Merge pull request #6128 from scorreard/update_codex_training

Creation of a learning pathway for the creation of a sig and codex

Author: shiltemann

CONTRIBUTORS.yaml

@@ -434,6 +434,9 @@ bfranicevic:
     affiliations:
       - elixir-europe
 
+BirdmanRidesAgain :
+    name : Keiler Collier
+    joined: 2025-08
 
 breakthewall:
     name: Joan Hérisson

_layouts/learning-pathway.html

@@ -82,3 +82,12 @@ <h2 id="funding">{{locale['references']| default: "Funding" }}</h2>
 	{% endif %}
 
 </section>
+
+<section>
+ {% if pathway.cited %}
+ <h2 id="bibliography">{{locale['references']| default: "References" }}</h2>
+ {% bibliography --cited %}
+ {% endif %}
+</section>
+
+

_plugins/gtn/scholar.rb

@@ -38,7 +38,7 @@ def self.render_citation(key)
     def self.discover_bib
       Jekyll.logger.info '[GTN/scholar] Creating global bib cache'
       global_bib = BibTeX::Bibliography.new
-      bib_paths = [Find.find('./topics'), Find.find('./faqs'), Find.find('./news')].lazy.flat_map(&:lazy).grep(/bib$/)
+      bib_paths = [Find.find('./topics'), Find.find('./faqs'), Find.find('./learning-pathways'), Find.find('./news')].lazy.flat_map(&:lazy).grep(/bib$/)
       bib_paths.each do |path|
         BibTeX.open(path).each do |x|
           x = x.convert_latex

learning-pathways/index.md

@@ -10,6 +10,12 @@ description: Learning pathways are sets of tutorials curated for you by communit
 
 Learning pathways are sets of tutorials curated for you by community experts to form a coherent set of lessons around a topic, building up knowledge as you go. We always recommend to follow the tutorials in the order they are listed in the pathway.
 
+Explore all pathways below, or jump directly to a section:
+
+- [For Scientists](#for-scientists)
+- [For Teachers, Developers and System Administrators](#for-teachers-developers-and-system-administrators)
+
+
 ## For Scientists
 
 

learning-pathways/references.bib

@@ -0,0 +1,18 @@
+@misc{codex-gcc,
+  doi = {10.7490/F1000RESEARCH.1119764.1},
+  url = {https://f1000research.com/slides/13-705},
+  author = {Batut,  Bérénice and Bacon,  Wendi and Zierep,  Paul and Bernt,  Matthias and Soranzo,  Nicola and Gustafsson,  Johan},
+  title = {Galaxy CoDex for finding tools,  workflows,  and training},
+  publisher = {F1000 Research Limited},
+  year = {2024}
+}
+
+@article{nasr2024,
+  title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data},
+  url = {http://dx.doi.org/10.1101/2024.12.23.629682},
+  DOI = {10.1101/2024.12.23.629682},
+  publisher = {Cold Spring Harbor Laboratory},
+  author = {Nasr,  Engy and Pechlivanis,  Nikos and Strepis,  Nikolaos and Amato,  Pierre and Bernt,  Matthias and Bhardwaj,  Anshu and Blankenberg,  Daniel and Brites,  Daniela and Cumbo,  Fabio and Do,  Katherine and Ferrari,  Emanuele and Griffin,  Timothy J. and Gruening,  Bjoern and Hiltemann,  Saskia and Hyde,  Cameron J and Jagtap,  Pratik and Mehta,  Subina and Métris,  Kimberly L. and Momin,  Saim and Nelson,  Tiffanie M. and Oba,  Asime and Pavloudi,  Christina and Péguilhan,  Raphaëlle and Price,  Gareth R and Psomopoulos,  Fotis and Rosic,  Nedeljka and Schatz,  Michael C and Schiml,  Valerie Claudia and Siguret,  Clea and Soranzo,  Nicola and Stubbs,  Andrew and Van Heusden,  Peter and Vohra,  Mustafa and Zierep,  Paul and Batut,  Bérénice},
+  year = {2024},
+  month = dec
+}

learning-pathways/sig-and-codex-creation.md

@@ -0,0 +1,67 @@
+---
+layout: learning-pathway
+title: Creation of a Community CoDex and lab (and optionally of a Special Interest Group (SIG))
+type: instructors
+description: |
+  The Galaxy Communities Dock or **Galaxy CoDex** is a centralized repository that ensures the versioning and documentation of the community components (Batut et al., 2024; Nasr et al., 2024).
+
+  The codex is composed of :
+  - A **GitHub repository** specific to each community with curated lists of tools, workflows and tutorials relevant to the community.
+  *For example : [The curated resources (tools, workflows, tutorials) for the microgalaxy codex](https://github.com/galaxyproject/galaxy_codex/tree/main/communities/microgalaxy/resources).*
+
+  - The **Community lab**, a centralised webpage that enables communities to rapidly aggregate, curate, integrate, display, and launch relevant tools, workflows, and training on different Galaxy servers. This user-friendly interface, built on the Galaxy framework, provides community members with data analysis capacity without requiring programming expertise. Users can run individual tools or create complex workflows, with full provenance tracking to ensure reproducibility, designed specifically for the community research (Nasr et al., 2024).
+  *For example, [the microgalaxy lab (Europe)](https://microbiology.usegalaxy.eu/).*
+
+  The **Special Interest Group (SIG)** refers to a dedicated scientific community that crosses individual lab boundaries and wants to collaborate, share resources, support each other, and/or collectively advocate on a given theme. We have SIGs based on region, domain of science, and more. You might consider that a SIG covers any group of like-minded Galaxy enthusiasts not currently combined into a Working Group.
+  Here is the list of [currently existing SIGs](https://galaxyproject.org/community/sig/) and the [microgalaxy community of practice webpage](https://galaxyproject.org/community/sig/microbial#microgalaxy-community)
+
+  For more information, see: {% cite codex-gcc %} and {% cite nasr2024 %}.
+
+  **Description of the learning pathway:**
+  - Module 1 : The creation of a community CoDex (including the lab interface). Generation of the CoDex includes the generation of three tables : A tool table, a tutorial table and a workflow table.
+  - Module 2: Creation a Special Interest Group (SIG) page (optional).
+
+tags: [community, codex, lab, sig]
+editorial_board:
+- scorreard
+- shiltemann
+- bebatut
+- BirdmanRidesAgain
+
+pathway:
+  - section: "Module 1: Create a Galaxy CoDex for your community"
+    description: |
+      The aim is this learning pathway is to create a Galaxy CoDex for your community (including the lab interface).
+      This module is composed of four tutorials :
+        - Tutorial 1 : Creation of resources listing all the tools and their metadata relevant to your community.
+        - Tutorial 2 : Creation of resources listing all the tutorials and their metadata relevant to your community.
+        - Tutorial 3 : Creation of resources listing all the workflows and their metadata relevant to your community.
+        - Tutorial 4 : Creation of the lab interface (in development)
+
+      Tutorials 1, 2 and 3 are stand alones one and they can be done in any order (or skipped altogether).
+      Tutorial 4 requires files generated by tutorials 1, 2 and 3 so should be done last.
+
+    tutorials:
+      - name: community-tool-table
+        topic: community
+      - name: community-tutorial-table
+        topic: community
+      - name: community-workflow-table
+        topic: community
+      #- name: community-lab
+      #  topic: community
+
+
+  - section: "Module 2: Create a Special Interest Group (SIG)"
+    description: |
+      The aim is this learning pathway is to create a Special Interest Group (SIG) webpage for your community.
+      You can see the list of [currently existing SIGs](https://galaxyproject.org/community/sig/) for insipration.
+    tutorials:
+#      - name: sig-define
+#        topic: community
+#      - name: sig-create
+#        topic: community
+      - name: community_content
+        topic: community
+
+---

topics/community/faqs/create_codex.md

@@ -0,0 +1,13 @@
+---
+title: What is a Codex?
+box_type: tip
+layout: faq
+contributors: [bebatut, scorreard]
+---
+
+The Galaxy Communities Dock or **Galaxy CoDex** is a centralized repository that ensures the versioning and documentation of the community components (Batut et al., 2024; NASR et al., 2025).
+The codex is composed of 
+  - A GitHub repository specific to each community with curated lists of tools, workflows and tutorials relevant to the community.
+  For example : [The curated resources (tools, workflows, tutorials) for the microgalaxy codex](https://github.com/galaxyproject/galaxy_codex/tree/main/communities/microgalaxy/resources).
+  - The **Community lab**, a centralised webpage that enables communities to rapidly aggregate, curate, integrate, display, and launch relevant tools, workflows, and training on different Galaxy servers. This user-friendly interface, built on the Galaxy framework, provides community members with data analysis capacity without requiring programming expertise. Users can run individual tools or create complex workflows, with full provenance tracking to ensure reproducibility, designed specifically for the community research (NASR et al., 2025). 
+  For example, [the microgalaxy lab (Europe)](https://microbiology.usegalaxy.eu/).