Table 1.
Topics available in the Galaxy training material website (https://training.galaxyproject.org) with their target users and available tutorials. Admin = Galaxy administrators, Biol = Biomedical researchers, Dev = Tool and software developers, Inst = Instructors and Tutorial developers. The scripts for the extraction of such information are available in GitHub (https://github.com/bebatut/galaxy-training-material-stats). This table displays content current as of 28th Sep, 2017.
| Topic | Target | Tutorials |
|---|---|---|
| Galaxy Server administration | Admin | Galaxy Database schema, Docker and Galaxy, Advanced customisation of a Galaxy instance |
| Assembly | Biol | Introduction to Genome Assembly, De Bruijn Graph Assembly, Unicycler Assembly |
| ChIP-Seq data analysis | Biol | Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1), Identification of the binding sites of the Estrogen receptor |
| Development in Galaxy | Dev | Contributing with GitHub, Tool development and integration into Galaxy, Tool Shed: sharing Galaxy tools, Galaxy Interactive Tours, Galaxy Interactive Environments, Visualizations: charts plugins, Galaxy Webhooks, Visualizations: generic plugins, BioBlend module, a Python library to use Galaxy API, Tool Dependencies and Conda, Tool Dependencies and Containers, Galaxy Code Architecture |
| Epigenetics | Biol | DNA Methylation |
| Introduction to Galaxy | Biol | Galaxy 101, From peaks to genes, Multisample Analysis, Options for using Galaxy, IGV Introduction, Getting data into Galaxy |
| Metagenomics | Biol | 16S Microbial Analysis with Mothur, Analyses of metagenomics data - The global picture |
| Proteomics | Biol | Protein FASTA Database Handling, Metaproteomics tutorial, Label-free versus Labelled - How to Choose Your Quantitation Method, Detection and quantitation of N-termini via N-TAILS, Peptide and Protein ID, Secretome Prediction, Peptide and Protein Quantification via Stable Isotope Labelling (SIL) |
| Sequence Analysis | Biol | Quality Control, Mapping, Genome Annotation, RAD-Seq Reference-based data analysis, RAD-Seq de-novo data analysis, RAD-Seq to construct genetic maps |
| Train the trainers | Inst | Creating a new tutorial - Writing content in markdown, Creating a new tutorial - Defining metadata, Creating a new tutorial - Setting up the infrastructure, Creating a new tutorial - Creating Interactive Galaxy Tours, Creating a new tutorial - Building a Docker flavor for a tutorial, Good practices to run a workshop |
| Transcriptomics | Biol | De novo transcriptome reconstruction with RNA-seq, Reference-based RNA-seq data analysis, Differential abundance testing of small RNAs |