BioConda and BioContainers

Galaxy relies on thousands of tools in Bioconda - the biggest repository of bio tools in the world. Learn how to add your own tools to Bioconda, and in turn Galaxy.

Room: Congress hall B

Beginner's Handbook: Intro to Galaxy

Join our beginner's training for the Galaxy Project to unlock the fundamentals of data analysis, workflow management, and essential tools, all while building a strong foundation for your future Galaxy endeavors.

Room: Congress hall C

Tools for Machine Learning pt 1

Part 1 of this multi-part training starts with the history of AI systems across 4 primary components: model, math, data, and use. Topics included are: cognitive science, probabilistic reasoning, GPUs vs. CPUs, and real-life applications (Kaggle competitions, Hugging Face collaborations).

In this tutorial: we begin the first part of the CNN tutorial with a standard dataset (MNIST).

Room: Congress hall D

Mass Spectrometry and Metaproteomics pt 1

Unlock the secrets of host-microbe interactions in disease with a new Galaxy-based workflow, combining mass spectrometry and customized bioinformatics for powerful and accessible protein analysis in clinical research.

Room: Meeting room 2

Advanced Workflow Development

Learn some of the more advanced techniques in order to develop large, scalable, and maintainable workflows in our training session! Gain hands-on experience with best practices and enhance your workflow development skills for efficient and robust solutions.

Room: Congress hall B

Beginner's Handbook: Admin

Join us for a fun and engaging training on the basics of Galaxy Administration, where you'll learn the essentials, discover helpful resources, and connect with fellow admins. Bring your questions and get ready to dive into the exciting world of Galaxy Administration!

Room: Congress hall C

Beginner's Handbook: Dev

Join our introductory training on Galaxy development and learn how to set up a local instance, make minor client or backend changes, and see your updates in action. Get a brief overview of the client and backend infrastructure to understand how your development efforts translate into the Galaxy platform.

Room: Congress hall C

Beginner's Handbook: Tools

Get ready to boost your galaxy toolkit with our intro tool wrapping training! This fun and comprehensive session will teach you how to integrate your own tools into Galaxy, covering all the basics from XML wrapper creation to dependency management and best practices for seamless functionality.

Room: Congress hall C

Tools for Machine Learning pt 2

Part 2 of this multi-part training continues with a focus on the Convolutional Neural Network (CNN) model for the purpose of image classification. After a brief summary of the history of AI systems, this lecture compares and contrasts the major neural networks (FNN, CNN, RNN, LSTM, GAN, and Transformers) before focusing an CNN image classifier use case.

In this tutorial: we complete the CNN tutorial for image classification with a choice of a standard dataset (MNIST) or pre-selected non-standard dataset (depending on time: fruit, asteroids, puppies).

[updated due to guest speaker schedule] Guest speaker: following the tutorial at 17:00 (5PM), the guest speaker discusses the advancements in bioinformatics that leverage deep learning to predict protein behavior and apply natural language-processing (NLP) methodologies to biological sequences. The speaker demonstrates how to fine-tune an LLM trained on protein sequences, specifically ProtT5 (using Hugging Face and JupyterLab in Galaxy Europe).

Room: Congress hall D

Assembly and Annotation

Assembly and annotation are crucial for processing and understanding genetic data, providing insights into the structure and function of genomes. Join our training to discover how Galaxy's powerful tools and workflows can tackle these complex tasks.

Room: Meeting room 1

Mass Spectrometry and Metaproteomics pt 2

Unlock the secrets of host-microbe interactions in disease with our new Galaxy-based workflow, combining mass spectrometry and customized bioinformatics for powerful and accessible protein analysis in clinical research.

Room: Meeting room 2

Ecology pt 1

Kick off GCC2024 with our first-ever Ecology-focused training session, where you'll explore the powerful tools available in the European Galaxy Ecology instance. Learn to manage ecological data, model species distribution, and produce stunning biodiversity indicators using genetics, GIS, and satellite remote-sensing data.

Room: Congress hall B

Interactive Visualization Development

They say a picture is worth a thousand words. Join this training to learn how Galaxy visualizations work, and how to add one of your own.

Room: Congress hall C

Tools for Machine Learning pt 3

Part 3 of this multi-part training assumes participants have some theoretical knowledge on an AI large language model (LLM) and seek more customization within established machine learning frameworks, specifically Google's TensorFlow. This lecture explores the benefits and challenges of using "vanilla" RNNs by delving into their algorithmic structures.

In this tutorial: we begin the first part of the RNN tutorial using the standard dataset (English and French words).

Room: Congress hall D

Galaxy Backend Development

Explore the essentials of server-side development in Galaxy, with a strong focus on Python. This training will introduce you to the skills and knowledge needed to effectively manage and enhance Galaxy's backend operations.

Room: Meeting room 1

Galaxy Tool Metadata Extractor

Join us for a fun dive into the Galaxy Tool Metadata Extractor workflow, crafted during the Biohackathon 2023 in Barcelona! Learn how to gather, organize, and share tools tailored to your scientific community, and discover how crowd-sourced improvements can enhance your projects—plus, we'll brainstorm ways to make this process even simpler and more effective.

Room: Meeting room 2

Ecology pt 2

Kick off GCC2024 with our first-ever Ecology-focused training session, where you'll explore the powerful tools available in the European Galaxy Ecology instance. Learn to manage ecological data, model species distribution, and produce stunning biodiversity indicators using genetics, GIS, and satellite remote-sensing data.

Room: Congress hall B

Exposomics

Dive into the world of mass spectrometry with Galaxy, where you'll master tools and workflows to study the exposome! Discover how to process high-resolution GC-MS and LC-MS data, detect low abundant analytes, and choose the right parameters for your projects—all while exploring additional open-source packages.

Room: Congress hall C

Tools for Machine Learning pt 4

Part 4 of this multi-part training shows how to apply a sequence-to-sequence model to translate short English sentences into short French sentences, character-by-character, using a Long Short-Term Memory (LSTM) model, which is a type of RNN. The primary tools used in this tutorial include Galaxy's Interactive Jupyter Notebook tool for Command Line Interface (CLI) and Google's TensorFlow.

In this tutorial: we complete the RNN tutorial (started in Part 3) using the standard dataset (English and French words).

Room: Congress hall D

Teaching with Galaxy using the GTN and TIaaS

Learn how to keep your training sessions and classes on track with Galaxy's dedicated resource pool known as TIaaS. This training also focuses on incorporating best practices in utilizing the Galaxy Training Network, the largest repository of Galaxy-related training materials.

Room: Meeting room 1

CSS Deep Dive for Frontend Developers

Unlock the magic of modern CSS and learn how to simplify your code while achieving intricate designs with minimal JavaScript! In this training, you'll create elaborate layouts, implement custom CSS properties, harness built-in reactivity, and build reusable reactive components

Room: Meeting room 2

Pathogen Detection from Sequencing Data

Join us for a deep dive into the PathoGFAIR workflow, where you'll learn how to detect and track foodborne pathogens using cutting-edge metagenomic Nanopore sequencing. This fun and informative workshop will have you mastering Galaxy-based FAIR workflows and creating clear, actionable visualizations and reports.

Room: Congress hall B

Run Alphafold in Galaxy Now

Exciting news—AlphaFold is now available in Galaxy! Join our training to learn how to leverage this cutting-edge tool for protein structure prediction, and see how it can supercharge your research with the power of AI right at your fingertips.

Room: Congress hall C

Genome Assembly with the VGP Workflows

Dive into the world of genome assembly with workflows from the Vertebrate Genome Project (VGP)! In this session, you'll learn how to assemble genomes, evaluate their quality, and discover tips to enhance your assemblies for top-notch results.

Room: Congress hall D

chatGXY - a Galaxy-specific Chatbot for Getting Answers

Come and learn about the galaxy specific llm ChatGXY! In this session, you'll learn about haow this tool can potentially be used to improve the galaxy platform, how the chatbot was created, and the potential problems that it can lead to.

Room: Meeting room 1

Working with Galaxy's Automated Testing

This tutorial delves into the diverse testing landscape of the Galaxy codebase, covering unit, functional, and end-to-end tests across both client and backend systems. You'll learn through a representative sample of tests and gain insights into key concepts and issues to consider when writing tests for software, whether for new features or as standalone contributions.

Room: Meeting room 2

Leveraging Public Single Cell Data

Unlock the treasure trove of public data and learn how to import it into Galaxy for your own single-cell analyses! Bring your own public dataset or use one of our reccomendations, and discover how to gain new insights with various Galaxy workflows in out training session.

Room: Congress hall B

Quantum Processing in Galaxy

Quantum computing is real and ready for you to explore! Join our training session to trial this cutting-edge technology and gain hands-on experience with quantum computing applications.

Room: Congress hall C

Advanced Tool Wrapping in Galaxy

Wrapping a tool in Galaxy might seem straightforward initially, but a myriad of issues can arise. Join our training to explore advanced aspects of tool wrapping and gain the knowledge needed to navigate and solve the problems that arise.

Room: Congress hall D

Earth Systems

This training unveils Galaxy's exciting platform for Earth System studies, making it easier to analyze the intricate dance between the atmosphere, oceans, land, and biosphere. With dedicated models, tools, and visualizations, researchers can dive into predicting and mitigating climate change impacts like never before!

Room: Meeting room 1

Metabolomics, via MS Data Processing

Dive into the world of Metabolomics with Galaxy, where you can tackle everything from raw data extraction to statistical analysis and annotation—all in one place! In this training, we'll use LC-MS analysis to showcase Galaxy's capabilities, supported by hands-on materials from the Galaxy Training Network.

Room: Meeting room 2