Smörgåsbord 2023

Free, Global, Online Week of Galaxy Training

Practical Information

Dates
22-26 May 2023
Location:
Online
Cost:
Free
Format:
Asynchronous (no live sessions, pre-recorded videos, support via Slack, YOU decide your schedule)
Supporting Institutions:
The Gallantries Project, The CINECA Project, Erasmus Medical Center, ELIXIR Europe, BY-COVID, The Galaxy Training Network, EOSC Euro Science Gateway, DataPLANT
Contact:
Saskia Hiltemann, Helena Rasche
Registration
Register Now!
Add to Google Calendar Add to Outlook Add to Office 365

Program

Below you will find all the tutorials for this course, everything you need to follow this course is listed here.

Welcome & Setup (Start Here!)

Practical information about this course and getting everything set up to follow this course.

Welcome Video

Description:

Start here! We will go over all the important things you need to know about this week!
Length: 15 minutes
Captions: Saskia Hiltemann
Created: 16 May 2023
Materials:
Support:
Go to the video page to see all versions.

Speakers

Galaxy logo
Register for a Galaxy Account


Create an account on one of the following Galaxy servers:

You will get an email with activation link. It may end up in your junk folder.


tiaas logo
Join TIaaS group


Training Infrastructure as a Service (TIaaS) helps Galaxy workshops run smoothly. Joining TIaaS will make your jobs run quicker.

After clicking this link you should see a green box, and then you are all set!


Slack Logo
Join Slack Chat!


Slack is where you can ask all your questions

You will find different channels here, one for each training session where you can ask your questions, as well as some more general channels for socializing, general discussions, feedback and more.


See our Slack Tips & Tricks page for some more info about Slack and how we use it.

Galaxy logo
GalaxyProject Code of Conduct

We are committed to providing a welcoming and inspiring community for all, and expect our code of conduct to be honored.

Please read the Code of Conduct and adhere to it throughout this event. If you witness any violations of this code of conduct, please report it to us.

Read the full Code of Conduct

Icon of a Certificate
Request a certificate of attendance.

For this event, we will use the GTN Certificate Slack Bot to keep track of your progress and request your certificate. (Instructions below).

NOTE: If your country blocks Slack, then please fill in this Certificate Request Form instead.

Deadline: no later than Sunday June 4, 2023.


Certificate Requirements
  1. Have a registration for this event.
  2. Save all your Galaxy Histories.
  3. Register completion of tutorials using the Certificate Bot (see below).
  4. Answer the icebreakers question on Slack every day!
  5. Be active on Slack!
    • Join the Slack channels for every training session you follow this week (see link below video)
    • Let us know when you are starting with a session in the session's dedicated Slack channel
    • Talk about the session! Get stuck? Have a question about the science? want to discuss anything? want to thank your instructors? do it in Slack!
    • Whenever you finish a session, let us know what you thought of it!
    • Enjoyed a tutorial? Take a moment to thank your (volunteer) instructors and speakers on Slack
    • And please, feel free to help other participants on Slack if you know the answer!
  6. Fill out our feedback survey (see "wrap-up" section of the program). This will help us improve this event in the future.

NOTE: You can follow as few or as many training sessions as you want, we will give you a personalized certificate listing all the sessions you attended.


Using the GTN Certificate Slack Bot

  • Completed a tutorial?
    1. Share your Galaxy history via URL
      • Instructions
      • The history URL will look something like: https://usegalaxy.xx/u/saskia/h/my-history-name
    2. Open the Slack channel for the tutorial you finished
      • The link to this channel is listed below the video

    3. Submit your history URL in this channel using the command:

      /completed https://link_to_your_history

    • NOTE: Your message must START with /completed, you cannot write this in the middle or end of the message.
    • NOTE: If a tutorial results in mulltiple histories, you can submit them all in the same command: - example: /completed history1_url history2_url
      1. Write a short message in the channel letting us know what you thought of the tutorial, and/or thanking the instructors!

  • Want to check your submissions?
    • At any time, use the /transcript command to see what you have already submitted
    • In any channel, or a message to @GTN Certificate Bot

  • Finished with the event? Use the command:
    • /request-certificate
      • to request a certificate for the course.
      • Enter your name as you would like it to appear on the Certificate
        • example: /request-certificate Saskia Hiltemann
    • In any channel, or a message to @GTN Certificate Bot
    • We will review your Galaxy histories, and send you your personalised certificate
      • We aim to do this within 2 weeks of the certificate deadline

Come say Hi in Slack! Let us know you are joining today and are getting started!

Icebreaker pictogram
Monday Icebreaker


1. Introduce yourself and tell us one fun fact about yourself!
2. What are you hoping to learn this week?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)

Note: Please do this every day if you would like to receive a certificate of attendance


Icebreaker pictogram
Tuesday Icebreaker


What is the coolest, most mind blowing fact (nature/people/animal etc.) you know?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Wednesday Icebreaker


What is your favorite dish (food or drink)? Bonus points for recipes!

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Thursday Icebreaker


1. What is one fun hobby, passion, skill or talent you have?
2. What is your favorite thing about the course so far?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Icebreaker pictogram
Friday Icebreaker


What is your favorite book, film, tv show or game you've enjoyed recently?

Post your answers in #social on Slack!

Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :)


Day 1: Introduction

Today we recommend you start by learning about the Galaxy platform (but nothing is mandatory!).

Learn Galaxy

New to Galaxy? please choose one of the two introductory modules. Already familiar with Galaxy? Deepen your knowledge of the Galaxy platform with the tutorials in the 'Advanced Galaxy Features' section

Intro to Galaxy Intro to Galaxy (Non Genomics) Advanced Galaxy Features

Sequence Analysis Basics

This module covers some common steps in -omics analysis, such as quality control, mapping to a reference genome, and genome assembly.

Sequence Analysis Basics

Day 2-5: YOU decide!

The schedule for this week is up to YOU. You can do as many or as few tutorials as you want, and YOU decide which topics you learn about! We have defined some training modules to help you choose your program this week.

Browse by Analysis Type

I'm interested in...

Genomics Transcriptomics Proteomics Single-Cell Analysis Meta -omics Genome Annotation Genome Assembly Machine Learning

Browse by Sample Type

I want to analyze...

One Health Data Plants Microbial Samples

Non-Genomics modules

I want to learn about...

Ecology Climate Computational Chemistry

Bioconductor & R

Bioconductor

FAIR data & Best Practices

RO-Crate

I'm new to Bioinformatics and unsure what to choose!

No problem! If you are unsure what you want to do, or just want to learn more about bioinformatics in general, we have defined a week's schedule for you, the Bioinformatics Buffet!

Bioinformatics Buffet

Looking for Something Else?

Browse All Videos Browse All GTN Tutorials Galaxy Tool & GTN Development

Or ask us for recommendations in Slack!

Wrap-up

Done for the week? Please take a moment to thank your volunteer instructors in Slack, and give us some feedback so that we can improve this event in the future.

Thank you for joining and we hope to keep seeing you around the Galaxy Community!

Galaxy logo
Let us know what you thought of this course!

Please share your thoughts, suggestions, complaints and compliments with us in one of the following ways:

  • About this event: Please fill out this Feedback Form to help us improve this event in the future!
  • About the Materials (slides, training manuals): use the feedback forms at the end of the tutorial on the GTN website.
  • Anything else? - Let us know in Slack (#feedback )

Icon of a Certificate
Request a certificate of attendance.

For this event, we will use the GTN Certificate Slack Bot to keep track of your progress and request your certificate. (Instructions below).

NOTE: If your country blocks Slack, then please fill in this Certificate Request Form instead.

Deadline: no later than Sunday June 4, 2023.


Certificate Requirements
  1. Have a registration for this event.
  2. Save all your Galaxy Histories.
  3. Register completion of tutorials using the Certificate Bot (see below).
  4. Answer the icebreakers question on Slack every day!
  5. Be active on Slack!
    • Join the Slack channels for every training session you follow this week (see link below video)
    • Let us know when you are starting with a session in the session's dedicated Slack channel
    • Talk about the session! Get stuck? Have a question about the science? want to discuss anything? want to thank your instructors? do it in Slack!
    • Whenever you finish a session, let us know what you thought of it!
    • Enjoyed a tutorial? Take a moment to thank your (volunteer) instructors and speakers on Slack
    • And please, feel free to help other participants on Slack if you know the answer!
  6. Fill out our feedback survey (see "wrap-up" section of the program). This will help us improve this event in the future.

NOTE: You can follow as few or as many training sessions as you want, we will give you a personalized certificate listing all the sessions you attended.


Using the GTN Certificate Slack Bot

  • Completed a tutorial?
    1. Share your Galaxy history via URL
      • Instructions
      • The history URL will look something like: https://usegalaxy.xx/u/saskia/h/my-history-name
    2. Open the Slack channel for the tutorial you finished
      • The link to this channel is listed below the video

    3. Submit your history URL in this channel using the command:

      /completed https://link_to_your_history

    • NOTE: Your message must START with /completed, you cannot write this in the middle or end of the message.
    • NOTE: If a tutorial results in mulltiple histories, you can submit them all in the same command: - example: /completed history1_url history2_url
      1. Write a short message in the channel letting us know what you thought of the tutorial, and/or thanking the instructors!

  • Want to check your submissions?
    • At any time, use the /transcript command to see what you have already submitted
    • In any channel, or a message to @GTN Certificate Bot

  • Finished with the event? Use the command:
    • /request-certificate
      • to request a certificate for the course.
      • Enter your name as you would like it to appear on the Certificate
        • example: /request-certificate Saskia Hiltemann
    • In any channel, or a message to @GTN Certificate Bot
    • We will review your Galaxy histories, and send you your personalised certificate
      • We aim to do this within 2 weeks of the certificate deadline

Welcome Video

Description:

This short video gives an overview of the worldwide Galaxy community, and different ways you can get involved! Video created by Beatriz Serrano-Solano.
Length: 5 minutes
Captions: Saskia Hiltemann
Created: 15 February 2021
Materials:
Support:
Go to the video page to see all versions.

Speaker



Acknowledgements

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This event was brought to you by..

This event was made possible thanks to the entire GTN and Galaxy community!
Organiser Information

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