From 52bb74754cd05dac35f293043cfa5f55b02eb010 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 6 Oct 2023 10:57:12 +0200 Subject: [PATCH 01/17] looks like bad copy/paste --- topics/teaching/tutorials/running-workshop/tutorial.md | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/topics/teaching/tutorials/running-workshop/tutorial.md b/topics/teaching/tutorials/running-workshop/tutorial.md index 1c73e2fcecee18..c1ee4e71648ec7 100644 --- a/topics/teaching/tutorials/running-workshop/tutorial.md +++ b/topics/teaching/tutorials/running-workshop/tutorial.md @@ -140,16 +140,13 @@ Not everyone is always outwardly enthusiastic about the course for any number of Find someone you haven't talked to yet today, and talk to them. Make sure all the helpers have the same goal. 6. Regularly ask questions of the trainees: + - What data formats work here? - Where is the data coming from? - What data transformation is being made? - What were the data formats used today? -repository_branch: "master" -eepository_branch: "master" -repository_branch: "master" -sitory_branch: "master" - - What were the main steps of today's workflow? + 7. Regularly remind trainees of things you've taught them Repeat again and again, in different ways, to reinforce concepts From 5410c3bf595166e45531d2903e8fa23d7a8a9722 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 6 Oct 2023 11:11:18 +0200 Subject: [PATCH 02/17] another copy paste issue --- _includes/default-footer.html | 4 ---- 1 file changed, 4 deletions(-) diff --git a/_includes/default-footer.html b/_includes/default-footer.html index 42f1b86c060639..1b7a4471896149 100644 --- a/_includes/default-footer.html +++ b/_includes/default-footer.html @@ -39,7 +39,3 @@ - - - - From 78d151fe1f34edb102cdca686c496aa66ceab99f Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 6 Oct 2023 13:06:15 +0200 Subject: [PATCH 03/17] ignore non-vue --- bin/validate-frontmatter.rb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bin/validate-frontmatter.rb b/bin/validate-frontmatter.rb index c29dfb577b412d..00d65b0f85c61a 100755 --- a/bin/validate-frontmatter.rb +++ b/bin/validate-frontmatter.rb @@ -227,7 +227,8 @@ def self.run .grep_v(/schema-*/) .select do |x| d = YAML.load_file(x) - d.key? 'editorial_board' or d.key? 'summary' or d.key? 'type' + # Ignore non-hashes + d.is_a?(Hash) && (d.key? 'editorial_board' or d.key? 'summary' or d.key? 'type') end errors += materials.map { |x| [x, lint_topic(x)] } From 12d429722cfb63788a050bab728ba9da7e9c9f2c Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 6 Oct 2023 13:06:29 +0200 Subject: [PATCH 04/17] add e+ LPs --- learning-pathways/io1.md | 134 +++++++++++++++++++++++++++++++++++++++ learning-pathways/io2.md | 96 ++++++++++++++++++++++++++++ learning-pathways/io3.md | 81 +++++++++++++++++++++++ learning-pathways/io4.md | 46 ++++++++++++++ 4 files changed, 357 insertions(+) create mode 100644 learning-pathways/io1.md create mode 100644 learning-pathways/io2.md create mode 100644 learning-pathways/io3.md create mode 100644 learning-pathways/io4.md diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md new file mode 100644 index 00000000000000..e9aae5ad04cc2e --- /dev/null +++ b/learning-pathways/io1.md @@ -0,0 +1,134 @@ +--- +layout: learning-pathway +tags: [beginner] +type: use + +editorial_board: +- fpsom +- shiltemann +- hexylena +funding: +- erasmusplus + +title: Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding + +priority: 1 +draft: true + +pathway: + - section: "Year 1: Coding in Python" + description: | + Intro to Coding in Python. Covers variables, functions, and data structures [SC1.1,2] + tutorials: + - name: python-basics + topic: data-science + - name: python-advaced-np-pd + topic: data-science + + - section: "Year 1: Coding in Python Modular (Avans)" + description: | + Intro to Coding in Python. Covers variables, functions, and data structures [SC1.1,2] + + In collaboration with Avans Hogeschool, an associated Partner we produced the following lessons + tutorials: + - topic: data-science + name: python-math + - topic: data-science + name: python-functions + - topic: data-science + name: python-types + - topic: data-science + name: python-iterables + - topic: data-science + name: python-flow + - topic: data-science + name: python-loops + - topic: data-science + name: python-exceptions + - topic: data-science + name: python-files + - topic: data-science + name: python-basics-recap + - topic: data-science + name: python-glob + - topic: data-science + name: python-argparse + - topic: data-science + name: python-subprocess + - topic: data-science + name: python-venv + - topic: data-science + name: python-conda + + - section: "Year 1: Coding in R" + description: | + Intro to Coding in R. Covers variables, functions, and data structures [SC1.1,2] + tutorials: + - name: r-basics + topic: data-science + - name: r-advanced + topic: data-science + - name: r-dplyr + topic: data-science + + - section: "Year 1: Intro to Command Line" + description: | + This submodule will cover the basics of the shell (variables, for loops), needed for data handling [SC1.1,2,6] + tutorials: + - name: cli-basics + topic: data-science + - name: cli-advanced + topic: data-science + - name: cli-bashcrawl + topic: data-science + - name: snakemake + topic: data-science + + - section: "Year 1: Intro to Git and GitHub" + description: | + This submodule will cover the basics of research software development and sharing (committing, branching, forking, GitHub, etc.) [SC1.1,2,6] + tutorials: + - name: bash-git + topic: data-science + - name: git-cli + topic: data-science + - name: github-command-line-contribution + topic: contributing + - name: github-interface-contribution + topic: contributing + + - section: "Year 2: Introduction to Genomics" + description: | + This submodule covers the biological background, as well as the technological concepts involved in genome sequencing, and their effects on downstream data analysis. [SC1.3,4,6] + + - section: "Year 2: Quality Control" + description: | + This submodule will cover the evaluation of the quality of datasets, and how to improve quality by a cyclic process of cleaning, trimming and filtering datasets and re-evaluating the quality. [SC1.3-5] + tutorials: + - name: quality-control + topic: sequence-analysis + + - section: "Year 2: Mapping" + description: | + This submodule will cover the comparison of genome sequencing samples to a reference genome. The concept of reference data is relevant in many data analyses across life sciences; connecting to online databases and incorporating this data into an analysis. [SC1.3,4] + tutorials: + - name: mapping + topic: sequence-analysis + + - section: "Year 3: Variant Analysis" + description: | + This submodule will cover the topic of variant calling; after mapping of sequences to the reference genome, the regions that are different from the reference genome (variants) must be determined, and evaluated for impact. As any two individuals will by definition show many differences, the challenge of distinguishing between healthy variation and potential disease-causing variants is one of the main challenges in variant calling. [SC1.3-5] + tutorials: + - name: bash-variant-calling + topic: data-science + + - section: "Year 3: Transcriptomics" + description: | + DNA only describes the potential of the genome; which genes are actually active within the cell and impacting the health and function of the organism, is determined via transcriptomics (RNA sequencing). By integrating data from these two levels of analysis (DNA and RNA), a clearer picture of the state of the cell can be obtained. [SC1.3-5] + tutorials: + - name: rna-seq-bash-star-align + topic: transcriptomics + +--- + +In total, this module will form a course of around 10 days (± 2 days depending on exact analysis stories we identify). Some of these introductory submodules will build on existing training material available in the GTN or Carpentries (~15%). diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md new file mode 100644 index 00000000000000..ede26ae0eb9957 --- /dev/null +++ b/learning-pathways/io2.md @@ -0,0 +1,96 @@ +--- +layout: learning-pathway +tags: [beginner] +type: use + +editorial_board: +- shiltemann +- hexylena +- bebatut +funding: +- erasmusplus + +title: Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling + +priority: 1 +draft: true + +pathway: + + + + - section: "Year 1: Introduction to large-scale analyses in Galaxy" + description: | + Galaxy offers support for the analysis of large collections of data. This submodule will cover the upload, organisation, and analysis of such large sets of data and files. [SC2.1; SC1.3,5] + tutorials: + - name: upload-rules + topic: galaxy-interface + - name: upload-rules-advanced + topic: galaxy-interface + - name: ncbi-sarf + topic: galaxy-interface + - name: history-to-workflow + topic: galaxy-interface + - name: collections + topic: galaxy-interface + - name: workflow-automation + topic: galaxy-interface + - name: workflow-editor + topic: galaxy-interface + - name: workflow-parameters + topic: galaxy-interface + + + - section: "Year 1: Introduction to the human microbiome analyses" + description: | + The human microbiome consists of a community of thousands of species of microorganisms. Sequencing of this community is often performed to identify which species of microorganism are present. This aids in diagnostics and treatment of patients. [SC2.1-3,6; SC1.4,5] + tutorials: + - name: beer-data-analysis + topic: metagenomics + - name: nanopore-16s-metagenomics + topic: metagenomics + + - section: "Year 1: Advanced microbiome analysis" + description: | + By using more complex sequencing techniques, it is possible to not only obtain information about which organisms are present in the microbiome, but also their activity. This can e.g. aid in identification of antibiotic resistance. This more complex sequencing requires more complex data analysis [SC2.1-4,6; SC1.4,5] + tutorials: + - name: pathogen-detection-from-nanopore-foodborne-data + topic: metagenomics + + - section: "Year 2: Cancer Analysis" + description: | + The previous submodules focused on scaling up in terms of number of samples. This submodule will focus on scaling up in terms of complexity. Cancer is a disease of the genome, it is a multifaceted and heterogeneous disease. This leads to complex datasets and analysis pipelines [SC2.3,4; SC1.5] + tutorials: + - name: mapping-by-sequencing + topic: variant-analysis + # https://github.com/galaxyproject/training-material/pull/3802 + + - section: "Year 2: Intro to machine learning" + description: | + Going beyond conventional statistics, many scientific data analyses benefit from machine learning techniques for modelling of datasets. This is widely used in biomedical domain. [SC2.4,5; SC1.4] + tutorials: + - name: intro-to-ml-with-r + topic: statistics + + - section: "Year 2: Introduction to the Galaxy visualisation framework" + description: | + ⚠️ **TODO** ⚠️ Galaxy has many options for visualisation of scientific data. This module will cover how to use this framework to create and share visualisation. [SC2.2-3; SC1.1,3,6] + tutorials: [] + + - section: "Year 3: Visualisation of complex multidimensional data" + description: | + For advanced visualisation, tools such as Circos may be utilized where Galaxy’s basic visualisation framework does not suffice. [SC2.2-3; SC1.5] + tutorials: + - name: circos + topic: visualisation + + - section: "Year 3: Introduction to Visualisation with R and Python" + description: | + When the available visualisation options do not suffice, custom plots and visualisations can be created using one of several extensive visualisation libraries available in R and Python. This module will cover the basics of using R and Python to create custom plots and visualisations. [SC2.3; SC1.1] + tutorials: + - name: data-manipulation-olympics-viz-r + topic: data-science + - name: python-plotting + topic: data-science + +--- diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md new file mode 100644 index 00000000000000..1a56f9c29a07f1 --- /dev/null +++ b/learning-pathways/io3.md @@ -0,0 +1,81 @@ +--- +layout: learning-pathway +tags: [beginner] +type: use + +editorial_board: +- abretaud +- hexylena +- shiltemann +funding: +- erasmusplus + +title: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration + +priority: 1 +draft: true + +pathway: + - section: "Year 1: Introduction to genomics and genome annotation" + description: | + 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] + tutorials: + - name: introduction + topic: genome-annotation + + - section: "Year 1: Prokaryotic annotation" + description: | + 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] + tutorials: + - name: annotation-with-prokka + topic: genome-annotation + - name: apollo + topic: genome-annotation + + - section: "Year 2: FAIR Data" + description: | + This submodule will focus specifically on how learners can make their data more FAIR (findable, accessible, interoperable, and reusable) [SC3.5] + tutorials: + - topic: fair + name: fair-intro + - topic: fair + name: fair-gtn + - topic: fair + name: data-management + - topic: fair + name: bioimage-metadata + - name: ro-crate-intro + topic: fair + - name: ro-crate-in-galaxy + topic: fair + - name: ro-crate-in-python + topic: fair + - name: ro-crate-galaxy-best-practices + topic: fair + - name: ro-crate-workflow-run-ro-crate + topic: fair + + - section: "Year 2: Automatic Annotation" + description: | + 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] + tutorials: + - name: funannotate + topic: genome-annotation + + - section: "Year 3: Eukaryotic annotation" + description: | + 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] + tutorials: + - name: repeatmasker + topic: genome-annotation + - name: lncrna + topic: genome-annotation + - name: apollo-euk + topic: genome-annotation + + - section: "Year 3: Official Gene Set" + description: | + ⚠️ **TODO** ⚠️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] + + +--- diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md new file mode 100644 index 00000000000000..4a7098636fe6a9 --- /dev/null +++ b/learning-pathways/io4.md @@ -0,0 +1,46 @@ + +--- +layout: learning-pathway +tags: [beginner] +type: use + +editorial_board: +- yvanlebras +- bebatut +funding: +- erasmusplus + +title: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery + +priority: 1 +draft: true + +pathway: + - section: "Year 1: Biodiversity data handling and visualisation" + description: | + learners will understand how to handle biodiversity data and analyse it, as well as elements of visualisation, identifying the optimal visualisation for a dataset. [SC1.1,SC1.4, SC2.1, SC2.3, SC4.1-3] + tutorials: + - name: PAMPA-toolsuite-tutorial + topic: ecology + - name: regionalGAM + topic: ecology + - name: biodiversity-data-exploration + topic: ecology + - name: gbif_cleaning + topic: ecology + + - section: "Year 2: Metabarcoding and environmental DNA data analysis" + description: | + analysis of environmental DNA samples requires integrative analysis of highly diversified samples, and new techniques to scale with the data [SC1.4, SC1.5, SC2.1, SC3.1, SC4.1-4] + tutorials: + - name: Obitools-metabarcoding + topic: ecology + + - section: "Year 3: Species distribution modeling" + description: | + As an application of data modeling, we will use species migration and biodiversity to teach learners how to build models for complex data and visualise the results. [SC1.1, SC2.4, SC4.1-4] + tutorials: + - name: species-distribution-modeling + topic: ecology + +--- From 2080f2979c361b9cea3c853760989b005bfea8b9 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Fri, 6 Oct 2023 14:10:07 +0200 Subject: [PATCH 05/17] draft LPs --- _includes/pathway-card.html | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/_includes/pathway-card.html b/_includes/pathway-card.html index d9e9f30c1128ba..ecdc2c675dcb9f 100644 --- a/_includes/pathway-card.html +++ b/_includes/pathway-card.html @@ -3,7 +3,7 @@ {% assign coverimage = path.coverimage | default: "/assets/images/GTNLogo1000.png" %} {% assign coverimagealt = path.coverimagealt | default: "GTN logo with a multi-coloured star and the words Galaxy Training Network"%} - +{% if path.draft != true or jekyll.environment != "production" %}
@@ -21,6 +21,11 @@
{{path.title}}

+ + {% if path.draft %} + Draft + {% endif %} + {% for tag in path.tags %} {{ tag }} {% endfor %} @@ -28,5 +33,4 @@
{{path.title}}
- - +{% endif %} From d0ee56c9c82134d84945d70e43ef3e100ded321a Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Oct 2023 12:13:09 +0200 Subject: [PATCH 06/17] add draft mode gallantries IOs --- learning-pathways/io1.md | 2 +- learning-pathways/io2.md | 2 +- learning-pathways/io3.md | 2 +- learning-pathways/io4.md | 2 +- learning-pathways/io5.md | 58 ++++++++ .../gallantries-async/helper-after.md | 1 + .../gallantries-async/helper-before.md | 1 + .../gallantries-async/helper-during.md | 3 + .../gallantries-async/instructor-after.md | 2 + .../gallantries-async/instructor-before.md | 7 + .../gallantries-async/instructor-during.md | 1 + .../gallantries-async/organizer-after.md | 3 + .../gallantries-async/organizer-before.md | 45 ++++++ .../gallantries-async/organizer-during.md | 6 + .../tutorials/gallantries-async/tutorial.md | 139 ++++++++++++++++++ .../gallantries-coursebuilder/tutorial.md | 103 +++++++++++++ 16 files changed, 373 insertions(+), 4 deletions(-) create mode 100644 learning-pathways/io5.md create mode 100644 topics/teaching/tutorials/gallantries-async/helper-after.md create mode 100644 topics/teaching/tutorials/gallantries-async/helper-before.md create mode 100644 topics/teaching/tutorials/gallantries-async/helper-during.md create mode 100644 topics/teaching/tutorials/gallantries-async/instructor-after.md create mode 100644 topics/teaching/tutorials/gallantries-async/instructor-before.md create mode 100644 topics/teaching/tutorials/gallantries-async/instructor-during.md create mode 100644 topics/teaching/tutorials/gallantries-async/organizer-after.md create mode 100644 topics/teaching/tutorials/gallantries-async/organizer-before.md create mode 100644 topics/teaching/tutorials/gallantries-async/organizer-during.md create mode 100644 topics/teaching/tutorials/gallantries-async/tutorial.md create mode 100644 topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index e9aae5ad04cc2e..ae7065c70dea48 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -12,7 +12,7 @@ funding: title: Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding -priority: 1 +priority: 5 draft: true pathway: diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index ede26ae0eb9957..3683d39c9ff97e 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -12,7 +12,7 @@ funding: title: Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling -priority: 1 +priority: 5 draft: true pathway: diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index 1a56f9c29a07f1..e9899620eb995d 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -12,7 +12,7 @@ funding: title: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration -priority: 1 +priority: 5 draft: true pathway: diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index 4a7098636fe6a9..08554c2f960669 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -12,7 +12,7 @@ funding: title: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery -priority: 1 +priority: 5 draft: true pathway: diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md new file mode 100644 index 00000000000000..44c52c2642c315 --- /dev/null +++ b/learning-pathways/io5.md @@ -0,0 +1,58 @@ +--- +layout: learning-pathway +tags: [beginner] +type: use + +editorial_board: +- bebatut +- fpsom +funding: +- erasmusplus + +title: Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme + +priority: 5 +draft: true + + + +pathway: + + - section: "Hybrid Lesson Development Guide" + description: | + Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] + tutorials: + - name: + topic: + + - section: "Train the Trainer Programme" + description: | + This submodule consists of an in depth training of hybrid workshop delivery methodology and risk management. We will base this on existing TtT programmes such as from Carpentries and ELIXIR due to our contact with both, using open methodology to ensure significant review of the materials before publication. This will be evaluated in the first round leveraging LTTAs for the new consortium members (INRAE, MNHN). These LTTAs are not included as a dedicated cost item in the budget, as they will be online and do not require travel for the learners. Lessons learned and feedback provided during this evaluation process will be integrated back into the TtT training module, before a second round of refinement in the mentorship period [SC5.2] + tutorials: + - name: learning-principles + topic: contributing + - name: design + topic: contributing + - name: learner_participation_engagement + topic: teaching + - name: motivation_demotivation + topic: teaching + - name: assessment + topic: teaching + + - section: "Gallantries Handbook" + description: | + A companion to the TtT programme, a handbook instructing in the delivery of hybrid training workshops, including checklists for instructors, hosts, and staff involved in the delivery of such events. [SC5.1-3] + tutorials: + - name: hybrid-training + topic: teaching + - name: gallantries-async + topic: teaching + + - section: "Course Builder" + description: | + Given the highly modular nature of the training content developed in IOs 1-4, the respective submodules can be combined and assembled into courses in different ways. Each submodule has defined prerequisite modules and suggested follow-up modules as well as a time estimate. This information can be used by instructors to "build" their own courses using these building blocks. To assist with this task, we will provide those instructors with a small web application for module selection and scheduling. [SC5.2-3] + tutorials: + - name: gallantries-coursebuilder + topic: teaching +--- diff --git a/topics/teaching/tutorials/gallantries-async/helper-after.md b/topics/teaching/tutorials/gallantries-async/helper-after.md new file mode 100644 index 00000000000000..e37b33204144a7 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/helper-after.md @@ -0,0 +1 @@ +- Fill the helper feedback form \ No newline at end of file diff --git a/topics/teaching/tutorials/gallantries-async/helper-before.md b/topics/teaching/tutorials/gallantries-async/helper-before.md new file mode 100644 index 00000000000000..5dae0457232e03 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/helper-before.md @@ -0,0 +1 @@ +- Test the training material \ No newline at end of file diff --git a/topics/teaching/tutorials/gallantries-async/helper-during.md b/topics/teaching/tutorials/gallantries-async/helper-during.md new file mode 100644 index 00000000000000..ac187940ec561a --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/helper-during.md @@ -0,0 +1,3 @@ +- Follow the relevant chat channels +- Answer student questions or help them figure out who they should ask +- Write up common questions into an FAQ document, or contribute these to the GTN. diff --git a/topics/teaching/tutorials/gallantries-async/instructor-after.md b/topics/teaching/tutorials/gallantries-async/instructor-after.md new file mode 100644 index 00000000000000..49200e70f3edb1 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/instructor-after.md @@ -0,0 +1,2 @@ +- Report any lesson errors or suggest improvements on GitHub +- Give feedback on [Galaxy Training Material GitHub issue](https://github.com/galaxyproject/training-material/issues/1452) diff --git a/topics/teaching/tutorials/gallantries-async/instructor-before.md b/topics/teaching/tutorials/gallantries-async/instructor-before.md new file mode 100644 index 00000000000000..e972366e923c68 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/instructor-before.md @@ -0,0 +1,7 @@ +- Decide on the order of the lessons and who will teach which modules +- Help the organizer set up the workshop webpage +- Review the training material and suggest changes at least 3 weeks before +- Record your lessons +- Provide the videos to the organiser who will organise captions for you +- Review and correct the captions +- Be prepared to help during the week diff --git a/topics/teaching/tutorials/gallantries-async/instructor-during.md b/topics/teaching/tutorials/gallantries-async/instructor-during.md new file mode 100644 index 00000000000000..aeb49d40815f99 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/instructor-during.md @@ -0,0 +1 @@ +- During asynchronous events Instructors are more like Helpers, as the instructing portion is already done! diff --git a/topics/teaching/tutorials/gallantries-async/organizer-after.md b/topics/teaching/tutorials/gallantries-async/organizer-after.md new file mode 100644 index 00000000000000..31efbbd0afcc3f --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/organizer-after.md @@ -0,0 +1,3 @@ +- Collect the participant feedback forms +- Setup a call with the instructors to discuss feedback. +- Report the feedback and notes diff --git a/topics/teaching/tutorials/gallantries-async/organizer-before.md b/topics/teaching/tutorials/gallantries-async/organizer-before.md new file mode 100644 index 00000000000000..154b91f38d290c --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/organizer-before.md @@ -0,0 +1,45 @@ +- Identify the desired workshop contents and topics + - Check the [Video Library](https://gallantries.github.io/video-library/) to identify which videos are available + - Some may be out of date and need to be re-recorded + - Other videos may not exist for a given tutorial and will need to be recorded +- Identify and contact instructors who will record lessons +- Choose a date in coordination with instructors +- Create a registration form, e.g. by copying [our template](https://docs.google.com/forms/d/1mWl34vyXyhO-M9rwrrF0I-Kb2clSW0QHOiFTauweWv8) + + Such a registration form should include: participant details, email, affiliation, location for the workshop, accessibility requirements, motivation for participating, participation on social event, agreement on privacy statement. + +- Setup a webpage to advertise the event + + This page should include: + - [code of conduct](https://galaxyproject.org/community/coc/) + - general information about the event, its format (async) + - registration details and deadline + - draft schedule + - what participants need to do before + - details about the instructors, helpers, hosts + - sponsors (if any) + + We created a [template of such a page](https://gallantries.github.io/video-library/events/testevent/test-event.html) that can easily adapted. + +- Identify places you can promote your event. [Galaxy Hub](https://github.com/galaxyproject/galaxy-hub) or [Carpentries Discuss List](https://carpentries.topicbox.com/groups/discuss) are the primary places to do this + + You should do this 1-3 month in advance of your event (if you can). + +- Collect contact details of the local hosts and instructors in case of last minute changes + +- Arrange the schedule given the content, the instructor availability and the different time zones + + With asynchronous events, students may be working on the training at all times of day and night, so if possible, identify instructors in all of the major world regions (APAC, EMEA, AMER) who can work together to promptly answer student questions online. + +- Identify the chat platform (e.g. a private Slack, or the GTN Slack) + +- Arrange a conference call(s) with instructors and hosts in order to: + - Meet in advance of the workshop + - Divide and document the responsibilities + - Share contact details + - Test the technical infrastructure + +- Request [TiaaS infrastructure](https://galaxyproject.eu/tiaas) if using usegalaxy.eu +- Contact participants to remind them of the workshop webpage where you have written the joining instructions, start/end times, and contact information +- Prepare the feedback form for participants, e.g. by copying our template +- Prepare the feedback form for hosts, helpers and instructors, e.g. by copying our template diff --git a/topics/teaching/tutorials/gallantries-async/organizer-during.md b/topics/teaching/tutorials/gallantries-async/organizer-during.md new file mode 100644 index 00000000000000..59d4669b4486dc --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/organizer-during.md @@ -0,0 +1,6 @@ +- Send daily welcome messages reminding participants what will happen today + - E.g. what materials should everyone be working on + - Where they can get help + - Remind them of the Code of Conduct + - Etc. +- Prepare the participation certificates, e.g. by copying [our template](https://docs.google.com/document/d/1SxvGyST4o5vevosj9H7s3EFnaJwl3Q1up9xPUZRu3r4/edit?usp=sharing), and send them to local hosts diff --git a/topics/teaching/tutorials/gallantries-async/tutorial.md b/topics/teaching/tutorials/gallantries-async/tutorial.md new file mode 100644 index 00000000000000..af23884f27fa14 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-async/tutorial.md @@ -0,0 +1,139 @@ +--- +layout: tutorial_hands_on + +title: Asynchronous training +subtopic: practises +draft: true +time_estimation: 1h +questions: +- What is asynchronous training? +- How to deliver asynchronous training using Galaxy? +- What should be prepared for an asynchronous training event? +- How is it different than hybrid training? +objectives: +- Describe asynchronous training +- Organize an asynchronous training event using Galaxy +key_points: +- With hybrid training events, remote instructors pair up with on-site helpers to deliver 1 training across multiple sites simultaneously +- With asynchronous events, instead the contents are prepared ahead of time +- Asynchronous, online training events reduce costs and improve accessibility, even further than hybrid trainings +contributions: + authorship: + - bebatut + - fpsom + - hexylena + funding: + - erasmusplus +--- + +**asynchronous training events**, i.e. MOOC style courses pair pre-recorded and written lesson materials with online participants following along at their own pace and convenience. + +With this model, we aim to bring training events to the trainees while **eliminate** environmental impact of instructor *and* participant travel. + +# What is an asynchronous training event? + +*To illustrate a typical Gallantries/Smörgåsbord event and the different roles (1 person can have several roles), we have decided to share a story with several fictional characters* + +**Taylor** is a training coordinator of an international research consortium. They recently surveyed researchers in the consortium on their need in HTS data analysis. The results were overwhelming: over 60 scientists at the several locations would like to learn how to analyze their own RNA-seq data. To fulfill this demand, Taylor decided to organize a Smörgåsbord style event: a 3-days online workshop. Taylor is the **global organizer** of this event, in charge of finding the date, contact and coordinate with the teachers, advertise the event, find the instructors, etc. After the event, Taylor will aggregate all feedback from participants, helpers and hosts and share them. + +Taylor recruited 2 **helpers** for each day, from amongst the participating incitations. One of the helpers, **Casey**, has some previous experience with RNA-seq data analysis and Galaxy. Before the workshop, they went through the training material and tested it. They will help participants during the workshop when they are stuck or get different results than the instructors. They will also give direct feedback to the instructor about the pace, any possible local issues etc. + +Taylor also recruited 4 **instructors**, **Farah** among them. Farah is a trained bioinformatician and experienced instructor, regularly giving training to scientists on HTS data analysis. She will give the introduction and the first steps of RNA-seq data analysis lessons. Farah is located in Germany and teaches from a room at her institute in front of her computer. **2 weeks** before an event she needs to record her lesson as she would normally teach it during a live training, and provide that video to Taylor. Taylor will generate captions (e.g. YouTube's auto-captions) to Farah who must review and manually correct any captioning mistakes, before returning those to Taylor. + +**Alex** is a PhD student in molecular biology based in Greece. They would like to learn about RNA-seq data analysis to be able to analyze the data they generated. They heard about the workshop and wish to join online. As a **participant**, Alex will actively participate in the workshop by running their first RNA-seq data analysis given the instructor's instructions, ask for help from helpers when stuck, will raise their questions on the participant chat, and will give feedback using sticky notes and the dedicated feedback form. + +# Cost of an event + +With the asynchronous training model, the cost of organizing and participating in the workshop are essentially eliminated: the instructors do not need to travel to the venue, participants can learn wherever is convenient for them, no rooms nor coffee must be organised. + +# Workshop Checklists + +To help you organize an asynchronous event, we have created some checklists, by timing but also [by role](#checklists-by-role). Most of the items in these checklists are not specific to Gallantries/Smörgåsbord events. + +## Before the workshop + +### Global organizers + +{% include topics/teaching/tutorials/gallantries-async/organizer-before.md %} + +### Local helpers + +{% include topics/teaching/tutorials/gallantries-async/helper-before.md %} + +### Instructors + +{% include topics/teaching/tutorials/gallantries-async/instructor-before.md %} + +## During the workshop + +- Chat online on Slack or another platform +- Enjoy! + +### Global organizers + +{% include topics/teaching/tutorials/gallantries-async/organizer-during.md %} + +### Local helpers + +{% include topics/teaching/tutorials/gallantries-async/helper-during.md %} + +### Instructors + +{% include topics/teaching/tutorials/gallantries-async/instructor-during.md %} + +## After the workshop + +Debrief + Sticky notes collection from sites + share experience back: feedback from sites (extract form from issue in github) + form feedback from instructors + helpers + +### Global organizers + +{% include topics/teaching/tutorials/gallantries-async/organizer-after.md %} + +### Instructors + +{% include topics/teaching/tutorials/gallantries-async/instructor-after.md %} + + + +# Checklists by role + +## Global organizers + +### Before the workshop + +{% include topics/teaching/tutorials/gallantries-async/organizer-before.md %} + +### During the workshop + +{% include topics/teaching/tutorials/gallantries-async/organizer-during.md %} + +### After the workshop + +{% include topics/teaching/tutorials/gallantries-async/organizer-after.md %} + +## Local helpers + +### Before the workshop + +{% include topics/teaching/tutorials/gallantries-async/helper-before.md %} + +### During the workshop + +{% include topics/teaching/tutorials/gallantries-async/helper-during.md %} + +## Instructors + +### Before the workshop + +{% include topics/teaching/tutorials/gallantries-async/instructor-before.md %} + +### During the workshop + +{% include topics/teaching/tutorials/gallantries-async/instructor-during.md %} + +### After the workshop + +{% include topics/teaching/tutorials/gallantries-async/instructor-after.md %} diff --git a/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md b/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md new file mode 100644 index 00000000000000..0985e4000c4a90 --- /dev/null +++ b/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md @@ -0,0 +1,103 @@ +--- +layout: tutorial_hands_on + +title: Course Builder +subtopic: prepare +time_estimation: 10m +questions: + - Is this service appropriate for my event? +objectives: + - Identify if it is appropriate +key_points: + - Can make hosting Gallantries/Smörgåsbord style courses easier +contributions: + authorship: + - hexylena + funding: + - erasmusplus +requirements: + - type: "internal" + topic_name: contributing +tags: + - cyoa +--- + +As part of the [Gallantries Project](https://gallantries.github.io) we developed a small "Course Builder" which can help you build a schedule of pre-existing videos from the GTN Video library to use with your courses. + +> +> +> In this tutorial, we will see: +> +> 1. TOC +> {:toc} +> +{: .agenda} + +# Try the Course Builder + +You can try the [course builder](https://gallantries.github.io/course-builder/) online. It works as follows: + +1. The "Welcome!" Tab + + Pick some modules from the left hand menu by clicking on them. They will turn blue when added to your event. + + > Add some modules + > Add the following modules: + > + > Basics: + > 1. Setup + > 1. Code of Conduct + > 1. Feedback + > Sessions: + > 1. Quality Control + > 1. Mapping + > Galaxy Intro: + > 1. A Very Short Introduction to Galaxy + > Transcriptomics: + > 1. Introduction to Transcriptomics + > 1. Reference based RNA-Seq data analysis + {: .hands_on} + +2. The "Session" Tab + + This tab allows you to organise your modules into sessions. Do you want to split up the materials by day? Or morning/afternoon? Or by week if you're running a longer course? + + > Create Sessions and Organise Content + > 1. Create a new section + > + > name: Galaxy Intro + > description: "Morning Session" + > + > 1. Create a new section + > + > name: RNA-Seq + > description: "Afternoon Session" + > + > 1. Add Very Short Introduction to Galaxy to the first session by dragging and dropping it. + > 1. Add RNA Seq modules to the second session + {: .hands_on} + +3. The "Configure Event" Tab + + This tab lets you add metadata to the event, it builds on the data in the video-library so you may not find your name in the list. + + > Update event metadata + > 1. Change the event title and description + > 1. Change the event dates + > 1. Select some trainers + > 1. Select some contacts (can be randomly, or yourself if you are present) + > 1. Select some affiliated institutions + {: .hands_on} + +3. The "Export" Tab + + If you've made it this far you're ready to contribute this file to the Video Library which will provide a workshop webpage for you! + + > Create the event webpage + > 1. Fork the [video-library repo](https://github.com/gallantries/video-library) + > 1. Add your file to `docs/events//index.md` + > 1. Create a pull request + > - If any instructors/institutes/organisers were missing from your + > selections, then write the missing information in the Pull Request + > and the maintainers will help you add it in the correct place. + {: .hands_on} From d137e8887218b86a14f12e20e4990791d03cba06 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Oct 2023 12:17:06 +0200 Subject: [PATCH 07/17] blah --- .../gallantries-async/instructor-before.md | 1 + .../tutorials/gallantries-async/tutorial.md | 16 ++++++++++++++++ 2 files changed, 17 insertions(+) diff --git a/topics/teaching/tutorials/gallantries-async/instructor-before.md b/topics/teaching/tutorials/gallantries-async/instructor-before.md index e972366e923c68..e9def72108a895 100644 --- a/topics/teaching/tutorials/gallantries-async/instructor-before.md +++ b/topics/teaching/tutorials/gallantries-async/instructor-before.md @@ -2,6 +2,7 @@ - Help the organizer set up the workshop webpage - Review the training material and suggest changes at least 3 weeks before - Record your lessons + - Be sure to review the [recording guidelines](https://gallantries.github.io/video-library/events/smorgasbord2/recording.html) - Provide the videos to the organiser who will organise captions for you - Review and correct the captions - Be prepared to help during the week diff --git a/topics/teaching/tutorials/gallantries-async/tutorial.md b/topics/teaching/tutorials/gallantries-async/tutorial.md index af23884f27fa14..b978f8b97d87e7 100644 --- a/topics/teaching/tutorials/gallantries-async/tutorial.md +++ b/topics/teaching/tutorials/gallantries-async/tutorial.md @@ -46,6 +46,22 @@ Taylor also recruited 4 **instructors**, **Farah** among them. Farah is a traine With the asynchronous training model, the cost of organizing and participating in the workshop are essentially eliminated: the instructors do not need to travel to the venue, participants can learn wherever is convenient for them, no rooms nor coffee must be organised. +# Event Timeline + +Here is an example event timeline we provided for a past Smörgåsbord event: + +Date | Time Left | What's happening +--- | --- | --- +31 January | 6 weeks | You tell us which sessions you want to record +4 February | 5 weeks | The final schedule is published +17 February | 4 weeks | GTN CoFest! Here we will help you create workflows + workflow tests for your tutorials. +28 February | 2 weeks | **Training Videos Due**. Final Course Materials online +7 March | 1 week | Captions deadline & 30-second intro videos due +14 March | 0 | It begins! + +We also provided instructors with an instructors guideline page [tailored to the event](https://gallantries.github.io/video-library/instructors) and more important, a set of recording guidelines [like the Gallantries'](https://gallantries.github.io/video-library/events/smorgasbord2/recording.html) which helped instructors know what was best practice during video recording. + + # Workshop Checklists To help you organize an asynchronous event, we have created some checklists, by timing but also [by role](#checklists-by-role). Most of the items in these checklists are not specific to Gallantries/Smörgåsbord events. From f83f29c8c7fdc84d408d3a508617943a0f8fb798 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Oct 2023 12:19:30 +0200 Subject: [PATCH 08/17] shouldve added this earlier --- videos/index.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/videos/index.md b/videos/index.md index 460a1b1d5adcdb..c3dc27ff82d671 100644 --- a/videos/index.md +++ b/videos/index.md @@ -1,5 +1,5 @@ --- -title: GTN Videos +title: GTN Automated Videos layout: page redirect_from: - /topics/admin/videos/index @@ -36,7 +36,8 @@ redirect_from: {% endif %} {% endfor %} -The GTN now generates videos for selected slide decks. Click on a topic below to jump to the video page for that topic! +The GTN now automatically generates videos for selected slide decks. Click on a topic below to jump to the video page for that topic! +Additionally there is a much larger [Video Library](https://gallantries.github.io/video-library/) available with recordings from human instructors teaching each tutorial. {% for topic in sorted_topics %} {% assign topic_id = topic[0] %} From d93402e31dcbe0e4e7927b8810f2a697cef394d7 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Oct 2023 12:20:58 +0200 Subject: [PATCH 09/17] logo ig --- learning-pathways/io1.md | 3 +++ learning-pathways/io2.md | 3 +++ learning-pathways/io3.md | 3 +++ learning-pathways/io4.md | 4 +++- learning-pathways/io5.md | 3 +++ 5 files changed, 15 insertions(+), 1 deletion(-) diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index ae7065c70dea48..edd5aebb31576a 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -12,6 +12,9 @@ funding: title: Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding +cover-image: ./shared/images/Gallantries_logo.png +cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." + priority: 5 draft: true diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index 3683d39c9ff97e..ff86db5012c5b4 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -12,6 +12,9 @@ funding: title: Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling +cover-image: ./shared/images/Gallantries_logo.png +cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." + priority: 5 draft: true diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index e9899620eb995d..efe5e9543b0268 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -12,6 +12,9 @@ funding: title: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration +cover-image: ./shared/images/Gallantries_logo.png +cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." + priority: 5 draft: true diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index 08554c2f960669..d5120fc622fdbf 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -1,4 +1,3 @@ - --- layout: learning-pathway tags: [beginner] @@ -12,6 +11,9 @@ funding: title: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery +cover-image: ./shared/images/Gallantries_logo.png +cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." + priority: 5 draft: true diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index 44c52c2642c315..c7d3493daac83d 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -11,6 +11,9 @@ funding: title: Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme +cover-image: ./shared/images/Gallantries_logo.png +cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." + priority: 5 draft: true From f4a59312626f24c23be773b7327a2fd0b4f0a6d8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 18 Oct 2023 12:32:09 +0200 Subject: [PATCH 10/17] fourth todo --- learning-pathways/io5.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index c7d3493daac83d..ba85f077b087e1 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -23,10 +23,8 @@ pathway: - section: "Hybrid Lesson Development Guide" description: | - Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] - tutorials: - - name: - topic: + ⚠️ **TODO** ⚠️ Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] + tutorials: [] - section: "Train the Trainer Programme" description: | From 114b334c2d5eb71d50ad933cac80e9b60a933c0b Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Thu, 19 Oct 2023 10:37:46 +0200 Subject: [PATCH 11/17] link to a draft tut --- learning-pathways/io3.md | 5 ++- .../tutorials/official-gene-set/tutorial.md | 42 +++++++++++++++++++ 2 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 topics/genome-annotation/tutorials/official-gene-set/tutorial.md diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index efe5e9543b0268..d752241ec0fa7a 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -78,7 +78,10 @@ pathway: - section: "Year 3: Official Gene Set" description: | - ⚠️ **TODO** ⚠️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] + 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] + tutorials: + - name: official-gene-set + topic: genome-annotation --- diff --git a/topics/genome-annotation/tutorials/official-gene-set/tutorial.md b/topics/genome-annotation/tutorials/official-gene-set/tutorial.md new file mode 100644 index 00000000000000..559afdca43ecca --- /dev/null +++ b/topics/genome-annotation/tutorials/official-gene-set/tutorial.md @@ -0,0 +1,42 @@ +-- +layout: tutorial_hands_on +title: Creating an Official Gene Set +zenodo_link: "" +questions: +- I have several genomes assemblies that are not annotated (or I do not trust annotations) +- I am interested to compare structure of a particular gene across these genome assemblies +- How do I do that? +objectives: +- Validate your genes and create an official gene set from them. +time_estimation: 30M +key_points: +- Genoest' OGS Tools makes it easy to validate and release a build of your genome and its annotations. +contributions: + authorship: + - abretaud + funding: + - erasmusplus + +draft: true +--- + +Here's how we manage annotations at BIPAA: + +- Automatic annotation with Maker +- Apollo server for manual curation, following our guidelines +- Each night, our Apollo report application checks that each annotated gene follows our guidelines. A report is available for each user with a list of errors and warnings that needs to be fixed, and a list of valid gene. +- Regularly we generate a new OGS by merging the automatic annotation with Apollo annotated genes (the valid ones only). We use the ogs_merge script to do that. +- To submit the OGS to ENA @ EBI in EMBL format, we (would like to) use gff2embl + + + +> +> +> In this tutorial, we will deal with: +> +> 1. TOC +> {:toc} +> +{: .agenda} + + From 399645d5f352fab6177ff850b725a83ea3c6fe84 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 23 Oct 2023 14:52:39 +0200 Subject: [PATCH 12/17] add SCs --- learning-pathways/io1.md | 9 +++++++++ learning-pathways/io2.md | 10 ++++++++++ learning-pathways/io3.md | 9 +++++++++ learning-pathways/io4.md | 6 ++++++ learning-pathways/io5.md | 6 ++++++ 5 files changed, 40 insertions(+) diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index edd5aebb31576a..e621336f690d26 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -135,3 +135,12 @@ pathway: --- In total, this module will form a course of around 10 days (± 2 days depending on exact analysis stories we identify). Some of these introductory submodules will build on existing training material available in the GTN or Carpentries (~15%). + +Success Criteria: + +- SC1.1) Basic coding skills. This module will cover the basics of the R and Python coding languages for novices. No coding experience will be assumed nor expected. Basic coding concepts will be introduced (variables, functions, data structures). +- SC1.2) Research software development. We will cover best practices for research software development. It will follow Open Science principles, and include topics such as collaborative code development (e.g. git), reproducible research, code review, and quality control. +- SC1.3) Familiarity with federated data analysis, management, and compute infrastructures. We will introduce the Galaxy platform, a user-friendly web-based analysis platform capable of distributing work across public/private clouds and High-Performance Computing (HPC) resources. +- SC1.4) Basic statistical analysis skills. This submodule will cover the basic concepts involved in statistical analysis of scientific data. +- SC1.5) Data acquisition and integration. Scientific data analyses often require interaction with external datasets. We will cover ways to retrieve data from online data sources, transform it to the required format, and integrate it into the analysis. +- SC1.6) Reproducibility and data sharing. A cornerstone of scientific research is reproducibility. We will cover how to effectively share data and analysis pipelines in order to make scientific results optimally reproducible. diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index ff86db5012c5b4..3f284dc81f0357 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -97,3 +97,13 @@ pathway: topic: data-science --- + +Success Criteria: + +- SC2.1) Large-scale data analyses and -handling. In this module, learners will gain competency in managing, organizing, and analysing large collections of datasets. +- SC2.2) Analysis of high-dimensional datasets. Real-world scientific studies often involve more complex datasets. For example, combining data from different experiments or timepoints. This more complex experimental setup translates to increased complexity in data analysis. +- SC2.3) Data visualisation. This module will cover the basics of data visualisation to aid with exploration, interpretation of complex datasets. +- SC2.4) Data modelling. This module will introduce learners to the basics data modelling techniques. This is often required for the identification of patterns in data required for e.g. classification. +- SC2.5) Machine learning. This module will also cover more advanced data modelling techniques such as machine learning. +- SC2.6) Reasoning about impact of computation on results. Many choices must be made during data analysis. This includes experimental design, choice of data analysis tools and their parameter settings, and external reference databases. Each of these choices will impact the results. Accurate interpretation of results is only possible with an understanding and awareness of the impact of these factors. + diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index d752241ec0fa7a..72cb432dd54047 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -85,3 +85,12 @@ pathway: --- + + +Success Criteria: + +- SC3.1) Data stewardship. This competency will provide learners with the necessary skills to evaluate data owned by their organisation, identify key metadata and content requirements, and establish controls and assurance metrics to ensure new data produced by their organisation is of sufficient quality. +- SC3.2) Data federation. While hosting data internally is good, sharing data with teams across the Union and around the world is even better. Students need to understand how to achieve data federation and interchange with other organisations. +- SC3.3) Data standardisation. A key component of stewardship and federation, standardisation of data allows it to be reused internally by common pipelines, but more importantly to be submitted to external databases. This is a key requirement of many data related projects. +- SC3.4) Data collaboration. Many projects now scale beyond the ability of an individual to work on alone. Students need to learn how to work together with large datasets. +- SC3.5) FAIR Data. For high quality, reproducible science, datasets should be FAIR; findable, accessible, interoperable, and reusable. This competency aids learners in ensuring their data is FAIR. diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index d5120fc622fdbf..bcb461bc61d265 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -46,3 +46,9 @@ pathway: topic: ecology --- + +Success Criteria: +- SC4.1) Statistical analysis. This will build on the basic statistics covered in IO1 to give a much better statistical comprehension often needed in more advanced analyses like modeling. +- SC4.2) Interactive data visualisation. For most cases, existing visualisations are sufficient, but knowing which visualisation is appropriate and why can be a key point often missed. Additionally sometimes analyses will require custom visualisation such as for geographic information system data. +- SC4.3) Hypothesis generation. When a researcher is handed a large pile of data, figuring out which questions to ask, and what the expected answer is, is the first step of good science. +- SC4.4) Advanced data modelling. Given a hypothesis for some data, a researcher should know how to model changes across some unknown variables, predicting into the future or filling in potential missing gaps in data. diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index ba85f077b087e1..9cfe5d78e8ff8f 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -57,3 +57,9 @@ pathway: - name: gallantries-coursebuilder topic: teaching --- + +Success Criteria: + +- SC5.1) Hybrid Training Material Development. Hybrid training brings new challenges, and instructors need to be familiar with the particular issues training materials may experience in the face of hybrid training delivery. +- SC5.2) Hybrid Training Methodology. This will enable instructors to effectively host hybrid events and be prepared to address potential issues which may arise there. +- SC5.3) Transnational Training Organisation. Instructors will need instruction in the additional constraints of organising events across countries and timezones. From 52605f93ab84cf5a58ccb0cb5d876b62614a7819 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Mon, 23 Oct 2023 16:34:14 +0200 Subject: [PATCH 13/17] link it --- learning-pathways/io5.md | 2 ++ .../faqs/remote-teaching-cyoa.md | 8 ++++++ .../faqs/remote-teaching-faqs.md | 8 ++++++ .../faqs/remote-teaching-selfstudy.md | 10 ++++++++ .../faqs/remote-teaching.md | 10 ++++++++ .../create-new-tutorial-content/tutorial.md | 25 ++++++++++++++++++- 6 files changed, 62 insertions(+), 1 deletion(-) create mode 100644 topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-cyoa.md create mode 100644 topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-faqs.md create mode 100644 topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-selfstudy.md create mode 100644 topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching.md diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index 9cfe5d78e8ff8f..2286a4e1837cb4 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -25,6 +25,8 @@ pathway: description: | ⚠️ **TODO** ⚠️ Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] tutorials: [] + - name: create-new-tutorial-content + topic: contributing - section: "Train the Trainer Programme" description: | diff --git a/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-cyoa.md b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-cyoa.md new file mode 100644 index 00000000000000..b8eb3a88daa530 --- /dev/null +++ b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-cyoa.md @@ -0,0 +1,8 @@ +--- +title: "Preparing materials for asynchronous learning: CYOA" +box_type: tip +layout: faq +contributors: [hexylena] +--- + +If you are running a remote training, and expect your users to follow a specific path, be **certain** to include the URL parameter to select the pathway to avoid student confusion. Please note that all tutorials using a CYOA *should* be tagged which will give you a heads up as a trainer. diff --git a/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-faqs.md b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-faqs.md new file mode 100644 index 00000000000000..e0036cea74ea15 --- /dev/null +++ b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-faqs.md @@ -0,0 +1,8 @@ +--- +title: "Preparing materials for asynchronous learning: FAQs" +box_type: tip +layout: faq +contributors: [hexylena] +--- + +When you are running a remote, asynchronous lesson, you'll want to be sure you collect all student questions and add them back to your tutorial afterwards, as FAQs. This will help other learners as they progress through the materials, and can give you a very easy URL to point your learners to if they get stuck on a particular task. diff --git a/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-selfstudy.md b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-selfstudy.md new file mode 100644 index 00000000000000..204ee330fcb078 --- /dev/null +++ b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-selfstudy.md @@ -0,0 +1,10 @@ +--- +title: "Preparing materials for asynchronous learning: Self-Study" +box_type: tip +layout: faq +contributors: [hexylena] +--- + +In the context of remote trainings, where a teacher isn't synchronously available, ensuring that you have questions throughout your materials for students to check their understanding is incredibly key. + +Additionally ensuring that solutions are provided, and are correct and up-to-date (or use a snippet explaining data variability along with with ways to check the results) is mandatory. Students will then use these questions to self-check their understanding against what you expected them to learn. diff --git a/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching.md b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching.md new file mode 100644 index 00000000000000..faa284dbdf83dd --- /dev/null +++ b/topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching.md @@ -0,0 +1,10 @@ +--- +title: "Preparing materials for asynchronous learning: Tips" +box_type: tip +layout: faq +contributors: [hexylena] +--- + +The use of snippets is **extremely** important for asynchronous, remote learning. In this situation as students do not have a teacher immediately on hand, and likely do not have friends or colleagues sitting working with them, they will rely on these boxes to refresh their knowledge and know what to do. + +Please ensure you test your learning materials with a learner or colleague not familiar the material, and if possible, (**silently**) watch them go through your lesson. You'll easily identify which portions need more explanations and details. diff --git a/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md b/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md index a7738b5ae02850..33cf51c4640433 100644 --- a/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md +++ b/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md @@ -21,6 +21,8 @@ contributions: editing: - bgruening - shiltemann + funding: + - gallantries abbreviations: API: Application Programming Interface JSON: JavaScript Object Notation @@ -283,6 +285,18 @@ The generated tutorial is structured with: > {: .hands_on} +## Self Study Tutorials + +By following all of the guidelines in this file you can be sure that your tutorial will be optimised for self-study. +The GTN framework encourages the use of snippets, and PTDK ensures tutorials have fully detailed parameters learners should configure. +If you make use of snippets in appropriate places, learners can easily follow a tutorial despite different skill levels with Galaxy. + +Additionally use of [Question and Solution boxes](#questions-and-solution-boxes) can ensure that students can self-check their understanding and progress as they progress through the tutorial. +Generally we recommend one or more questions (and associated correct solutions!) after every hands-on box (which might have a one or more steps to follow.) +These questions will let students be sure their work is correct before they proceed too far. +As such you should design your questions carefully in order to catch common and likely failure modes that learners may encounter. +If a student might forget to select a less-common or deeply-nested parameter, be sure that your question following that hands on tests that properly, and if possible explain that in the solutions. + ## Adding images with captions To add an image in Markdown file, we need to use the markdown syntax for this: {% raw %}`!​[proper alt text describing the image for visually impaired learners](../../images/image.png)`{% endraw %}. @@ -590,7 +604,7 @@ which, when rendered, look like: > - *"param1"*: `42` {: .hands_on} -## **Questions** and **solution** boxes +## **Questions** and **Solutions** boxes Questions can be added to force trainees to think about what they are currently doing, and to put things in perspective. They can also help the instructors by exposing and clarifying common scenarios, errors, or applications. @@ -632,6 +646,8 @@ With well chosen wrong answers, MCQs can do much more than just measure how much In the box below, initially hidden, we add the correct answer and possibly any additional explanation. Self-trainees can then check the solution and its explanation. +{% snippet topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-selfstudy.md %} + ## **Tips** box @@ -889,6 +905,8 @@ The alternative is to figure out the ID for the tool you want to use: Many common questions or instructions may be useful to share between different tutorials. For example instructions on how to start a new history or importing data. To make these types of snippets easier to re-use and avoid duplication, they are available in the form of *snippets*. +{% snippet topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching.md %} + ### Finding snippets These are available in folders named `faqs`, either at the project level, topic level, or tutorial level. @@ -935,6 +953,7 @@ or without a box altogether: {% snippet faqs/galaxy/histories_create_new.md box_type="none" %} + ### Creating new FAQs/snippets Do you want to include something in your tutorial that you think might be useful in other tutorials as well? Or are you answering a frequently asked question? Consider creating a snippet for it @@ -962,6 +981,8 @@ Here you can write the snippet / answer to the FAQ in Markdown {% assign kid_val = site.data['schema-faq'] %} {% include _includes/schema-render.html key=kid_key value=kid_val %} +{% snippet topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-faqs.md %} + ### FAQ pages All FAQs will also be collected on their own page, this makes it easy for and teachers to prepare the session, and for participants to quickly find the answers to common questions. @@ -1122,6 +1143,8 @@ The branch can be selected via URL parameter e.g. for courses, to prevent users - [See this page with Ananas](?gtn-cyoa=Ananas#choose-your-own-tutorial) - [See this page with Avocados](?gtn-cyoa=Avocados#choose-your-own-tutorial) +{% snippet topics/contributing/tutorials/create-new-tutorial-content/faqs/remote-teaching-cyoa.md %} + # Citations If you would like to cite any articles, books or websites in your tutorial, you can do so by adding a file called `tutorial.bib` next to your `tutorial.md` file. In this file you may enter [bibtex](http://www.bibtex.org/Using/) formatted citations. An example is given below: From 9240097c45bf32aeb358ebf5b1cb70781ffdc5e8 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 1 Nov 2023 16:58:25 +0100 Subject: [PATCH 14/17] fix username for main --- learning-pathways/io1.md | 2 +- learning-pathways/io2.md | 4 ++-- learning-pathways/io3.md | 2 +- learning-pathways/io4.md | 2 +- learning-pathways/io5.md | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index e621336f690d26..11dce21b1a2c6f 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -8,7 +8,7 @@ editorial_board: - shiltemann - hexylena funding: -- erasmusplus +- gallantries title: Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index 3f284dc81f0357..4053ba04b2b890 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -8,7 +8,7 @@ editorial_board: - hexylena - bebatut funding: -- erasmusplus +- gallantries title: Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling @@ -77,7 +77,7 @@ pathway: - section: "Year 2: Introduction to the Galaxy visualisation framework" description: | - ⚠️ **TODO** ⚠️ Galaxy has many options for visualisation of scientific data. This module will cover how to use this framework to create and share visualisation. [SC2.2-3; SC1.1,3,6] + (This module was cancelled due to insufficiencies in the Galaxy Visualisation Framework.) Galaxy has many options for visualisation of scientific data. This module will cover how to use this framework to create and share visualisation. [SC2.2-3; SC1.1,3,6] tutorials: [] - section: "Year 3: Visualisation of complex multidimensional data" diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index 72cb432dd54047..e935bb1aa4237e 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -8,7 +8,7 @@ editorial_board: - hexylena - shiltemann funding: -- erasmusplus +- gallantries title: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index bcb461bc61d265..f69d08ae0fa97b 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -7,7 +7,7 @@ editorial_board: - yvanlebras - bebatut funding: -- erasmusplus +- gallantries title: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index 2286a4e1837cb4..98637130b6750b 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -7,7 +7,7 @@ editorial_board: - bebatut - fpsom funding: -- erasmusplus +- gallantries title: Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme @@ -23,7 +23,7 @@ pathway: - section: "Hybrid Lesson Development Guide" description: | - ⚠️ **TODO** ⚠️ Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] + Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] tutorials: [] - name: create-new-tutorial-content topic: contributing From d9b718014ed5d83c8434c101946d3cf1cb0e4ac7 Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 1 Nov 2023 17:03:10 +0100 Subject: [PATCH 15/17] linting --- .../genome-annotation/tutorials/official-gene-set/tutorial.md | 4 ++-- topics/teaching/tutorials/gallantries-async/tutorial.md | 2 +- .../teaching/tutorials/gallantries-coursebuilder/tutorial.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/topics/genome-annotation/tutorials/official-gene-set/tutorial.md b/topics/genome-annotation/tutorials/official-gene-set/tutorial.md index 559afdca43ecca..c0cfd3b4c087a8 100644 --- a/topics/genome-annotation/tutorials/official-gene-set/tutorial.md +++ b/topics/genome-annotation/tutorials/official-gene-set/tutorial.md @@ -1,4 +1,4 @@ --- +--- layout: tutorial_hands_on title: Creating an Official Gene Set zenodo_link: "" @@ -15,7 +15,7 @@ contributions: authorship: - abretaud funding: - - erasmusplus + - gallantries draft: true --- diff --git a/topics/teaching/tutorials/gallantries-async/tutorial.md b/topics/teaching/tutorials/gallantries-async/tutorial.md index b978f8b97d87e7..abe8aee74e1b55 100644 --- a/topics/teaching/tutorials/gallantries-async/tutorial.md +++ b/topics/teaching/tutorials/gallantries-async/tutorial.md @@ -23,7 +23,7 @@ contributions: - fpsom - hexylena funding: - - erasmusplus + - gallantries --- **asynchronous training events**, i.e. MOOC style courses pair pre-recorded and written lesson materials with online participants following along at their own pace and convenience. diff --git a/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md b/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md index 0985e4000c4a90..b52a00fa89ac72 100644 --- a/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md +++ b/topics/teaching/tutorials/gallantries-coursebuilder/tutorial.md @@ -14,7 +14,7 @@ contributions: authorship: - hexylena funding: - - erasmusplus + - gallantries requirements: - type: "internal" topic_name: contributing From 577183df8a982476e0095450b99bee9a68f539cd Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 1 Nov 2023 17:11:49 +0100 Subject: [PATCH 16/17] linting, docs of LPs --- bin/schema-learning-pathway.yaml | 38 ++++++++++++++++++++++++++- learning-pathways/climate-learning.md | 4 +++ learning-pathways/io1.md | 3 +++ learning-pathways/io2.md | 4 +++ learning-pathways/io3.md | 3 +++ learning-pathways/io4.md | 3 +++ learning-pathways/io5.md | 8 +++--- 7 files changed, 58 insertions(+), 5 deletions(-) diff --git a/bin/schema-learning-pathway.yaml b/bin/schema-learning-pathway.yaml index dd98eb832a5d56..9793edd7eb6c5c 100644 --- a/bin/schema-learning-pathway.yaml +++ b/bin/schema-learning-pathway.yaml @@ -49,11 +49,48 @@ mapping: - type: str #enum: #- CONTRIBUTORS + tags: type: seq + description: Any relevant tags that would help a user discover this LP sequence: - type: str required: true + + type: + type: str + description: | + 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 + required: true + enum: + - admin-dev + - basics + - data-science + - use + - instructors + + draft: + type: bool + description: | + `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. + pathway: type: seq required: true @@ -67,7 +104,6 @@ mapping: type: str tutorials: type: seq - required: true sequence: - type: map mapping: diff --git a/learning-pathways/climate-learning.md b/learning-pathways/climate-learning.md index 6caa00da78e405..af5a5130abeaa4 100644 --- a/learning-pathways/climate-learning.md +++ b/learning-pathways/climate-learning.md @@ -6,6 +6,10 @@ description: | How to have a complete overview of how Galaxy works going from the user welcome page to use batch tools and finishing by conducting interactive analysis. These set of 3 Climate tutorials allow you to understand and see plenty of the multiple features of Galaxy and learning about the cool subject of climate analysis. tags: [Climate, Overview] +editorial_board: +- Marie59 + +type: use pathway: - section: "Following 3 climate tutorials" diff --git a/learning-pathways/io1.md b/learning-pathways/io1.md index 11dce21b1a2c6f..73483777fa8b91 100644 --- a/learning-pathways/io1.md +++ b/learning-pathways/io1.md @@ -12,6 +12,9 @@ funding: title: Gallantries Grant - Intellectual Output 1 - Introduction to data analysis and -management, statistics, and coding +description: | + This Learning Pathway collects the results of Intellectual Output 1 in the Gallantries Project + cover-image: ./shared/images/Gallantries_logo.png cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." diff --git a/learning-pathways/io2.md b/learning-pathways/io2.md index 4053ba04b2b890..4683db53a7de6c 100644 --- a/learning-pathways/io2.md +++ b/learning-pathways/io2.md @@ -12,6 +12,10 @@ funding: title: Gallantries Grant - Intellectual Output 2 - Large-scale data analysis, and introduction to visualisation and data modelling + +description: | + This Learning Pathway collects the results of Intellectual Output 2 in the Gallantries Project + cover-image: ./shared/images/Gallantries_logo.png cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." diff --git a/learning-pathways/io3.md b/learning-pathways/io3.md index e935bb1aa4237e..50585528d16e31 100644 --- a/learning-pathways/io3.md +++ b/learning-pathways/io3.md @@ -12,6 +12,9 @@ funding: title: Gallantries Grant - Intellectual Output 3 - Data stewardship, federation, standardisation, and collaboration +description: | + This Learning Pathway collects the results of Intellectual Output 3 in the Gallantries Project + cover-image: ./shared/images/Gallantries_logo.png cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." diff --git a/learning-pathways/io4.md b/learning-pathways/io4.md index f69d08ae0fa97b..4e988a85a33d2a 100644 --- a/learning-pathways/io4.md +++ b/learning-pathways/io4.md @@ -11,6 +11,9 @@ funding: title: Gallantries Grant - Intellectual Output 4 - Data analysis and modelling for evidence and hypothesis generation and knowledge discovery +description: | + This Learning Pathway collects the results of Intellectual Output 4 in the Gallantries Project + cover-image: ./shared/images/Gallantries_logo.png cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." diff --git a/learning-pathways/io5.md b/learning-pathways/io5.md index 98637130b6750b..5e5b467087b923 100644 --- a/learning-pathways/io5.md +++ b/learning-pathways/io5.md @@ -11,20 +11,20 @@ funding: title: Gallantries Grant - Intellectual Output 5 - Train-the-Trainer and mentoring programme +description: | + This Learning Pathway collects the results of Intellectual Output 5 in the Gallantries Project + cover-image: ./shared/images/Gallantries_logo.png cover-image-alt: "Gallantries logo with the carpentries wrench in galaxy 2 stripes 1 strip colour scheme." priority: 5 draft: true - - pathway: - - section: "Hybrid Lesson Development Guide" description: | Covers an introduction to pedagogy for instructors and how to adapt training materials to hybrid methodology and key points and indicators that instructors should use when evaluating or adapting training materials to hybrid training delivery [SC5.1] - tutorials: [] + tutorials: - name: create-new-tutorial-content topic: contributing From fec28bdbe75e0eff31e51bbae74119f971ed7feb Mon Sep 17 00:00:00 2001 From: Helena Rasche Date: Wed, 1 Nov 2023 17:15:43 +0100 Subject: [PATCH 17/17] break link tags because raw isn't doing enough --- .../tutorials/create-new-tutorial-content/tutorial.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md b/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md index 33cf51c4640433..282a11c9fce708 100644 --- a/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md +++ b/topics/contributing/tutorials/create-new-tutorial-content/tutorial.md @@ -403,7 +403,7 @@ The rendered table is then given as a minimum-width and centred matrix: ## Internally linking to other training material -If you want to link to other training material within your text, please use the {%raw%}`{% link path/to/file.ext %}`{%endraw%} tag: +If you want to link to other training material within your text, please use the {%raw%}`{​% link path/to/file.ext %​}`{%endraw%} tag: {%raw%} ```markdown @@ -413,7 +413,7 @@ If you want to link to other training material within your text, please use the (Note the `.md` extension, and not `.html`, always provide the file name here, it will automatically be converted to the correct link) -If you want to link to a specific section in a tutorial using an anchor (e.g. `#getting-started`), place it outside of the {%raw%}`{% link %}`{%endraw%} tag: +If you want to link to a specific section in a tutorial using an anchor (e.g. `#getting-started`), place it outside of the {%raw%}`{​% link %​}`{%endraw%} tag: {%raw%} ```markdown