2025-10-14-foodborne.md

---

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: [e-mail]
# 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:
  geo:
    lat: 47.5348573
    lon: 7.6419454
  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]) or Anna Henger ([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).