutorial, but it will not be included in the notebook, giving you a bit better control over mixing setup content which is relevant for Galaxy, with notebook content that can be easy to run for students.

Example(s)
snippet: topics/climate/tutorials/pangeo-notebook/preamble.md
List of Items

list of learning objectives for the tutorial

A learning objective is a single sentence describing what a learner will be able to do once they have done the tutorial. Generally it is best to follow a 2C or 3C learning objective such as:

Compute (Skill)

multiple whole genome assemblies (Objective)

in such a way to develop big data processing skills (Result)

Example(s)
objectives:
- Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*
- Explore Biodiversity data with taxonomic, temporal and geographical informations
- Generate a DotPlot emulating the original paper using a different analysis tool
Free Text

A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter)

Example(s)
og_image: /assets/images/gat.png
Required Pattern: Must match the following regular expression
/^\/.*/
Integer Number

This field allows ordering tutorials within the tutorial list. Tutorials with lower numbered priority come before tutorials with higher numbers.

Example(s)
List of Items

list of questions that will be addressed in the tutorial

Example(s)
questions:
- How does Genome assembly work?
- How do I change Galaxy configs?
- How to detect and quantify differentially abundant proteins in a HEK-Ecoli Benchmark DIA datatset?
- What kinds of data do programs store?
List of Items

If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible.

Example(s)
redirect_from:
- /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial
List of Items

List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to follow_up_training.

Example(s)
requirements:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml
  
- type: external
  title: The Unix Shell
  link: "http://swcarpentry.github.io/shell-novice/"
  
- type: none
  title: "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04."
  
Sequence Value (List of items)
A dictionary/map
type
Free Text

the type of link

Possible Values:

internal

external

none

Example(s)
type: "internal"
type: "external"
type: "none"
Free Text

URL of the external resource

Free Text

Title of the external resource

Free Text

[Internal Only] The name of the topic

List of Items

[Internal Only] List of required tutorials inside that topic
Free Text

if the topic has multiple subtopics defined, you can assign your tutorial to one of those subtopics here. Without this, the tutorial will appear in the “Other tutorials” section on the topic page.

Example(s)
subtopic: single-cell
List of Items

A free form list of tags that are relevant for your tutorial.

Example(s)
tags:
- covid-19
- git-gat
List of Items

If alternative translations of a material are available, then use this key to indicate which languages have been manually translated.

Example(s)
translations:
- en
A dictionary/map

For materials which are automatically converted into videos via the available mechanisms, this field declares which voice should be used. If this field is not declared, a random voice will be chosen from a list of the best available voices from AWS Polly.

Example(s)
voice:
    id: Lupe
    lang: es-US
    neural: true
id
Free Text

lang
Free Text

neural
Boolean
Free Text

link on Zenodo to the input data for the tutorial

Example(s)
zenodo_link: https://zenodo.org/record/3706539
Required Pattern: Must match the following regular expression
/(^$|^https://zenodo.org/records?/[0-9]+/?$|^https://doi.org/10.5281/zenodo.[0-9]+/?$)/

A dictionary/map
layout
Free Text

The layout to use. Generally you should use tutorial_slides and no other value.

Possible Values:

tutorial_slides

introduction_slides

tutorial_slides_ai4life

Example(s)
layout: "tutorial_slides"
layout: "introduction_slides"
layout: "tutorial_slides_ai4life"
title
Free Text

Title of the slides (it will appear on the slides and the topic listing)

Example(s)
title: Introduction to CRISPR screen analysis
title: High Performance Computing for Pairwise Genome Comparison
title: Circos
contributions
A dictionary/map

List of slide contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial.

Example(s)
contributions:
    authorship:
        - shiltemann
        - bebatut
    editing:
        - hexylena
        - bebatut
        - natefoo
    testing:
        - bebatut
    infrastructure:
        - natefoo
    translation:
        - shiltemann
    funding:
        - gallantries
List of Items

These entities wrote the bulk of the training material, they may have done the analysis, built the workflow, and wrote the text themselves.

List of Items

These entities edited the text, either for spelling and grammar, flow, GTN-fit, or other similar editing categories

List of Items

These entities provided funding support for the development of this resource

List of Items

These entities managed and provided infrastructure to the GTN or for training purposes

List of Items

These entities tested the tutorial to ensure it works correctly for students, or reported issues with the tutorial.

List of Items

These entities did translation and localisation work on this resource

List of Items

These entities contributed UX or Design improvements to this tutorial or the GTN as a whole
logo
Free Text

A logo identifier (e.g. GTN) should be used by default, but may be swapped out for special logos from the assets folder.

Possible Values:

GTN

assets/images/gat.png

assets/images/gga.png

assets/images/ncbi.png

/assets/images/elixir-uk.png

/assets/images/BioNT_Logo.png

topics/ai4life/images/AI4Life-logo_giraffe-nodes.png

assets/images/genomics_intro.png

Example(s)
logo: "GTN"
logo: "assets/images/gat.png"
logo: "assets/images/gga.png"
logo: "assets/images/ncbi.png"
logo: "/assets/images/elixir-uk.png"
logo: "/assets/images/BioNT_Logo.png"
logo: "topics/ai4life/images/AI4Life-logo_giraffe-nodes.png"
logo: "assets/images/genomics_intro.png"
Free Text

A default CSS class applied to slides
List of Items

List of tutorial contributors. Please use contributions instead as it provides more detailed accounting of tutorial history.

Example(s)
contributors:
- hexylena
- shiltemann
Free Text

A copyright attribution string, as required by some licenses.

Example(s)
copyright: © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors
Boolean

true to hide your tutorial from the topic page (optional). This is useful if you need a tutorial for a workshop, but have not finished making it up to GTN standards.

List of Items
List of Items

list of resources that the reader of the material could follow at the end of the tutorial

Example(s)
follow_up_training:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml
  
- type: external
  title: The Unix Shell
  link: "http://swcarpentry.github.io/shell-novice/"
  
- type: none
  title: "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04."
  
Sequence Value (List of items)
A dictionary/map
type
Free Text

the type of link

Possible Values:

internal

external

none

Example(s)
type: "internal"
type: "external"
type: "none"
Free Text

URL of the external resource

Free Text

Title of the external resource

Free Text

[Internal Only] The name of the topic

List of Items

[Internal Only] List of required tutorials inside that topic
Free Text

Possible Values:

external

Example(s)
hands_on: "external"
Free Text
List of Items

List of take-home messages. This information will appear at the end of the slides. These should really be a key point, something that should stick in their mind; what you want them to take home from the slides.

Example(s)
key_points:
- Pangeo is an inclusive community promoting open, reproducible and scalable science.
- Balanced batches and replicates allow bioinformatic batch correction
- Galaxy workflows can download images from the IDR, selecting specific channels, time points, z-stack positions and crop the image in different ways.
Free Text

The document language.

Possible Values:

es

en

Example(s)
lang: "es"
lang: "en"
Free Text

Here give a feeling of what level the material is at.

Possible Values:

Introductory

Intermediate

Advanced

Example(s)
level: "Introductory"
level: "Intermediate"
level: "Advanced"
Free Text

An SPDX identifier for the alternative license that is used for that particular material. This is only relevant for materials which have been imported from an external source and were originally licensed under another license. For new materials we strongly encourage contributors to not use this key as materials are CC-BY, by default.
List of Items

list of learning objectives for the tutorial

A learning objective is a single sentence describing what a learner will be able to do once they have done the tutorial. Generally it is best to follow a 2C or 3C learning objective such as:

Compute (Skill)

multiple whole genome assemblies (Objective)

in such a way to develop big data processing skills (Result)

Example(s)
objectives:
- Understand the basic concepts behind phylogenetic trees, as applied to *Mycobacterium tuberculosis*
- Explore Biodiversity data with taxonomic, temporal and geographical informations
- Generate a DotPlot emulating the original paper using a different analysis tool
Free Text

A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter)

Example(s)
og_image: /assets/images/gat.png
Required Pattern: Must match the following regular expression
/^\/.*/
Integer Number

This field allows ordering resources within the topic list. Learning resources with lower numbered priority come before those with higher numbers.

Example(s)
List of Items

list of questions that will be addressed in the slides

Example(s)
questions:
- What is ATAC-Seq?
- What are Galaxy Interactive Environments (GIEs)?
- How to visualize your genome after automated annotations have been performed?
List of Items

If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible.

Example(s)
redirect_from:
- /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial
List of Items

List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to follow_up_training.

Example(s)
requirements:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml
  
- type: external
  title: The Unix Shell
  link: "http://swcarpentry.github.io/shell-novice/"
  
- type: none
  title: "A VM with at least 2 vCPUs and 4 GB RAM, preferably running Ubuntu 18.04 - 20.04."
  
Sequence Value (List of items)
A dictionary/map
type
Free Text

the type of link

Possible Values:

internal

external

none

Example(s)
type: "internal"
type: "external"
type: "none"
Free Text

URL of the external resource

Free Text

Title of the external resource

Free Text

[Internal Only] The name of the topic

List of Items

[Internal Only] List of required tutorials inside that topic
Free Text

if the topic has multiple subtopics defined, you can assign your tutorial to one of those subtopics here. Without this, the tutorial will appear in the “Other tutorials” section on the topic page.

Example(s)
subtopic: single-cell
List of Items

A free form list of tags that are relevant for your tutorial.

Example(s)
tags:
- covid-19
- git-gat
Free Text

An estimation of the time needed to complete the hands-on. It should look like 10M or 1H30M

Required Pattern: Must match the following regular expression
/^(?:([0-9]*)[Hh])*(?:([0-9]*)[Mm])*(?:([0-9.]*)[Ss])*$/
List of Items

If alternative translations of a material are available, then use this key to indicate which languages have been manually translated.

Example(s)
translations:
- en
Boolean

This enables automatic slide-to-video conversion. See the documentation of that feature for more information about this feature. If enabled, you must provide good speaker notes for every single slide.
A dictionary/map

For materials which are automatically converted into videos via the available mechanisms, this field declares which voice should be used. If this field is not declared, a random voice will be chosen from a list of the best available voices from AWS Polly.

Example(s)
voice:
    id: Lupe
    lang: es-US
    neural: true
id
Free Text

lang
Free Text

neural
Boolean

Decimal Number

Decimal Number
Free Text

link on Zenodo to the input data for the tutorial

Example(s)
zenodo_link: https://zenodo.org/record/3706539

GTN Resources

A dictionary/map
layout
Free Text

This must be set to faq

Possible Values:

faq

Example(s)
layout: "faq"
title
Free Text

Title of the FAQ

Example(s)
title: How does the GTN implement the 'Ten simple rules for collaborative lesson development'
title: How can I give feedback?
title: Ways to use Galaxy
box_type
Free Text

The type of box that should be used when rendering this FAQ. Use none if it should not be in a box, but just plain text.

Possible Values:

tip

hands_on

question

comment

warning

details

none

Example(s)
box_type: "tip"
box_type: "hands_on"
box_type: "question"
box_type: "comment"
box_type: "warning"
box_type: "details"
box_type: "none"
contributors
List of Items

Who contributed to this FAQ

Example(s)
contributors:
- shiltemann
- hexylena
Free Text

A text key used for sorting related FAQs together in the visual interface for users.

Example(s)
area: contributors
area: learners
area: features
Free Text

A short, one line description to provide additional context of the FAQ

Example(s)
description: Galaxy may have several reference genomes built-in, but you can also create your own.
description: Quickly learn what the identifiers are in any **BAM** dataset that is the result from mapping
description: Finding and Correcting Metadata
List of Items

If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible.

Example(s)
redirect_from:
- /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial

A dictionary/map
name
Free Text

The internal identifier for a topic, it should be the same as the folder name.

Example(s)
name: epigenetics
name: sequence-analysis
name: admin
Required Pattern: Must match the following regular expression
/^[a-z0-9_-]+$/
type
Free Text

The type of topic, some have subtly different behaviours.

admin-dev

should be used for admin and developer topics that are not scientifically focused.

basics

Only used for galaxy-interface type topics

data-science

Topics which are not necessarily Galaxy focused but expand into broader communities

use

These topics use galaxy for some analysis

instructors

Specific to topics related to instruction of Galaxy

Possible Values:

admin-dev

basics

data-science

use

instructors

Example(s)
type: "admin-dev"
type: "basics"
type: "data-science"
type: "use"
type: "instructors"
title
Free Text

Title of the topic, this is displayed for users to see.

Example(s)
title: Proteomics
title: Variant Analysis
summary
Free Text

A longer description of the contents of this topic

Example(s)
summary: Statistical Analyses for omics data and machine learning using Galaxy tools
editorial_board
List of Items
Free Text

Any custom CSS you might want to apply to a specific topic. This could be overriding e.g. the masthead colour (beware, will potentially conflict with themes.)

This is generally not a recommended property to set on topics, and something that is only used as part of outreach efforts to import content into the GTN.

Example(s)
custom_css: - :root { --brand-color: red; }
Free Text

The image ID for an image which contains all of the tools and data for this topic.

Example(s)
docker_image: quay.io/galaxy/sequence-analysis-training
Boolean

true to hide your tutorial from the topic page (optional). This is useful if you need a tutorial for a workshop, but have not finished making it up to GTN standards.

List of Items
Free Text

Link to a gitter channel that is more relevant for this topic than the default. E.g. a single cell topic, you could use Galaxy-Training-Network/galaxy-single-cell to link to their specific chat room in all of the child tutorials by default.

Example(s)
gitter: Galaxy-Training-Network/galaxy-single-cell
gitter: galaxy-genome-annotation/Lobby
Free Text

The specific learning path you wish to reference as a call-to-action for views who aren’t sure where to get started.

It must be the name of a file in learning-pathways, without the .md suffix. This is not validated so, please make sure it’s correct :)

Example(s)
learning_path_cta: intro-to-galaxy-and-genomics
learning_path_cta: admin-training
Free Text

A logo identifier (e.g. GTN) should be used by default, but may be swapped out for special logos from the assets folder.

Free Text

The alt text for the logo (MANDATORY).
Free Text

A custom image to show on the link preview in external applications (e.g. when the URL is pasted into Twitter)

Example(s)
og_image: /assets/images/gat.png
Required Pattern: Must match the following regular expression
/^\/.*/
List of Items

Example(s)
references:
- - |
    authors: "Vaudel M, et al."
    title: "Shedding light on black boxes in protein identification."
    link: "https://www.ncbi.nlm.nih.gov/pubmed/24678044"
    summary: "An extensive tutorial for peptide and protein identification, available at http://compomics.com/bioinformatics-for-proteomics. The material is completely based on freely available and open-source tools."
  
Sequence Value (List of items)
A dictionary/map

authors
Free Text

title
Free Text

link
Free Text

Free Text
List of Items

List of resources that the reader of the material should be familiar with before starting this training. The structure is identical to follow_up_training.

Example(s)
requirements:
- type: internal
  topic_name: statistics
  tutorials:
      - age-prediction-with-ml
  
Sequence Value (List of items)
A dictionary/map
type
Free Text

the type of link

Possible Values:

internal

Example(s)
type: "internal"
Free Text

The name of the topic

List of Items

List of required tutorials inside that topic
List of Items

For large topics, we can define subtopics and create multiple tutorial lists, which separates the tutorials to help users find content that interests them more quickly.
A dictionary/map
id
Free Text

Subtopic ID, this should match what is used in tutorials.

Example(s)
id: single-cell
Required Pattern: Must match the following regular expression
/^[A-Za-z0-9_-]+$/
title
Free Text

Subtopic title, which is displayed for users to see.

Example(s)
title: Maintaining a Production Galaxy
title: Single-cell RNA-seq
description
Free Text

A human readable textual description of a subtopic.

Example(s)
description: - "Start here if you are new to RNA-Seq analysis in Galaxy"
- "These tutorials take you from raw sequencing reads to pathway analysis"
- "Tutorials about analysis of single-cell RNA-seq data"
- "Tutorials using a single published single-cell RNA-seq dataset for a variety of analyses"
Boolean

false to hide your topic from the production GTN. This is useful if you need a topic for a workshop, but have not finished making it up to GTN standards.
Boolean

If this is a tag based topic (no tutorials of it’s own) then you must set this flag to indicate it as such, otherwise you will find yourself with an empty topic page.
Free Text

These are used to organise the home page tutorials only, not used anywhere else.

Possible Values:

technology

field

Example(s)
topic_type: "technology"
topic_type: "field"

A dictionary/map
title
Free Text

Title of the Quiz

Example(s)
title: Diagnostic Assessment
title: SQL Basics Recap
contributors
List of Items

Who contributed to this FAQ

Example(s)
contributors:
- shiltemann
- hexylena
questions
List of Items

The questions that are part of the quiz
A dictionary/map
title
Free Text

The question title, displayed on the teacher and student screens simultaneously

Example(s)
title: How you could collect information from learners at the beginning of a course or lesson and how you can use it?
title: What keyword do you use to retrieve data in SQL
timeout
Integer Number

How long the students have to answer the question
type
Free Text

What type of question to display.

Possible Values:

choose-1

choose-many

free-text

poll

Example(s)
type: "choose-1"
type: "choose-many"
type: "free-text"
type: "poll"
List of Items

The possible answers to the question you’ve asked. Consider including common wrong answers, or answers based on common mistakes to help students identify where they went wrong.

Example(s)
answers:
- OBTAIN
- SELECT
- RETRIEVE
- RETURN
The correct answer, it MUST be part of the answers list. It can be a list of correct answers if it is a choose-many question

Example(s)
correct: SELECT
correct: AB
Free Text

Path to an image, if you’d like to include one along with the question. Should be the full path starting with /

Example(s)
image: /training-material/topics/data-science/images/carpentries-sql/sql-join-structure.svg
Boolean

Used ONLY with the poll type questions to enable displaying the results as they come in. Great for polling audiences for how they’re feeling.

A dictionary/map
title
Free Text

Title of the pathway

Example(s)
title: Clustering in Machine Learning
title: Breve introducción a Galaxy - en español
title: Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
description
Free Text

Description of the pathway
type
Free Text

The type of topic, some have subtly different behaviours.

admin-dev

should be used for admin and developer topics that are not scientifically focused.

basics

Only used for galaxy-interface type topics

data-science

Topics which are not necessarily Galaxy focused but expand into broader communities

use

These topics use galaxy for some analysis

instructors

Specific to topics related to instruction of Galaxy

Possible Values:

admin-dev

basics

data-science

use

instructors

Example(s)
type: "admin-dev"
type: "basics"
type: "data-science"
type: "use"
type: "instructors"
editorial_board
List of Items

tags
List of Items

Any relevant tags that would help a user discover this LP
pathway
List of Items
A dictionary/map

section
Free Text

Free Text
List of Items
A dictionary/map

name
Free Text

Boolean

Free Text
Free Text

Possible Values:

admin

covid19

ai4life

assembly

climate

computational-chemistry

contributing

data-science

dev

ecology

epigenetics

evolution

fair

galaxy-interface

genome-annotation

imaging

introduction

metabolomics

microbiome

proteomics

sequence-analysis

single-cell

statistics

synthetic-biology

teaching

transcriptomics

variant-analysis

visualisation

Example(s)
topic: "admin"
topic: "covid19"
topic: "ai4life"
topic: "assembly"
topic: "climate"
topic: "computational-chemistry"
topic: "contributing"
topic: "data-science"
topic: "dev"
topic: "ecology"
topic: "epigenetics"
topic: "evolution"
topic: "fair"
topic: "galaxy-interface"
topic: "genome-annotation"
topic: "imaging"
topic: "introduction"
topic: "metabolomics"
topic: "microbiome"
topic: "proteomics"
topic: "sequence-analysis"
topic: "single-cell"
topic: "statistics"
topic: "synthetic-biology"
topic: "teaching"
topic: "transcriptomics"
topic: "variant-analysis"
topic: "visualisation"
Free Text

Possible Values:

hands_on

slides

Example(s)
type: "hands_on"
type: "slides"
Free Text

cover image

Free Text

cover image alt text

Boolean

true to hide your LP from the LP list (optional). This is useful if you need an LP for a workshop, but have not finished making it up to GTN standards.

List of Items

These entities provided funding support for the development of this resource
Free Text

Possible Values:

learning-pathway

Example(s)
layout: "learning-pathway"
Integer Number

priority within learning path list

A dictionary/map
layout
Free Text

Possible Values:

news

Example(s)
layout: "news"
title
Free Text

Title of the news post

Example(s)
title: BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More
title: New Tutorial Feature: Choose Your Own Tutorial
contributions
A dictionary/map

List of tutorial contributors. Here we break them down into several broad categories to help contributors identify how they contributed to a specific tutorial.

Example(s)
contributions:
    authorship:
        - shiltemann
        - bebatut
    editing:
        - hexylena
        - bebatut
        - natefoo
    testing:
        - bebatut
    infrastructure:
        - natefoo
    translation:
        - shiltemann
    funding:
        - gallantries
List of Items

These entities wrote the bulk of the training material, they may have done the analysis, built the workflow, and wrote the text themselves.

List of Items

These entities edited the text, either for spelling and grammar, flow, GTN-fit, or other similar editing categories

List of Items

These entities provided funding support for the development of this resource

List of Items

These entities managed and provided infrastructure to the GTN or for training purposes

List of Items

These entities tested the tutorial to ensure it works correctly for students, or reported issues with the tutorial.

List of Items

These entities did translation and localisation work on this resource

List of Items

These entities contributed UX or Design improvements to this tutorial or the GTN as a whole
A dictionary/map

A dictionary of abbreviations and their expansions.

Example(s)
abbreviations:
    SQL: Structured Query Language
    API: Application Programming Interface
Free Text

The expansion of the abbreviated term.
List of Items

List of tutorial contributors. Please use contributions instead as it provides more detailed accounting of tutorial history.

Example(s)
contributors:
- hexylena
- shiltemann
Free Text

link to a picture that will be used as the cover for the article

Example(s)
cover: assets/images/BYCOVID_logo_tagline.png
Free Text

If a cover is provided, then alt text is Mandatory.

Example(s)
coveralt: logo of by covid with subtitle reading beyond covid
Boolean

Whether clicking on the “read story link” goes directly to another site.

Possible Values:

true

false

Example(s)
external: true
external: false
Boolean

A boolean tracking in an automated way if this news post was generated via the GTN’s News Google Form. Please do not add this manually.

Possible Values:

true

false

Example(s)
from_google_form: true
from_google_form: false
Free Text

Basically an alias for tutorial, except requiring a full URL

Example(s)
link: https://example.org
List of Items

If a tutorial is renamed to a new location, use this field to list prior locations from which this tutorial was accessible.

Example(s)
redirect_from:
- /topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial
List of Items

A free form list of tags that are relevant for your tutorial.

Example(s)
tags:
- new topic
- new tutorial
- new feature
- covid-19
- git-gat
Free Text

Include a link to a specific page as a call to action button at the bottom of the page.

Example(s)
tutorial: topics/sequence-analysis/tutorials/de-novo-rad-seq/tutorial.html

Contributors

A dictionary/map

Example(s)
hexylena:
    name: Helena
    twitter: hexylena
    bio: I wrote this documentation! I do super cool things.
A dictionary/map

This ideally is your GitHub handle. If you do not have, or do not wish to provide a GitHub username, you may make up another identifier here, but then you must set github: false as described below.
name
Free Text

Your preferred name. If you prefer an alias or another name, this is welcome, it does not need to be your legal name.

Example(s)
name: 张三
name: Alice
name: Jane Doe
name: Madame Tout-le-Monde
name: Γιάννης Παπαδόπουλος
joined
Free Text

The year and month in which you joined

Example(s)
joined: 2020-01
Required Pattern: Must match the following regular expression
/[0-9]{4,}-[0-9]{2}/
List of Items

A set of organisations or grants your are affiliated with

Free Text
Free Text

A short biography of yourself, if you wish to add additional details or context.

Example(s)
bio: Research at the [South African National Bioinformatics Institute](https://www.sanbi.ac.za/)
Free Text

Your bluesky handle

Example(s)
bluesky: gtn.bsky.social
Required Pattern: Must match the following regular expression
/[0-9a-zA-Z.]+/
Boolean

Are you open to being contacted for hosting training, or being involved with local training events? Instructors might use this to contact you, if they are looking for regional trainers who can help with their event.
Free Text

The 2 letter code identifying the ELIXIR node to which you are a member or are associated with. If you are from norway, you will need to quote your value, "no", unlike everyone else, due to the Norway Problem with YAML

Possible Values:

au

be

ch

cz

de

dk

ee

es

fi

fr

gr

hu

ie

il

it

lu

nl

no

pt

se

si

uk

Example(s)
elixir_node: "au"
elixir_node: "be"
elixir_node: "ch"
elixir_node: "cz"
elixir_node: "de"
elixir_node: "dk"
elixir_node: "ee"
elixir_node: "es"
elixir_node: "fi"
elixir_node: "fr"
elixir_node: "gr"
elixir_node: "hu"
elixir_node: "ie"
elixir_node: "il"
elixir_node: "it"
elixir_node: "lu"
elixir_node: "nl"
elixir_node: "no"
elixir_node: "pt"
elixir_node: "se"
elixir_node: "si"
elixir_node: "uk"
Free Text

Your email address, if you wish to provide it.

Example(s)
email: jane.doe@gmail.com
Required Pattern: Must match the following regular expression
/@/
Free Text

The URL to your fediverse profile

Example(s)
fediverse: http://genomic.social/@abretaud
Required Pattern: Must match the following regular expression
/^https:\/\/[0-9a-zA-Z.]+/@?[0-9a-zA-Z.]+$/
Free Text

The flavor of the fediverse server (used in our webfinger endpoint.)

Possible Values:

mastodon

akkoma

Example(s)
fediverse_flavor: "mastodon"
fediverse_flavor: "akkoma"
List of Items

A set of organisations you were previously affiliated with

Boolean

If your identifier in this file is not a GitHub account (or not your account), then this must be set to true, so we do not link to that account.
Free Text

Set this to no if you would like to be excluded from the hall of fame.

Possible Values:

no

Example(s)
halloffame: "no"
Free Text

If this community member is deceased, you can use this field to write a small in memoriam section that will display in their Hall of Fame profile.
Free Text

Required Pattern: Must match the following regular expression
/[0-9a-zA-Z]+/
A dictionary/map
Free Text

The country you work in, ISO-3166-2 code.

Example(s)
country: NL
country: DE
Decimal Number

Latitude in decimal numbers

Example(s)
lat: 4.12
Decimal Number

Longitude in decimal numbers

Example(s)
lon: 55.0
Free Text

Preferred contact method
Free Text

Your matrix identifier and home server

Example(s)
matrix: hexylena:matrix.org
Required Pattern: Must match the following regular expression
/[0-9a-zA-Z]+:.*/
Free Text

Your identifier at orcid.org

Example(s)
orcid: 0000-0001-9760-8992
Required Pattern: Must match the following regular expression
/[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}-[0-9A-Z]{4}/
Free Text

Your twitter handle, without the @

Example(s)
twitter: gxytraining
Required Pattern: Must match the following regular expression
/[0-9a-zA-Z]+/

Frequently Asked Questions

Have questions about this tutorial? Check out the FAQ page for the Contributing to the Galaxy Training Material topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help Forum

Feedback

Did you use this material as an instructor? Feel free to give us feedback on how it went.
Did you use this material as a learner or student? Click the form below to leave feedback.

Citing this Tutorial

Helena Rasche, GTN Metadata (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/contributing/tutorials/schemas/tutorial.html Online; accessed TODAY
Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

@misc{contributing-schemas,
author = "Helena Rasche",
	title = "GTN Metadata (Galaxy Training Materials)",
	year = "",
	month = "",
	day = ""
	url = "\url{https://training.galaxyproject.org/training-material/topics/contributing/tutorials/schemas/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol} Computational Biology}
}

                   

Congratulations on successfully completing this tutorial!

Developing GTN training material
This tutorial is part of a series to develop GTN training material, feel free to also look at:

Creating a new tutorial

Creating Slides

Hands-on: Hands-on: Contributing with GitHub via command-line

Overview of the Galaxy Training Material

Hands-on: Hands-on: Contributing with GitHub via its interface

Hands-on: Hands-on: Principles of learning and how they apply to training and teaching

Hands-on: Hands-on: Adding auto-generated video to your slides

Hands-on: Hands-on: Tools, Data, and Workflows for tutorials

Hands-on: Hands-on: Adding Quizzes to your Tutorial

GTN Metadata

Running the GTN website locally

Generating PDF artefacts of the website

Creating content in Markdown

Running the GTN website online using GitPod

Teaching Python

Creating Interactive Galaxy Tours

Including a new topic

Design and plan session, course, materials

Updating diffs in admin training

FAIR Galaxy Training Material

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.
shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/contributing/tutorials/schemas/tutorial.json | jq .admin_install_yaml -r)
Alternatively you can copy and paste the following YAML
---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []