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
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Welcome & Course Information | Saskia Hiltemann | Lecture | Video | 25m | Slides | link | #general |
| Get set up for the course | setup | ||||||
| Meet & Join the Galaxy Community! | The Global Galaxy 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 |
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.
Day 1: Introduction to Galaxy and NGS analysis
Today we start by introducing the Galaxy Platform, and show you how to analyze your NGS data using Galaxy. Today we have a mixture of lecutres, demos, and hands-on tutorials.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Icebreaker: Introduce yourself in Slack! | icebreaker | ||||||
| A Very Short Introduction to Galaxy | Anton Nekrutenko | Lecture/Demo | Video | 10m | Slides | link | #1-1_galaxy-intro |
| Your First Galaxy Analysis | Dave Clements | Tutorial | Video | 1h30m | Slides Tutorial Tutorial | link | #1-1_galaxy-intro |
| Demo: NGS Data Logistics using SARS-CoV-2 data | Anton Nekrutenko | Demo | Video | 15m | Tutorial | link | #1-2_ngs-intro |
| Quality Control: Intro | Florian Heyl | Lecture | Video | 40m | Slides | link | #1-3_quality-control |
| Quality Control: Hands-on! | Florian Heyl | Tutorial | Video | 1h10m | Tutorial | link | #1-3_quality-control |
| Mapping: Introduction | Peter van Heusden | Lecture | Video | 10m | Slides | link | #1-4_mapping |
| Mapping: Hands-on! | Peter van Heusden | Tutorial | Video | 20m | Tutorial | link | #1-4_mapping |
| Genome Assembly: Introduction | Simon Gladman | Lecture | Video | 25m | Slides | link | #1-5_assembly |
| Genome Assembly: Hands-on! | Anna Syme | Tutorial | Video | 35m | Tutorial | link | #1-5_assembly |
| Wrap up & Socialize | wrapup |
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.
Day 2: Introduction to RNA-Seq analysis with Galaxy and R
Today we dive into (bulk) RNA-seq analysis. We will walk you through an end-to-end analysis and Galaxy, and show you how to perform downstream analysis on the results using Rstudio in Galaxy.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Icebreaker: Say Hi in Slack! | icebreaker | ||||||
| Introduction to RNA-Seq | Fotis E. Psomopoulos | Lecture | Video | 30m | Slides | link | #2-1_ref-based-rna-seq |
| Reference-based RNA-seq Analysis | Bérénice Batut | Tutorial | Video | 2h30m | Tutorial | link | #2-1_ref-based-rna-seq |
| Starting Rstudio in Galaxy | Fotis E. Psomopoulos | Demo | Video | 20m | link | #2-2_intro-to-r | |
| Introduction to R | Fotis E. Psomopoulos | Tutorial | Video | 50m | Tutorial | link | #2-2_intro-to-r |
| Advanced R in Galaxy | Fotis E. Psomopoulos | Tutorial | Video | 1h | Tutorial | link | #2-3_advanced_r |
| Visualisation: RNASeq postprocessing with R | Fotis E. Psomopoulos | Tutorial | Video | 30m | Tutorial | link | #2-4_visualisation-with-r |
| Wrap up & Socialize | wrapup |
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.
Day 3: Single-cell RNA-Seq Analysis
Today's videos provide a short demo of the analysis, please work through the tutorials on your own first to get all the details and background information, and refer to the videos if you get stuck.
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Icebreaker: Let us know you've joined in Slack! | icebreaker | ||||||
| An introduction to scRNA-seq data analysis | These slides are narrated by AWS Polly. | Lecture | Video | 20m | Slides | link | #3-0_single-cell-rnaseq |
| Understanding Barcodes | Wendi Bacon | Demo | Video | 10m | Tutorial | link | #3-1_understanding-barcodes |
| Pre-processing of 10X Single-Cell RNA Datasets | Wendi Bacon | Demo | Video | 5m | Tutorial | link | #3-2_preprocessing-10x-single-cell-rna-datasets |
| Clustering 3K PBMCs with Scanpy | Wendi Bacon | Demo | Video | 45m | Tutorial | link | #3-3_clustering-3k-pbmcs-with-scanpy |
| Wrap up & Socialize | wrapup |
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.
Day 4: Proteomics
Today 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 |
|---|---|---|---|---|---|---|---|
| Icebreaker: Say Hi in Slack! | icebreaker | ||||||
| Introduction to mass spectrometry based proteomics data analysis | These slides are narrated by AWS Polly. | Lecture | Video | 20m | Slides | link | #4-0_introduction-to-ms-proteomics |
| Maxquant + MSstats on a clinical cohort | Melanie Föll | Tutorial | Video | 1h15m | Tutorial | link | #4-1_maxquant-and-msstats |
| Introduction to Proteogenomics | Timothy J. Griffin | Lecture | Video | 20m | Slides | link | #4-2_protegenomics |
| Proteogenomics 1: Database Creation | James Johnson | Tutorial | Video | 40m | Tutorial | link | #4-2_protegenomics |
| Proteogenomics 2: Database search | Andrew Rajczewski | Demo | Video | 30m | Tutorial Slides | link | #4-2_protegenomics |
| Proteogenomics 3: Novel peptide analysis | Subina Mehta | Demo | Video | 40m | Tutorial | link | #4-2_protegenomics |
| Metaproteomics | Pratik Jagtap | Tutorial | Video | 1h | Tutorial | link | #4-3_metaproteomics |
| Wrap up & Socialize | wrapup |
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.
Choose Your Own Adventure!
Today YOU create the program. Below are set of suggested tutorials. Some have videos, some are self-study tutorials. All have experienced instructors online for support. Want to try something else from the GTN website? Also fine! We will do our best to help you with it.
Video Tutorials
| Topic | Presentor | Type | Video | Length | GTN material | FAQ | Slack |
|---|---|---|---|---|---|---|---|
| Icebreaker: Say Hi in Slack! | icebreaker | ||||||
| Variant Analysis: M. Tuberculosis Variant Analysis (Lecture) | Peter van Heusden | Lecture | Video | 20m | Slides | link | #5-n_tuberculosis-variant-analysis |
| Variant Analysis: M. Tuberculosis Variant Analysis (Hands-on!) | Peter van Heusden | Tutorial | Video | 40m | Tutorial | link | #5-n_tuberculosis-variant-analysis |
| Metagenomics: 16S Microbial Analysis with mothur (Lecture) | Saskia Hiltemann | Lecture | Video | 15m | Tutorial | link | #5-b_16s-microbial-analysis |
| Metagenomics: 16S Microbial Analysis with mothur (Hands-on!) | Saskia Hiltemann | Tutorial | Video | 1h40m | Tutorial | link | #5-b_16s-microbial-analysis |
| Wetlab Demo: Genomic DNA sequencing by Oxford Nanopore MinIon | Miaomiao Zhou | Demo | Video | 20m | link | #5-a_antibiotic-resistance-detection-nanopore | |
| Clinical Microbiomics: Nanopore Whole Bacterial Genome Sequencing | Astrid Heikema | Lecture | Video | 30m | Tutorial | link | #5-a_antibiotic-resistance-detection-nanopore |
| Metagenomics: Antibiotic Resistance Detection with Nanopore Data | Willem de Koning | Tutorial | Video | 45m | Tutorial | link | #5-a_antibiotic-resistance-detection-nanopore |
| Assembly: Unicycler assembly of SARS-CoV-2 genome | Cristóbal Gallardo | Tutorial | Video | 25m | Slides Tutorial | link | #5-h_unicycler-assembly-sars-cov2-genome |
| Climate: Functionally Assembled Terrestrial Ecosystem Simulator (FATES): Lecture | These slides are narrated by AWS Polly. | Lecture | Video | 8m | Slides | link | #5-f_climate-fates |
| Climate: Functionally Assembled Terrestrial Ecosystem Simulator (FATES): Hands-on! | Anne Fouilloux | Tutorial | Video | 1h20m | Tutorial | link | #5-f_climate-fates |
| Circos Visualisation in Galaxy: Intro | Helena Rasche | Lecture | Video | 6m | Tutorial | link | #5-c_circos-visualisation |
| Circos Visualisation in Galaxy: Hands-on! | Helena Rasche | Tutorial | Video | 50m | Tutorial | link | #5-c_circos-visualisation |
| Genome Annotation: Annotation of a prokaryotic genome: Slides | These slides are narrated by AWS Polly. | Lecture | Video | 3m | Tutorial | link | #5-g_annotation-prokaryotic-genome |
| Genome Annotation: Annotation of a prokaryotic genome: Hands-on! | Anthony Bretaudeau | Tutorial | Video | 20m | Tutorial Slides | link | #5-g_annotation-prokaryotic-genome |
| Proteomics: ProteoRE tool for Functional Analysis of a Protein List | Yves Vandenbrouck | Tutorial | Video | 30m | Tutorial | link | #5-i_proteore-protein-list-annotation |
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.
Supported Tutorials (Self-Study)
These tutorials do not have videos, but experienced instructors will be online today to help you with them
| Topic | Presentor | GTN material | FAQ | Slack |
|---|---|---|---|---|
| Genomic Data Visualization with JBrowse | Helena Rasche | Slides Tutorial | link | #5-e_jbrowse |
| Ecology: Compute and analyze biodiversity metrics with PAMPA toolsuite | Coline Royaux Yvan Le Bras | Tutorial | link | #5-d_ecology_pampa-toolsuite |
| Epigenetics: ATAC-Seq data analysis | Hans-Rudolf Hotz Lucille Delisle Florian Heyl | Tutorial | link | #5-k_atac-seq |
| Proteomics: ProteoRE tool for biomarker discovery | Yves Vandenbrouck Florence Combes | Tutorial | link | #5-j_proteore-biomarkers-discovery |
| Cheminformatics: Protein-ligand docking | Simon Bray | Tutorial | link | #5-m_cheminformatics |
| Cheminformatics: Running molecular dynamics simulations using GROMACS | Simon Bray | Tutorial | link | #5-m_cheminformatics |
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 Galaxy 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 & GCC2021 | 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.