Merge branch 'main' into yvanlebras-patch-4-1

Author: bgruening

CONTRIBUTORS.yaml

@@ -77,12 +77,17 @@ abretaud:
       - eurosciencegateway
       - elixir-europe
 
+abdullahkahraman:
+    name: Abdullah Kahraman
+    github: false
+    joined: 2025-10
+
 abdulrahmanazab:
     name: Abdulrahman Azab
     joined: 2019-01
     affiliations:
       - eurosciencegateway
-
+      
 abueg:
     name: Linelle Abueg
     twitter: llabueg
@@ -193,6 +198,12 @@ andrewr:
       - minnesotauni
     joined: 2024-05
 
+
+annahenger:
+    name: Anna Henger
+    github: false
+    joined: 2025-10
+
 annatrigos:
     name: Anna Trigos
     github: false
@@ -1113,6 +1124,11 @@ hannahkimincompbio:
     name: Hannah Kim
     joined: 2024-09
 
+haswane:
+    github: false
+    name: Haswane Chei
+    joined: 2025-06
+
 hchiapello:
     name: Hélène Chiapello
     elixir_node: fr
@@ -2584,6 +2600,11 @@ santamccloud:
     affiliations:
       - uni-freiburg
 
+santinofaack:
+    name: Santino Faack
+    github: false
+    joined: 2025-10
+
 saramorsy:
     name: Sara Morsy
     joined: 2021-10

_layouts/tutorial_hands_on.html

@@ -377,7 +377,35 @@ <h1 id="gtn-feedback">{{locale['feedback'] | default: "Feedback" }}</h1>
                 <br>{{ locale['feedback-text-learner'] | default: "Did you use this material as a learner or student? Click the form below to leave feedback." }}<i class="fas fa-hand-point-down"></i>
                 </p>
 
-                <iframe id="feedback-google" class="google-form" src="https://docs.google.com/forms/d/e/1FAIpQLSd4VZptFTQ03kHkMz0JyW9b6_S8geU5KjNE_tLM0dixT3ZQmA/viewform?embedded=true&entry.1235803833={{ own_material_id }}"><a href="https://docs.google.com/forms/d/e/1FAIpQLSd4VZptFTQ03kHkMz0JyW9b6_S8geU5KjNE_tLM0dixT3ZQmA/viewform?embedded=true&entry.1235803833={{ own_material_id }}">Feedback Form</a></iframe>
+                <div id="feedback-button">
+                    <img src="{{ site.baseurl }}/shared/images/feedback.png" title="Click to activate feedback form" alt="Click here to load feedback form" />
+                </div>
+                <div id="feedback-form">
+                </div>
+
+                <script type="text/javascript">
+                (function (window, document) {
+                    function onDocumentReady(fn) {
+                        if (document.attachEvent ? document.readyState === "complete" : document.readyState !== "loading") {
+                            fn();
+                        } else {
+                            document.addEventListener('DOMContentLoaded', fn);
+                        }
+                    }
+
+                    onDocumentReady(function () {
+                        var feedbackButton = document.getElementById('feedback-button');
+                        var feedbackForm = document.getElementById('feedback-form');
+
+                        if (feedbackButton && feedbackForm) {
+                            feedbackButton.addEventListener('click', function() {
+                                feedbackButton.style.display = 'none';
+                                feedbackForm.innerHTML = '<iframe id="feedback-google" class="google-form" src="https://docs.google.com/forms/d/e/1FAIpQLSd4VZptFTQ03kHkMz0JyW9b6_S8geU5KjNE_tLM0dixT3ZQmA/viewform?embedded=true&entry.1235803833={{ own_material_id }}"><a href="https://docs.google.com/forms/d/e/1FAIpQLSd4VZptFTQ03kHkMz0JyW9b6_S8geU5KjNE_tLM0dixT3ZQmA/viewform?embedded=true&entry.1235803833={{ own_material_id }}">Loading feedback form...</a></iframe>';
+                            });
+                        }
+                    });
+                })(window, document);
+                </script>
 
                 <h1>{{locale['citing-tutorial'] | default: "Citing this Tutorial"}}</h1>
                 <p>

events/2025-10-14-foodborne.md

@@ -0,0 +1,131 @@
+---
+layout: event
+title: "A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy"
+
+description: |
+    The purpose of this workshop is to gain knowledge on detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy. The workshop will be on October 14th 2024 as a 1-day F2F at FHNW Muttenz, Switzerland, free and practical workshop.
+
+date_start: 2025-10-14
+date_end: 2025-10-14
+
+
+cost: free
+audience: Whoever is interested in generating sequencing data to detect pathogens
+    and is interested to learn how to use Galaxy to detect pathogens from sequencing data.
+
+contact_email: [email protected]
+# async: false
+mode: onsite
+
+#registration:
+  #link: https://galaxyproject.org/events/2023-02-02-foodborne-pathogen-detection-workshop/ # needs to be updated if the registration is still open!!!
+#  deadline: 2025-10-14
+
+contributions:
+  organisers: [annahenger, abdullahkahraman]
+  instructors: [wm75, EngyNasr, santinofaack]
+
+location:
+  name: FHNW University of Applied Sciences and Arts Northwestern Switzerland
+  address:  Hofackerstrasse 30
+  postcode: 4132
+  city: Muttenz
+  country: Switzerland
+
+infrastructure:
+  tiaas: true    # tiaas = Training Infrastructure as a Service, and can be requested (for free) from all major Galaxies
+
+  servers:
+    - server: https://usegalaxy.eu
+      name: Galaxy EU
+
+tags:
+- introduction
+- sequence-analysis
+- metagenomics
+- foodborne
+
+# Program of your course
+# Add GTN tutorials by supplying the topic and tutorial name
+program:
+  - section: "Preliminary schedule"
+    description: The workshop will take place on site in Room 02.W.03
+    tutorials:
+      - type: custom
+        name: "Welcome"
+        time: "09:30 to 10:00"
+      - name: galaxy-intro-peaks2genes
+        topic: introduction
+        time: "10:00 to 12:00"
+      - type: custom
+        time: "12:00 to 13:00" 
+        name: Lunch
+      - name: pathogen-detection-from-nanopore-foodborne-data
+        topic: microbiome
+        time: "13:00 to 15:30"
+      - type: custom
+        name: "Q&A and Closing"
+        time: "15:30 to 16:00"
+
+---
+# A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy
+
+Biolytix and the Freiburg Galaxy team teamed up over the last year to develop Galaxy-based workflows for accessible and scalable detection and identification of foodborne pathogens, thanks to an EOSC-Life internal grant for academia-industry collaborations.
+
+To share about the workflows and (foodborne) pathogen detection in general, we organize a 1-day F2F at FHNW Muttenz, Switzerland , free and practical workshop on October 14th, 2025 to learn how to detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy, an open-source platform for FAIR data analysis.
+
+## Topics
+
+- Galaxy Introduction
+- Sequence-analysis
+- Foodborne
+
+## Requirements:
+- Knowledge about sequencing techniques
+- Knowledge about pathogens
+
+
+## Learning Outcome
+
+By the end of this workshop, participants will be able to:
+- Name bioinformatics tools and steps required to
+    - Preprocess pathogen sequencing data
+    - Identify pathogens in sequencing data
+    - Track pathogen contamination sources using different sequencing data
+- Repeat steps in Galaxy to preprocess, identify and track pathogens from sequencing data
+
+
+## Schedule
+
+Please see the Program tab.
+
+## Registration
+
+
+The number of places in this workshop is limited. 
+
+
+
+If you want to register, please contact Diana Hormisch ([[email protected]](mailto:[email protected])) or Anna Henger ([[email protected]](mailto:[email protected]))
+
+
+## Getting to FHNW Muttenz
+
+### Using Public transport
+
+The FHNW Muttenz Campus is well served by public transport.
+
+- From Muttenz railway station: A six-minute or so walk via Hofackerstrasse or Grenzacherstrasse and through the campus park.
+- By bus: Bus 46 (from/to Kleinhüngingen) or 47 (from/to Bottmingen) to the "Fachhochschule" stop, then a two-minute walk
+- From the 'Zum Park' tram stop in Muttenz: Tram 14 from Basel and Pratteln, then a 10-minute or so walk via Zwinglistrasse and Kriegackerstrasse
+- By train: 5 minutes by train from Basel (S3 direction Olten or S1 direction Frick) and a 5 minute walk from the train station to the campus (see above)
+
+
+### By road
+
+- Car/motorcycle
+    - At the Hagnau junction on the A2 motorway take the A18 towards Delémont then leave by the Muttenz-Nord exit. At the 'Pantheon' turn left into Hofackerstrasse.
+    - 232 parking spaces are available on Hofackerstrasse (the car park is located on the right-hand side just before the campus). Payment can be made using the FH Card or cash.
+    - Parking spaces on the south side of the campus are available for persons with a mobility impairment.
+    - More than 50 covered motorcycle parking spaces are available on the west side of the campus (ramp to basement 1)
+- Bicycles: More than 500 covered and uncovered cycle parking spaces are available along Hofackerstrasse and in front of the PTC (Process Technology Centre).

events/2025-11-24-gat-brno.md

@@ -34,7 +34,7 @@ contributions:
   organisers: [martenson]
   instructors: [mvdbeek, bgruening, mira-miracoli, martenson, martindemko, pauldg]
   infrastructure: []
-  funding: [elixir-europe, deKCD]
+  funding: [elixir-europe, deKCD, deNBI]
 
 infrastructure:
   custom:

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@@ -1,3 +1,20 @@
+GTN_GTN:1760088022
+
+_layouts/tutorial_hands_on.html
+GTN_GTN:1759939295
+
+news/_posts/2025-10-08-joined-teachV.md
+GTN_GTN:1759847177
+
+events/2025-11-24-gat-brno.md
+GTN_GTN:1759740708
+
+metadata/shortlinks.yaml
+GTN_GTN:1759740660
+
+metadata/git-mod-e0b11612e2c5a441841ccb15b1016765c15c91bd.txt
+metadata/git-pub-e0b11612e2c5a441841ccb15b1016765c15c91bd.txt
+metadata/github.yml
 GTN_GTN:1759600222
 
 learning-pathways/sig-and-codex-creation.md

…1612e2c5a441841ccb15b1016765c15c91bd.txt …925f9b0ec6b29ee01365ad8e8538f990ab2b.txtmetadata/git-pub-e0b11612e2c5a441841ccb15b1016765c15c91bd.txt renamed to metadata/git-pub-d94a925f9b0ec6b29ee01365ad8e8538f990ab2b.txt metadata/git-pub-e0b11612e2c5a441841ccb15b1016765c15c91bd.txt renamed to metadata/git-pub-d94a925f9b0ec6b29ee01365ad8e8538f990ab2b.txt

@@ -1,3 +1,10 @@
+GTN_GTN:1759939295
+
+A	news/_posts/2025-10-08-joined-teachV.md
+GTN_GTN:1759740660
+
+R099	metadata/git-mod-aab96da72e1fbd40955935885a077245b3841788.txt	metadata/git-mod-e0b11612e2c5a441841ccb15b1016765c15c91bd.txt
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 GTN_GTN:1759600222
 
 A	topics/community/tutorials/community-lab/tutorial.md