Let's get Started!
Welcome everybody, and thank you for joining this course!
Everything you need for this course can be found on this webpage. More information including links to all training materials can be found by clicking on each session
Note: You can also switch to the rich view version of this page.
Welcome & Practical Information
Start here. This will cover all the logistics and practical information for this training week.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Welcome & Course Information | Helena Rasche Saskia Hiltemann | Lecture | Video | Slides | link | #event-gcc2021 | |
| Get set up for the course | custom | Video | |||||
| About Certificates | custom | Video | |||||
| Meet & Join the Galaxy Community! | The Global GTN Community | Video | GalaxyProject Home Galaxy servers Galaxy Training Network Support Galaxy Publications Galaxy Communities Events Mailing Lists Galaxy Working Groups GitHub Gitter Chat GTN Gitter PaperCuts GTN CoFest Twitter Twitter | ||||
| Daily Icebreaker Questions | custom | Video |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Introduction to Galaxy
Start here if you are new to Galaxy. These videos will introduce you to the Galaxy platform, and walk you through your first analyses
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| A Very Short Introduction to Galaxy | Anton Nekrutenko | Lecture/Demo | Video | Related Slides | link | #galaxy_first_analysis | |
| Your First Galaxy Analysis (genomics-based) | Dave Clements | Hands-on Tutorial | Video | Slides Tutorial1 Tutorial2 | link | #galaxy_first_analysis | |
| Galaxy Intro for Everyone (non-genomics) | Anne Fouilloux | Hands-on Tutorial | Video | Tutorial | link | #galaxy_intro_101-for-everyone | |
| Webinar Series: Galaxy Resources For.. | Webinar Series: Galaxy Resources For.. | Video | Galaxy Webinar Page | #event-gcc2021 |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Advanced Galaxy Features
These tutorials cover some more advanced Galaxy features
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Uploading data with the Rule Based Uploader | Assunta DeSanto | Hands-on Tutorial | Video | Tutorial Tutorial | link | #galaxy-rule-builder | |
| Running Workflows from the Command Line using Planemo | Simon Bray | Hands-on Tutorial | Video | Get Set Up (Windows) Tutorial | link | #galaxy-workflow-automation |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Introduction to NGS Analysis
This module will introduce the basics of NGS analysis, from cleaning your data to mapping and assembly
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Demo: NGS Data Logistics using SARS-CoV-2 data | Anton Nekrutenko | Demo | Video | Tutorial | link | #ngs_data-logistics | |
| Quality Control | Florian Heyl | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_quality-control | |
| Mapping | Peter van Heusden | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_mapping | |
| Genome Assembly | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_assembly |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Advanced NGS Analysis
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Assembly: Unicycler assembly of SARS-CoV-2 genome | Cristóbal Gallardo | Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_advanced_unicycler-assembly-sars-cov2-genome | |
| Genome Annotation: Annotation of a prokaryotic genome | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_advanced_annotation-prokaryotic-genome | ||
| Genome Annotation: Refining Genome Annotations with Apollo | Anthony Bretaudeau | Lecture & Hands-on Tutorial | Video | Slides Tutorial Apollo User's Guide | link | #genome_annotation_apollo | |
| Epigenetics - ATAC-Seq data analysis | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_advanced_epigenetics_atac-seq | ||
| SRA Aligned Read Formats to Speed Up SARS-CoV-2 Analysis | Jonathan Trow | Lecture & Hands-on Tutorial | Video | Slides Tutorial Related Tutorial | link | #ngs_advanced_sra-aligned-read-format |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Transcriptomics
The following module cover transcriptomic analysis in Galaxy, from bulk RNA-seq to Single-cell RNA-Seq, from Quality control to Visualisation
Introduction to RNA-Seq
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Introduction to RNA-Seq | Fotis E. Psomopoulos | Lecture | Video | Slides | link | #transcriptomics_ref-based-rna-seq | |
| Reference-based RNA-seq Analysis | Bérénice Batut | Hands-on Tutorial | Video | Tutorial | link | #transcriptomics_ref-based-rna-seq | |
| De novo transcriptome reconstruction with RNA-Seq | Mallory Freeberg | Hands-on Tutorial | Video | Tutorial Publication Training data Related Slides Related Slides Related Slides | link | #transcriptomics_de-novo-transcriptome-reconstruction | |
| Whole transcriptome analysis of Arabidopsis thaliana | Cristóbal Gallardo | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #transcriptomics_mirna-data-analysis |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
RNA-Seq analysis using Rstudio in Galaxy
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Starting Rstudio in Galaxy | Fotis E. Psomopoulos | Demo | Video | Rstudio in Galaxy not available? | link | #transcriptomics_intro-to-r | |
| Introduction to R | Fotis E. Psomopoulos | Hands-on Tutorial | Video | Tutorial | link | #transcriptomics_intro-to-r | |
| Advanced R in Galaxy | Fotis E. Psomopoulos | Hands-on Tutorial | Video | Tutorial | link | #transcriptomics_advanced_r | |
| Visualisation: RNASeq postprocessing with R | Fotis E. Psomopoulos | Hands-on Tutorial | Video | Tutorial | link | #transcriptomics_visualisation-with-r | |
| Visualization of RNA-Seq results with Volcano Plot in Galaxy and R | Maria Doyle | Duo of Hands-on Tutorials | Video | Tutorial 1 Tutorial 2 | link | #transcriptomics_volcano-plot |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Single-cell RNA-Seq Analysis
Why smash tissues up to analyse them, when you can find what’s inside each individual cell? In these scRNA-seq tutorials, you’ll move from FASTQ to trajectory using the same dataset throughout – a case study of previously published, real mouse data. And for the plant enthusiasts, you’ll do the same thing in Arabidopsis! Enjoy life at a single cell scale!
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| An introduction to scRNA-seq data analysis | These slides are narrated by AWS Polly. | Lecture | Video | Slides | link | #transcriptomics_single-cell-rnaseq | |
| Generating a single cell matrix using Alevin | Wendi Bacon | Self-Study with Video Walkthrough | Video | Tutorial | link | #transcriptomics_single-cell-matrix-alevin | |
| Filter, Plot and Explore Single-cell RNA-seq Data | Wendi Bacon | Self-study with Video Walkthrough | Video | Tutorial | link | #transcriptomics_single-cell-filter-plot-explore | |
| Trajectory Analysis using Python (Jupyter Notebook) in Galaxy | Wendi Bacon | Self-study with Video Walkthrough | Video | Tutorial | link | #transcriptomics_single_cell_trajectory-analysis-jupyter | |
| Analysis of plant scRNA-Seq Data with Scanpy | Mehmet Tekman | Hands-on Tutorial | Video | Tutorial | link |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Proteomics
In this module we explore the world of proteomics! Today we have a mixture of lectures, hands-on tutorials, and workflow demonstrations. The FAQ document provides links to example histories if you would like to explore the outputs of the demos yourself.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Introduction to mass spectrometry based proteomics data analysis | These slides are narrated by AWS Polly. | Lecture | Video | Slides | link | #proteomics_introduction-to-ms | |
| Maxquant + MSstats on a clinical cohort | Melanie Föll | Hands-on Tutorial | Video | Tutorial Example History | link | #proteomics_maxquant-and-msstats | |
| DIA Mass-spectrometry with EncyclopeDIA | Emma Leith James Johnson Pratik Jagtap | Lecture & Hands-on Tutorial | Video | Tutorial | link | #proteomics_ms-encyclopedia | |
| ProteoRE tool for Functional Analysis of a Protein List | Yves Vandenbrouck | Tutorial | Video | Tutorial | link | #proteomics_proteore-protein-list-annotation | |
| ProteoRE tool for biomarker discovery | Tutorial | Video | Tutorial | link | #proteomics_proteore-biomarkers-discovery | ||
| Metaproteomics Introduction | Pratik Jagtap | Video Demo | Video | Tutorial | link | #proteomics_metaproteomics | |
| Pandemics Research using Mass Spectrometry | Timothy J. Griffin Subina Mehta Andrew Rajczewski Pratik Jagtap | Lecture and Demo | Video | Slides Workflow | link | #proteomics_pandemics_research_ms |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Proteogenomics
Proteogenomics utilizes a combination of proteomics, genomics, and transcriptomics to aid in the discovery and identification of peptides
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Introduction to Proteogenomics | Timothy J. Griffin | Lecture | Video | Slides | link | #proteomics_protegenomics | |
| Proteogenomics 1: Database Creation | James Johnson | Tutorial | Video | Tutorial | link | #proteomics_protegenomics | |
| Proteogenomics 2: Database search | Andrew Rajczewski | Demo | Video | Tutorial Slides | link | #proteomics_protegenomics | |
| Proteogenomics 3: Novel peptide analysis | Subina Mehta | Demo | Video | Tutorial | link | #proteomics_protegenomics |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Microbial Analysis using Galaxy
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Variant Analysis: M. Tuberculosis Variant Analysis | Peter van Heusden | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #microbial_tuberculosis-variant-analysis | |
| 16S Microbial Analysis with mothur | Saskia Hiltemann | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #microbiome_16s-microbial-analysis | |
| Antimicrobial Resistance Detection using Nanopore long-read sequencing | Wetlab Demo, Lecture & Hands-on Tutorial | Video | Tutorial Related Tutorial | link | #microbiome_antibiotic-resistance-detection-nanopore | ||
| Metatranscriptomics analysis using microbiome RNA-seq data | Pratik Jagtap Timothy J. Griffin Subina Mehta Saskia Hiltemann | Tutorial | Video | Slides from video Related Slides Tutorial | link | #microbiome_metatranscriptomics | |
| Metaproteomics Introduction | Pratik Jagtap | Video Demo | Video | Tutorial | link | #proteomics_metaproteomics |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Machine Learning
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Introduction to Machine Learning | Anup Kumar | Lecture | Video | Slides | link | #machine_learning_introduction | |
| Classification in Machine Learning | Anup Kumar | Tutorial | Video | Tutorial Slides | link | #machine_learning_classification | |
| Regression in Machine Learning | Anup Kumar | Video | Tutorial Slides | link | #machine_learning_regression | ||
| Machine Learning using R in Galaxy | Fotis E. Psomopoulos | Video | Tutorial | link | #machine_learning_with_r | ||
| Deep Neural Networks Demystified | Kaivan Kamali | Trio of Hands-on Tutorials | Video | FNN Slides FNN Tutorial RNN Slides RNN Tutorial CNN Slides CNN Tutorial | link | #machine_learning_deep-neural-networks-demystified |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
SARS-CoV-2 analysis
Here we have collected all the training sessions that cover SARS-CoV-2 analysis. These sessions also appear in other modules and cover a range of topics, but one thing they have in common is that they use SARS-CoV-2 or COVID-19 data.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Demo: NGS Data Logistics using SARS-CoV-2 data | Anton Nekrutenko | Demo | Video | Tutorial | link | #ngs_data-logistics | |
| SRA Aligned Read Formats to Speed Up SARS-CoV-2 Analysis | Jonathan Trow | Lecture & Hands-on Tutorial | Video | Slides Tutorial Related Tutorial | link | #ngs_advanced_sra-aligned-read-format | |
| Assembly: Unicycler assembly of SARS-CoV-2 genome | Cristóbal Gallardo | Hands-on Tutorial | Video | Slides Tutorial | link | #ngs_advanced_unicycler-assembly-sars-cov2-genome | |
| Pandemics Research using Mass Spectrometry | Timothy J. Griffin Subina Mehta Andrew Rajczewski Pratik Jagtap | Lecture and Demo | Video | Slides Workflow | link | #proteomics_pandemics_research_ms |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Plant data analysis
Here we have collected all the training sessions that cover plant data analysis. These sessions also appear in other modules and cover a range of topics, but one thing they have in common is that they use plant datasets.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Whole transcriptome analysis of Arabidopsis thaliana | Cristóbal Gallardo | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #transcriptomics_mirna-data-analysis | |
| Analysis of plant scRNA-Seq Data with Scanpy | Mehmet Tekman | Hands-on Tutorial | Video | Tutorial | link |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Visualisation in Galaxy
This module will cover various ways of visualizing your data in Galaxy
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Circos Visualisation | Helena Rasche | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #visualisation_circos | |
| Genomic Data Visualization with JBrowse | Video | Slides Tutorial | link | #visualisation_jbrowse | |||
| Visualization of RNA-Seq results with Volcano Plot in Galaxy and R | Maria Doyle | Duo of Hands-on Tutorials | Video | Tutorial 1 Tutorial 2 | link | #transcriptomics_volcano-plot |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
Galaxy for Non-Genomics
Galaxy is widely used for analysis of genomics data, but is not limited to any scientific domain. This module covers some non-genomics topics such as Climate research and cheminformatics.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Climate: Functionally Assembled Terrestrial Ecosystem Simulator (FATES) | Lecture & Hands-on Tutorial | Video | Slides Tutorial | link | #climate_fates | ||
| Cheminformatics: High Throughput Molecular Dynamics and Analysis | Simon Bray Chris Barnett | Video | Tutorial | link | #cheminformatics | ||
| Cheminformatics: Protein-ligand docking | Video | Tutorial | link | #cheminformatics | |||
| Cheminformatics: Running molecular dynamics simulations using GROMACS | Video | Tutorial | link | #cheminformatics | |||
| Ecology: Compute and analyze biodiversity metrics with PAMPA toolsuite | Tutorial | Video | Tutorial | link | #ecology_pampa-toolsuite |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
All other Tutorials
Please also feel free to explore all the other tutorials on the GTN website, and do any that sound interesting to you. Our instructors will do their best to support you in any of these tutorials.
All done?
Please feel free to hang around in Slack and talk to us and the rest of the Galaxy community! Thanks for joining!!
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Wrap up & Socialize | wrapup | ||||||
| Useful links: Stay involved in the Galaxy Community! | The Global GTN Community | Video | 5m | GalaxyProject Home Galaxy servers Galaxy Training Network Support Galaxy Publications Galaxy Communities Events Mailing Lists Galaxy Working Groups GitHub Gitter Chat GTN Gitter PaperCuts GTN CoFest Twitter Twitter | |||
| Feedback Survey & Certificates | post-event | Video |
Note: Length indicates the duration of the video. If you want to follow along and/or perform the tutorial yourself, it will likely take longer to complete.
After the Course
All these materials will remain online, so you can continue working on them for as long as you want. The only difference will be that you should ask your questions on the GTN Gitter channel, instead of Slack.