Course Builder (Beta!)
Library
admin
- Galaxy Installation with Ansible (Tutorial)
- Ansible (Lecture)
- Ansible (Tutorial)
- Connecting Galaxy to a compute cluster (Tutorial)
- Reference Data with CVMFS (Tutorial)
- Reference Data with CVMFS (Tutorial)
- Data Libraries (Tutorial)
- Galaxy Monitoring with gxadmin (Tutorial)
- Galaxy Interactive Tools (Tutorial)
- Mapping Jobs to Destinations using TPV (Tutorial)
- Recording Job Metrics (Tutorial)
- admin/maintenance/slides (Lecture)
- Galaxy Monitoring with Telegraf and Grafana (Lecture)
- Galaxy Monitoring with Telegraf and Grafana (Tutorial)
- Distributed Object Storage (Tutorial)
- Running Jobs on Remote Resources with Pulsar (Lecture)
- Running Jobs on Remote Resources with Pulsar (Tutorial)
- Use Apptainer containers for running Galaxy jobs (Tutorial)
- Training Infrastructure as a Service (TIaaS) (Tutorial)
- Galaxy Tool Management with Ephemeris (Lecture)
- Galaxy Tool Management with Ephemeris (Tutorial)
- Performant Uploads with TUS (Tutorial)
- Upgrading Galaxy (Tutorial)
- User, Role, Group, Quota, and Authentication managment (Lecture)
- Admin Training Week Overview (Tutorial)
- Admin Welcome (Lecture)
assembly
- Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads (Tutorial)
- Large genome assembly and polishing (Tutorial)
- Chloroplast genome assembly (Lecture & Tutorial)
- An Introduction to Genome Assembly (Lecture)
- Running the VGP Genome Assembly workflows (Demo)
- Assembly of metagenomic sequencing data
climate
community
computational-chemistry
contributing
event
data-science
galaxy-interface
- Running RStudio on Galaxy (Demo)
- Demo: Understanding the Galaxy History System (Demo)
- Using dataset collections (Tutorial)
- SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Lecture)
- SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (Tutorial)
- Rule Based Uploader (Tutorial)
- Uploading data to ENA (Lecture & Tutorial)
- Automating Galaxy workflows using the command line (Tutorial)
- Using Workflow Parameters (Tutorial)
- Workflow Reports (Tutorial)
dev
- Galaxy Code Architecture: app and Dependency Injection (Lecture) đ§ââď¸
- Galaxy Code Architecture: Galaxy Ecosystem (Lecture) đ§ââď¸
- Galaxy Code Architecture: Files and Directories (Lecture Series) đ§ââď¸
- Galaxy Code Architecture: Models and Managers (Lecture) đ§ââď¸
- Galaxy Code Architecture: Pluggable Components (Lecture) đ§ââď¸
- Galaxy Code Architecture: Principles (Lecture)
- Galaxy Code Architecture: Project Management (Lecture)
- Galaxy Code Architecture: Web Client (Lecture) đ§ââď¸
- Galaxy Code Architecture: Web Requests (Lecture) đ§ââď¸
- API tests (Tutorial)
- Client Linting (Tutorial)
- Client Unit Tests (Tutorial)
- Introduction (Tutorial)
- Runtime Errors (Tutorial)
- Selenium (Tutorial)
- Debugging Wisdom (Lecture)
- Unit Testing (Tutorial)
- Galaxy Tool Development (Tutorial)
- ToolFactory: Generating Tools From More Complex Scripts
- ToolFactory: Generating Tools From Simple Scripts
ecology
epigenetics
galaxy-intro
galaxy
sars-cov2
genome-annotation
- Genome annotation with Prokka (Lecture)
- Genome annotation with Prokka (Tutorial)
- Refining Genome Annotations with Apollo (prokaryotes) (Lecture)
- Refining Genome Annotations with Apollo (prokaryotes) (Tutorial)
- Genome annotation with Funannotate (Tutorial)
- Masking repeats with RepeatMasker (Tutorial)
- Essential genes detection with Transposon insertion sequencing (Lecture) (Lecture)
crispr
introduction
variant-analysis
- From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis (Demo)
- Sequencing data analysis for a spectrum of viral genomes (Lecture)
- Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (Tutorial)
- M. tuberculosis Variant Analysis (Lecture)
- M. tuberculosis Variant Analysis (Tutorial)
- Trio Analysis using Synthetic Datasets from RD-Connect GPAP (Tutorial)
metagenomics
- Nanopore Whole Bacterial Genome Sequencing in a Clinical Setting (Lecture)
- Introduction to metagenomics (Lecture)
- Metatranscriptomics analysis using microbiome RNA-seq data (Tutorial)
- Taxonomic Profiling and Visualization of Metagenomic Data
- 16S Microbial Analysis with mothur (short) (Tutorial)
- Antibiotic resistance detection (Tutorial)
- Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition
- Identification of the micro-organisms in a beer using Nanopore sequencing (Tutorial)
- Assembly of metagenomic sequencing data
proteogenomics
proteomics
- EncyclopeDIA (Lecture)
- EncyclopeDIA (Tutorial)
- Introduction to proteomics, protein identification, quantification and statistical modelling (Lecture)
- MaxQuant and MSstats for the analysis of label-free data (Tutorial)
- Metaproteomics tutorial (Demo)
- Pandemics Research using Mass Spectrometry (Lecture & Demo)
- Proteogenomics 1: Database Creation (Tutorial)
- Proteogenomics 2: Database Search (Demo)
- Proteogenomics 3: Novel peptide analysis (Demo)
- Annotating a protein list identified by LC-MS/MS experiments (Tutorial)
virology
one-health
sequence-analysis
statistics
- Convolutional Neural Networks (CNN) (Tutorial)
- Feedforward Neural Networks (FNN) (Tutorial)
- Recurrent Neural Networks (RNN) (Tutorial)
- Classification in Machine Learning (Tutorial)
- Image classification in Galaxy with fruit 360 dataset (Tutorial)
- Introduction to Machine Learning using R (Tutorial)
- Introduction to Machine Learning (Lecture)
- Regression in Machine Learning (Lecture & Tutorial)
synthetic-biology
transcriptomics
- Bulk RNA Deconvolution with MuSiC (Tutorial)
- De novo transcriptome reconstruction with RNA-Seq (Tutorial)
- Inferring trajectories using Monocle3 (Tutorial)
- Generating a single cell matrix using Alevin (Demo)
- Combining datasets after pre-processing (Demo)
- Introduction to Transcriptomics (Lecture)
- Whole transcriptome analysis of Arabidopsis thaliana (Lecture)
- Whole transcriptome analysis of Arabidopsis thaliana (Tutorial)
- Reference-based RNA-Seq data analysis (Tutorial)
- RNA Seq Counts to Viz in R (Tutorial)
- Visualization of RNA-Seq results with Volcano Plot in R (Tutorial)
- Visualization of RNA-Seq results with Volcano Plot (Tutorial)
- Inferring Trajectories using Scanpy (Python) (Demo)
- An introduction to scRNA-seq data analysis (Lecture)
- Analysis of plant scRNA-Seq Data with Scanpy (Tutorial)
- Pre-processing of 10X Single-Cell RNA Datasets (Demo)
- Clustering 3K PBMCs with Scanpy (Demo)
- Filter, Plot and Explore Single-cell RNA-seq Data (Demo)
- Understanding Barcodes (Demo)
single-cell
- Bulk RNA Deconvolution with MuSiC (Tutorial)
- Inferring trajectories using Monocle3 (Tutorial)
- Generating a single cell matrix using Alevin (Demo)
- Combining datasets after pre-processing (Demo)
- Inferring Trajectories using Scanpy (Python) (Demo)
- An introduction to scRNA-seq data analysis (Lecture)
- Analysis of plant scRNA-Seq Data with Scanpy (Tutorial)
- Pre-processing of 10X Single-Cell RNA Datasets (Demo)
- Clustering 3K PBMCs with Scanpy (Demo)
- Filter, Plot and Explore Single-cell RNA-seq Data (Demo)
visualisation
tuberculosis
webinar
wetlab
ro-crate
python
workflowhub
bioconductor
- Getting set up for the Bioconductor SmĂśrgĂĽsbord tutorials (Demo)
- Interactive visualization of SummarizedExperiment objects with iSEE (Tutorial) đ§ââď¸
- Epidemiology for Bioinformaticians (Tutorial) đ§ââď¸
- Tidy Transcriptomics For Single-Cell RNA Sequencing Analyses (Tutorial) đ§ââď¸
- Comparative Genomics with DECIPHER and SynExtend (Tutorial) đ§ââď¸
r
- Interactive visualization of SummarizedExperiment objects with iSEE (Tutorial) đ§ââď¸
- Epidemiology for Bioinformaticians (Tutorial) đ§ââď¸
- Tidy Transcriptomics For Single-Cell RNA Sequencing Analyses (Tutorial) đ§ââď¸
- Comparative Genomics with DECIPHER and SynExtend (Tutorial) đ§ââď¸
Welcome to the Course Builder!
Here you can design your own course from the GTN and Gallantries' Library of Video Content. Follow the steps below to build your course
- Start by selecting some modules from the left.
- Then re-order your content until you're happy on the next tab.
- Configure the event settings like the title, start and end time, etc.
- Preview the daily schedule.
- And receive a Markdown file that can be contributed back to this repository to host your event.
Here you can control the ordering of the content in your schedule
Who all is involved in teaching this event?
When does the course start each day
Daily lunch time
When does the course end each day
Please open a Pull Request against this repository with the following content: