Galaxy Training Academy 2024

Asynchronous, Virtual course

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.

Welcome to the Galaxy Training Academy

Do you want to learn how to use Galaxy, a open source data analysis platform? Then you are at the right place. We offer here a 5-day Global Online and Asynchronous learning event.

We provide you with training materials which you can study at your own pace and on your own time throughout the week. Don’t worry, asynchronous does not mean that you are alone! If you ever need help, you can contact one of our many trainers worldwide via Slack chat .

On the first day you can make yourself familiar with the Galaxy platform. In the next days you can follow different tracks, please go to the program tab for more informaiton.

You can set your own pace on your learning journey using our provided self-learning materials. Next to the program, you will find Slack channels you can join to exchange with the trainers and other participants during the event. Here you will also find help if you have qustions or run into an issue during the training. We try to cover all time zones with helpers for each topic, but please be patient if you do not get an immediat response.

You only need a browser and an account on one of the galaxy instances registered for this event. Please have a look at the setup tab.

Certificates: You can earn a certificate for the tracks you attended by answering a short questionnaire to verify your participation.

Who is this course for?

Everyone who would like to get to know Galaxy and learn bioinformatics data analysis, whether you want to master a specific analysis or learn a new skill.

Organisers & Instructors

This event is brought to you by:

Organisers(s) orcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton NekrutenkoDannon Baker avatar Dannon Bakerorcid logoDelphine Lariviere avatar Delphine LariviereGareth Price avatar Gareth Priceorcid logoJohn Davis avatar John DavisMichael Schatz avatar Michael SchatzNatalie Whitaker-Allen avatar Natalie Whitaker-AllenNatalie Kucher avatar Natalie Kucherorcid logoSaskia Hiltemann avatar Saskia HiltemannTeresa Müller avatar Teresa Müller
Instructor(s) orcid logoAhmed Hamid Awan avatar Ahmed Hamid Awanorcid logoAnika Erxleben avatar Anika Erxlebenorcid logoAnna Syme avatar Anna SymeAnup Kumar avatar Anup Kumarorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBérénice Batut avatar Bérénice Batutorcid logoBjörn Grüning avatar Björn Grüningorcid logoClea Siguret avatar Clea SiguretDannon Baker avatar Dannon Bakerorcid logoDiana Chiang Jurado avatar Diana Chiang JuradoDeepti Varshney avatar Deepti Varshneyorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoEli Chadwick avatar Eli Chadwickorcid logoEngy Nasr avatar Engy NasrEmmanuel Augustine avatar Emmanuel AugustineGareth Price avatar Gareth PriceIgor Makunin avatar Igor Makuninorcid logoJohn Davis avatar John Davisorcid logoLucille Delisle avatar Lucille DelisleMatthias Bernt avatar Matthias Berntorcid logoMelanie Föll avatar Melanie FöllMichael Schatz avatar Michael SchatzNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoNate Coraor avatar Nate Coraororcid logoPaul Zierep avatar Paul Ziereporcid logoPavankumar Videm avatar Pavankumar Videmorcid logoPolina Polunina avatar Polina Poluninaorcid logoPratik Jagtap avatar Pratik Jagtaporcid logoRand Zoabi avatar Rand Zoabiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSaim Momin avatar Saim Mominorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSubina Mehta avatar Subina MehtaTeresa Müller avatar Teresa Müllerorcid logoTimothy J. Griffin avatar Timothy J. GriffinTyler Collins avatar Tyler Collinsorcid logoWendi Bacon avatar Wendi Baconorcid logoWolfgang Maier avatar Wolfgang Maier

Before you start

Before starting the course, make sure to follow the setup instructions

Monday: Introduction

When you are ready to start, just work your way through the program below by watching videos and/or following the text-based tutorials. There are no live sessions, so you can determine your own schedule. A large team of instructors is available on Slack to answer your questions 24/7! Enjoy!

Course introduction

Lesson Slides Hands-on Recordings

Welcome & Course logistics

Video: Welcome to the course!

Daily Icebreaker

Please take a moment to introduce yourself and tell us one fun fact about yourself!

Post your answer to Slack #social channel. (See the setup tab for instructions for joining Slack).

Galaxy introduction

Kick off the week with a hands-on introduction to Galaxy, covering everything from basic navigation and data manipulation to reproducing published analyses, quality control, and mapping sequences to a reference genome. Whether you’re new to Galaxy or looking to strengthen your skills, today’s sessions will equip you with the foundational knowledge needed for more advanced topics. In the morning you can take part in the Icebreaker by joining us in the Slack introduction channel. Or you can directly start with the tutorials.

Need help with these tutorials? Ask your questions via the Slack introduction channel.

Start to get to know Galaxy

Lesson Slides Hands-on Recordings
Galaxy Basics for genomics
Understanding Galaxy history system
Using dataset collections
Data Manipulation Olympics
NGS data logistics

Quick start or fresh up your Galaxy knowledge

Lesson Slides Hands-on Recordings
A short introduction to Galaxy

Fundamentals of Sequences analysis

Lesson Slides Hands-on Recordings
Quality Control
Mapping

Tuesday to Thursday: Choose your own Adventure!

Lesson Slides Hands-on Recordings

Daily Icebreakers

Tuesday: For today’s ice breaker, we would love to know one weird fact that you know for no reason. Wednesday: We would love to hear where you find inspiration. Maybe you find inspirtaiton through nature or maybe you have a prominant role model in your life—we’d love to learn more about you! Thursday: if you could take any one movie prop from a movie set, what would it be?

Post your answers each day to Slack #social channel.

Pick a track

Over the course of these three days, you can choose your preferred track and learn how to use Galaxy for data analysis in this research field. If you find multiple topics interesting, feel free to explore more than one track. Each track will guide you through the process, from basic to more advanced analyses, to accommodate learners of all levels.

For assistance, you can access support through the Slack channel associated with each track module. Please note that while we strive to accommodate all time zones, responses to specific questions may take a bit longer depending on the availability of experts in your time zone.

Proteomics Assembly Transcriptomics Single Cell Microbiome Bacterial Genomics BY-COVID Machine Learning

Friday: Grab bag

Can’t get enough? Then please pick one of our FAIR tutorials below, or any of the tutorials of the GTN. Please be aware that only trainings that are part of the introduction day or a learning track have been tested on all instances for the event. The trainers present on Slack will do their best to help you if you have a problem and answer questions, but they may not be expert in the topic you selected. You can directly start with you prefered tutorial.

Need help with these tutorials? Ask your questions via the Slack Channel #gta_friday-grab-bag.

Fair training

Lesson Slides Hands-on Recordings

Daily Icebreaker

For the last ice breaker, we would love to know what the most interesting or exciting thing you learned this week is!!

Post your answer on Slack #social channel

An overview of the RO-Crate concept and its implementations

Lecture Video

RO-Crate - Introduction

Registering Galaxy workflows in WorkflowHub

Lecture Video

Best practices for workflows in GitHub repositories

Explore the GTN!

Feel free to try any other tutorials you see on the GTN, and we will do our best to guide you!

Go to the GTN!

Get set up for the course!

Follow the steps below to get set up with everything you need to participate in the course!

Galaxy logo
Create 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.

Note: If you already have a Galaxy account you can skip this step and just log in to your existing account.

cartoon of a person standing in front of a blackboard
Join Galaxy Training Group (TIaaS)

Join TIaaS by clicking on the link below matching your Galaxy server:

  • Galaxy EU TIaaS
  • Galaxy Main is not using TIaaS
  • Galaxy AU is not using TIaaS

This will give your analysis jobs priority on Galaxy for the duration of the event. Make sure you are logged in before clicking the link. You should see a green message box if all went well.

cartoon of a person leaning against a laptop
Join Slack!

We will provide support via Slack. Here you can ask any questions you may have during the course, and socialize with your fellow participants and instructors. The following steps will get you set up with Slack:

  1. Join Slack via this Invite Link
  2. Join the event channel: #general
  3. Introduce yourself here!

Instructor Zone

Check out our checklists for

Request TIaaS

Training Infrastructure as a Service (TIaaS) is a service that allows you to request space for your course on a server, it helps ensure courses run smoothly by separating your trainee's jobs into a separate queue. Learn more about TIaaS in our tutorial.

The following links will open a (mostly) pre-filled out TIaaS form, if that server supports TIaaS. Otherwise you might see "page not found".

Once you receive a URL from the admins, please set it as a tiaas_link in your event metadata.

Add your event to the Galaxy Hub Event Horizon

To also list your event on the Galaxy Event Horizon, copy the text below, and add your event to the Galaxy Hub GitHub Repo. Create a folder for your event here, and add an index.md file with the following contents:

---
title: "Galaxy Training Academy 2024"
date: '2024-10-07'
days: 5
tease: The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.



#continent: EU
location: "online"
external_url: "https://training.galaxyproject.org/training-material/events/galaxy-academy-2024.html"
gtn: true
contact: "academy@galaxyproject.org"
subsites: [all]
---

Promote the Event

Tootable/Tweetable version:


Galaxy Training Academy 2024! 📢

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.




📅 October 7 – 11, 2024
➡️ https://gxy.io/GTN:E00005
📝 Registration is open until 2024-10-04! https://forms.gle/cxzVatt7MAgiMX12A

Slack-compatible version:


Galaxy Training Academy 2024! 📢

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.




:calendar: October 7 – 11, 2024
:arrow_right: https://gxy.io/GTN:E00005
:pencil: Registration is open until 2024-10-04! https://forms.gle/cxzVatt7MAgiMX12A

Version with schedule:


Galaxy Training Academy 2024! 📢

The Galaxy Academy is a self-paced online training event for beginners as well as learners who would like to improve their Galaxy data analysis skills. Over the course of one week, we will have a different topic and focus every day.




**Agenda**:
- Monday: Introduction
- Tuesday to Thursday: Choose your own Adventure!
- Friday: Grab bag

📅 October 7 – 11, 2024
➡️ https://gxy.io/GTN:E00005
📝 Registration is open until 2024-10-04! https://forms.gle/cxzVatt7MAgiMX12A