Description
Galaxy is a user-friendly web application that enables you to run complex data analysis (NGS, proteomics, images, metabolomics…) without learning programming. Whether you run standard workflows or perform custom and interactive analysis, Galaxy seamlessly executes these analysis on high performance clusters (HPC, like the one we have at EMBL) for you. Galaxy is used by research groups and companies as a collaborative analysis platform and by international projects as a workhorse (e.g. PhenoMeNal). It is one of the few tools that can be easily deployed in (secure) clouds (next to the data) enabling researchers to easily work remotely. It is also a powerful environment to quickly prototype analysis and workflows, deploy tools, share pipelines and teach.
During this 2 day workshop, participants will learn how to efficiently work with the Galaxy platform using both the usegalaxy.eu and our local EMBL Galaxy servers (galaxy.embl.de). During the first day, participants will learn the Galaxy basics like running jobs, managing their datasets, organizing their work in analysis histories, how to assemble workflows and parallelize data processing. During the second day, participants will analyze the data of their choice by selecting from a large choice of tutorials. Tutorials cover usual sequencing technologies (ATAC-seq, ChIP-seq, RNA-seq, DNA-meth & Variant calling), single-cell transcriptomic and image analysis. Finally, an overview of the EMBL IT infrastructure and how to best work with our local EMBL Galaxy platform will be demonstrated.
Available Topics for Day 2
Due to limited capacity we will only be able to offer 4 of the 7 sessions listed below. When registering, please select your first and second preference from the following list:
- Single-Cell Transcriptomics (3K PBMCs with Scanpy)
- ChIP-seq (Formation of the Super-Structures on the Inactive X)
- DNA methylation data analysis
- RNA-seq (Reference-based RNA-Seq data analysis)
- Variant Calling (Identification of somatic and germline variants from tumor and normal sample pairs)
- Imaging (Tracking of dividing fluorescent nuclei in a Drosophila embryo) – "Object tracking using CellProfiler: The workflow will analyze a time-lapse recording of a Drosophila embryo expressing histone-GFP and track dividing nuclei"
- Metagenomics (16S microbial analysis with mothur)
What you will learn
• General concepts and formats used with Galaxy
• Use both the public (usegalaxy.eu) and EMBL (galaxy.embl.de) Galaxy platforms
• Run jobs and assemble workflows in Galaxy
• Use advanced Galaxy features available on collections and workflows
• Understand EMBL infrastructure (servers, file servers, HPC…)
• How to best use our local EMBL Galaxy server and how it integrates with STOCKS
• Discover the Galaxy self-learning material (Galaxy Training Network) to continue autonomous learning after this training
Audience
The course is free and open to EMBL researchers from all experience levels, both wet and dry.
Bookings
Bookings are closed for this event.