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A practical workshop for (foodborne) pathogen detection from (direct Nanopore) sequencing data using Galaxy

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 February 2nd 2023 as a 1-day hybrid (F2F at FHNW Muttenz, Switzerland and online), free and practical workshop.

Flyer for the 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 hybrid (F2F at FHNW Muttenz, Switzerland and online), free and practical workshop on February 2nd, 2023 to learn how to detect (foodborne) pathogens from (direct Nanopore) sequencing data using Galaxy, an open-source platform for FAIR data analysis.

Registration closed

General information

  • Date: February 2nd, 2023
  • Format: Hybrid
  • Location

    • Online on Zoom
    • F2F2 at FHNW University of Applied Sciences and Arts Northwestern Switzerland, Room 01.S.01, Muttenz, Switzerland
  • Time: 9am-4pm CET (see in your timezone)
  • Cost: Free
  • Contact: berenice.batut@gmail.com if you have questions, or special requirements

Pedagogical information

  • Target Audience: Whoever who

    • Generates sequencing data to detect pathogens
    • Is interested in learning how to use Galaxy to detect pathogens from sequencing data
  • 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
  • Requirements:

    • Knowledge about sequencing techniques
    • Knowledge about pathogens

Preliminary schedule

Start End Duration Title Format Instructors
9:00am 9:30am 30min Welcome Talk Anna Henger, Bérénice Batut, Abdullah Kahraman
9:30am 10:00am 30min Galaxy introduction Talk Bérénice Batut
10:00am 12:00pm 2h Galaxy introduction Hands-on Bérénice Batut, Engy Nasr, Hans-Rudolf Hotz
12:00pm 1:00pm 1h Lunch
1:00pm 1:30pm 30min Foodborne pathogen detection Talk Anna Henger
1:30pm 3:30pm 2h Foodborne pathogen detection Hands-on Bérénice Batut, Engy Nasr
3:30pm 4:00pm 30min Q\&A and Closing Anna Henger, Bérénice Batut, Abdullah Kahraman

Registration

  • Registration: Before January 15th
  • Capacity: Maximum 40 participants with

    • Maximum 20 onsite
    • Maximum 20 online
  • Selection: If more participants applied than we have the capacity, the "first applied - first served" approach will be used. Participants will be informed on the 16th of January

Logistics

  • Infrastructure: European Galaxy server and the Galaxy Training Material. Both will stay accessible and open after the training.
  • Support: Zoom, Chat, and Shared Google document

Venue

The workshop will take place at:

FHNW University of Applied Sciences and Arts Northwestern Switzerland
Room 01.S.01
Hofackerstrasse 30
4132 Muttenz
Switzerland

It will be streamed for online participants via Zoom (link will be send before the event)

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).

Lodging

Coop Tagungszentrum

  • Address

    Seminarstrasse 12 – 22
    4132 Muttenz

  • Location: 20 min walking distance
  • Prices

    • Double room incl. breakfast: CHF 197.–
    • City tax CHF 3.50.
  • Contact

    • tagungszentrum@coop.ch
    • +41 61 466 11 11

Hotel City Inn

  • Address

    Centralbahnplatz 14
    4002 Basel

  • Location: 10 minutes by train from Basel and a 5 minute walk from the train station to the campus
  • Prices

    • Single room: 110 CHF per night
    • Double room: 140 CHF per night
  • Contact

    • reservation@cityinn.ch
    • +41 61 275 80 00

Event rules and regulations

CoC

The workshop will abide by the Galaxy Project Code of Conduct. Please, make sure that you read it before the event.

COVID-19 policy

In the context of the COVID-19 pandemic, there is no "zero risk" when it comes to any kind of gathering – especially events that bring groups of people together. To try to limit these risks as much as possible, the organizers team has enabled the following safety measures throughout the event. Please make sure to respect them and request support if at any given time you need it.

If you don't feel well or show any symptoms of COVID-19, please avoid joining the event. Online participation is possible at all given times. If you choose to attend in person, please make sure you:

  • wear a FFP2 mask during the conference sessions,
  • clean your hands frequently,
  • cover coughs and sneezes with bent elbow or tissues,
  • try to keep distance from other people when sitting.

Before the workshop

Some important steps to consider before joining the workshop:

  1. Create an account in the European Galaxy server to perform the analysis.
  2. Get ready for using Slack

    • Register at the Galaxy Training Network Slack space:
    • Join the workshop channel named #event-foodborne-pathogen-detection-2023
    • Say hello to other participants.
  3. Bring a computer with a recent web browser
  4. [Optional] Take one of Galaxy interactive tours to guide you stepwise through the Galaxy user interface and the history.

    They will help you to follow the Galaxy introduction, and ensure everyone has a basic understanding of how Galaxy works. It is recommended to go through the following two Galaxy interactive tours before beginning the training, but it is not mandatory

After the workshop

This workshop is over, all the training materials will stay online at https://training.galaxyproject.org/

Instructors and helpers

  • Bérénice Batut, University of Freiburg, Germany
  • Engy Nasr, University of Freiburg, Germany
  • Anna Henger, Biolytix, Switzerland
  • Hans-Rudolf Hotz, Friedrich Miescher Institute for Biomedical Research, Switzerland

Organizers

  • Bérénice Batut, University of Freiburg, Germany
  • Anna Henger, Biolytix, Switzerland
  • Abdullah Kahraman, FHNW University of Applied Sciences and Arts Northwestern Switzerland

Supporters

This workshop is possible thanks to EOSC-Life internal grant for academia-industry collaborations.

logo Biolytix logo FHNW logo EOSC Life logo ELIXIR logo Gallantries logo Erasmus+ logo FMI