GTN Metadata

Authors: orcid logoAvatarHelena Rasche

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:
Last modification: May 20, 2022
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License The GTN Framework is licensed under MIT

Tutorial Schema

A dictionary/map

layout required

Free Text

This must be set to tutorial_hands_on

Possible Values:

  • tutorial_hands_on

Example(s)

layout: "tutorial_hands_on"

title required

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 required

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
    funding:
        - erasmusplus

authorship

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.

editing

List of Items

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

funding

List of Items

These entities provided funding support for the development of this resource

infrastructure

List of Items

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

testing

List of Items

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

ux

List of Items

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

time_estimation required

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])*$/

abbreviations

A dictionary/map

A dictionary of abbreviations and their expansions.

Example(s)

abbreviations:
    SQL: Structured Query Language
    API: Application Programming Interface

Any key permitted

Free Text

The expansion of the abbreviated term.

contributors

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

edam_ontology

Free Text

An edam ontology id that describes the topic or tutorial.

Example(s)

edam_ontology: topic_3173

Required Pattern: Must match the following regular expression

/^topic_[0-9]+$/

enable

Boolean

false 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.

follow_up_training

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 required

A dictionary/map

type required

Free Text

the type of link

Possible Values:

  • internal
  • external
  • none

Example(s)

type: "internal"
type: "external"
type: "none"

link

Free Text

URL of the external resource

title

Free Text

Title of the external resource

topic_name

Free Text

[Internal Only] The name of the topic

tutorials

List of Items

[Internal Only] List of required tutorials inside that topic

galaxy_version

Decimal Number

Currently unused.

gitter

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

key_points

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

lang

Free Text

The document language.

Possible Values:

  • es
  • en

Example(s)

lang: "es"
lang: "en"

level

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"

license

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

notebook

A dictionary/map

Example(s)

notebook:
    language: python
    pyolite: true

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

language required

Free Text

Possible Values:

  • python
  • bash
  • r
  • sql

Example(s)

language: "python"
language: "bash"
language: "r"
language: "sql"

pyolite

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.

snippet

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

objectives

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

priority

Integer Number

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

Example(s)

questions

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?

redirect_from

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

requirements

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 required

A dictionary/map

type required

Free Text

the type of link

Possible Values:

  • internal
  • external
  • none

Example(s)

type: "internal"
type: "external"
type: "none"

link

Free Text

URL of the external resource

title

Free Text

Title of the external resource

topic_name

Free Text

[Internal Only] The name of the topic

tutorials

List of Items

[Internal Only] List of required tutorials inside that topic

subtopic

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

tags

List of Items

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

Example(s)

tags:
- covid-19
- git-gat

translations

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

voice

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 required

Free Text

lang required

Free Text

neural required

Boolean

zenodo_link

Free Text

link on Zenodo to the input data for the tutorial

Example(s)

zenodo_link: https://zenodo.org/record/3706539

Contributor Schema

A dictionary/map

Example(s)

hexylena:
    name: Helena
    twitter: hexylena
    bio: I wrote this documentation! I do super cool things.

Any key permitted

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 required

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 required

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}/

avatar

Free Text

bio

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/)

elixir_node

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"

email

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

/@/

funder

Boolean

Set this to true if this entity is a funding agency.

funding_id

Free Text

The short identifier for your grant.

Example(s)

funding_id: 2020-1-NL01-KA203-064717

funding_statement

Free Text

A short statement about the funder, markdown is supported.

Example(s)

funding_statement: This project ([`2020-1-NL01-KA203-064717`](https://ec.europa.eu/programmes/erasmus-plus/projects/eplus-project-details/#project/2020-1-NL01-KA203-064717)) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

github

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.

gitter

Free Text

Your gitter

Example(s)

gitter: hexylena

Required Pattern: Must match the following regular expression

/[0-9a-zA-Z]+/

halloffame

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"

linkedin

Free Text

Required Pattern: Must match the following regular expression

/[0-9a-zA-Z]+/

maintainer_contact

Free Text

Preferred contact method

matrix

Free Text

Your matrix identifier

Example(s)

matrix: @hexylena:matrix.org

Required Pattern: Must match the following regular expression

/@[0-9a-zA-Z]+:.*/

orcid

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}/

twitter

Free Text

Your twitter handle, without the @

Example(s)

twitter: gxytraining

Required Pattern: Must match the following regular expression

/[0-9a-zA-Z]+/

Slides Schema

A dictionary/map

layout required

Free Text

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

Possible Values:

  • base_slides
  • tutorial_slides
  • rdmbites_slides

Example(s)

layout: "base_slides"
layout: "tutorial_slides"
layout: "rdmbites_slides"

title required

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 required

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
    funding:
        - erasmusplus

authorship

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.

editing

List of Items

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

funding

List of Items

These entities provided funding support for the development of this resource

infrastructure

List of Items

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

testing

List of Items

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

ux

List of Items

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

logo required

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.

Example(s)

logo: GTN
logo: assets/images/gat.png

class

Free Text

A default CSS class applied to slides

contributors

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

edam_ontology

Free Text

An edam ontology id that describes the tutorial.

Example(s)

edam_ontology: topic_3173

Required Pattern: Must match the following regular expression

/^topic_[0-9]+$/

enable

Boolean

false 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.

follow_up_training

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 required

A dictionary/map

type required

Free Text

the type of link

Possible Values:

  • internal
  • external
  • none

Example(s)

type: "internal"
type: "external"
type: "none"

link

Free Text

URL of the external resource

title

Free Text

Title of the external resource

topic_name

Free Text

[Internal Only] The name of the topic

tutorials

List of Items

[Internal Only] List of required tutorials inside that topic

hands_on

Free Text

Possible Values:

  • external

Example(s)

hands_on: "external"

hands_on_url

Free Text

key_points

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.

lang

Free Text

The document language.

Possible Values:

  • es
  • en

Example(s)

lang: "es"
lang: "en"

level

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"

objectives

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

priority

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)

questions

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?

redirect_from

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

requirements

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 required

A dictionary/map

type required

Free Text

the type of link

Possible Values:

  • internal
  • external
  • none

Example(s)

type: "internal"
type: "external"
type: "none"

link

Free Text

URL of the external resource

title

Free Text

Title of the external resource

topic_name

Free Text

[Internal Only] The name of the topic

tutorials

List of Items

[Internal Only] List of required tutorials inside that topic

subtopic

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

tags

List of Items

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

Example(s)

tags:
- covid-19
- git-gat

time_estimation

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])*$/

translations

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

video

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.

voice

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 required

Free Text

lang required

Free Text

neural required

Boolean

endOfSentencePause

Decimal Number

endOfSlidePause

Decimal Number

zenodo_link

Free Text

link on Zenodo to the input data for the tutorial

Example(s)

zenodo_link: https://zenodo.org/record/3706539

FAQ Schema

A dictionary/map

layout required

Free Text

This must be set to faq

Possible Values:

  • faq

Example(s)

layout: "faq"

title required

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 required

Free Text

The type of box that should be used when rendering this FAQ.

Possible Values:

  • tip
  • hands_on
  • question
  • comment

Example(s)

box_type: "tip"
box_type: "hands_on"
box_type: "question"
box_type: "comment"

contributors required

List of Items

Who contributed to this FAQ

Example(s)

contributors:
- shiltemann
- hexylena

area

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

description

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

Topic Schema

A dictionary/map

name required

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 required

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 required

Free Text

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

Example(s)

title: Proteomics
title: Variant Analysis

summary required

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

maintainers required

List of Items

docker_image

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

edam_ontology

Free Text

An edam ontology id that describes the topic.

Example(s)

edam_ontology: topic_3173

Required Pattern: Must match the following regular expression

/^topic_[0-9]+$/

enable

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.

gitter

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

references

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 required

A dictionary/map

authors required

Free Text

title required

Free Text

link required

Free Text

summary

Free Text

requirements

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 required

A dictionary/map

type required

Free Text

the type of link

Possible Values:

  • internal

Example(s)

type: "internal"

topic_name

Free Text

The name of the topic

tutorials

List of Items

List of required tutorials inside that topic

subtopics

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.

Sequence Value

A dictionary/map

id required

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 required

Free Text

Subtopic title, which is displayed for users to see.

Example(s)

title: Maintaining a Production Galaxy
title: Single-cell RNA-seq

description required

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"

enable

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.

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

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Citing this Tutorial

  1. Helena Rasche, 2022 GTN Metadata (Galaxy Training Materials). https://training.galaxyproject.org/archive/2022-08-01/topics/contributing/tutorials/schemas/tutorial.html Online; accessed TODAY
  2. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

details BibTeX

@misc{contributing-schemas,
author = "Helena Rasche",
title = "GTN Metadata (Galaxy Training Materials)",
year = "2022",
month = "05",
day = "20"
url = "\url{https://training.galaxyproject.org/archive/2022-08-01/topics/contributing/tutorials/schemas/tutorial.html}",
note = "[Online; accessed TODAY]"
}
@article{Batut_2018,
    doi = {10.1016/j.cels.2018.05.012},
    url = {https://doi.org/10.1016%2Fj.cels.2018.05.012},
    year = 2018,
    month = {jun},
    publisher = {Elsevier {BV}},
    volume = {6},
    number = {6},
    pages = {752--758.e1},
    author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning},
    title = {Community-Driven Data Analysis Training for Biology},
    journal = {Cell Systems}
}
                

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:
  1. Overview of the Galaxy Training Material
  2. Adding auto-generated video to your slides
  3. Adding Quizzes to your Tutorial
  4. Contributing with GitHub via command-line
  5. Contributing with GitHub via its interface
  6. Creating a new tutorial
  7. Creating content in Markdown
  8. Creating Interactive Galaxy Tours
  9. Creating Slides
  10. Generating PDF artefacts of the website
  11. GTN Metadata
  12. Including a new topic
  13. Running the GTN website locally
  14. Running the GTN website online using GitPod
  15. Tools, Data, and Workflows for tutorials
  16. Updating diffs in admin training