Daily Updates

📚 Tutorials

• Creating community content

❓ Faqs

• How do I add a news feed to a Matrix channel?
• How do I find the Maintainer Home pages?
• How do I find the Community Home pages?
• How can I add my SIG meetings to the Galaxy Community Activities calendar?

📰 News

• GTN's Gift for 2024

📰 News

• 🖖🏾Galaxy SPOC Community: Year in Review

📅 Events

• Galaxy at SURF Research Cloud workshop
• Code & Collaborate: The FAIRytale of Software Development

📚 Tutorials

• Galaxy usage on SURF Research Cloud
• Pulsar usage on SURF Research Cloud

📰 News

• Organizing GTA2025: Give us feedback and your availability!

📚 Tutorials

• Data submission using ENA upload Tool
• Building the LORIS LLR6 PanCancer Model Using PyCaret

❓ Faqs

• Slow incremental builds
• What is an Architectural Decision Record (ADR)?
• GTN Architectural Decision Record Template
• GTN ADR: Why Jekyll and not another Static Site Generator (SSG)
• GTN ADR: Image Storage

🛠️ Workflows

• scRNA Plant Analysis
• Ludwig - Image recognition model - MNIST

📰 News

• SPOC CoFest 2024: How did it go?

❓ Faqs

• How do I add my community to the Galaxy CoDex?

🛠️ Workflows

• Seurat Filter, Plot and Exlore tutorial

🛤️ Learning pathways

• Tool development for a nice & shiny subdomain

📚 Tutorials

• Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy

❓ Faqs

• Syncing your Fork of the GTN
• Updating the default branch from master to main
• Forking the GTN repository

📚 Tutorials

• Make your tools available on your subdomain

📰 News

• Credit where it's due: GTN Reviewers in the spotlight

🖼️ Slides

• An earth-system RO-Crate

🧑‍🏫 Contributors

• @yuliiaorlova
• @Swathi266
• @mirelaminkova
• @GokceOGUZ
• @dometto
• @adairama
• @adya29

💰 Grants

• @nfdi4bioimage

🏢 Organisations

• @dfg

📰 News

• New Tutorial: Tracking of mitochondria and capturing mitoflashes

📚 Tutorials

• Updating tool versions in a tutorial

📚 Tutorials

• Create a subdomain for your community on UseGalaxy.eu

📅 Events

• 🖖🏾 SPOC II: the Write-a-Than

📚 Tutorials

• Tracking of mitochondria and capturing mitoflashes

🛠️ Workflows

• Capturing mitoflashes

❓ Faqs

• Add Toolshed category to a tool

📅 Events

• Galaxy at Congresso Brasileiro de Biologia Evolutiva

📚 Tutorials

• Running the GTN website online using GitHub CodeSpaces

📚 Tutorials

• Alternative Celery Deployment for Galaxy
• Single Cell Publication - Data Analysis
• Single Cell Publication - Data Plotting

❓ Faqs

• Supporting Tutorial Mode (GTN-in-Galaxy) in a tutorial

🧑‍🏫 Contributors

• @rmassei

🛤️ Learning pathways

• Applying single-cell RNA-seq analysis in Coding Environments

❓ Faqs

• Why isn't my history updating?
• Using answer key histories
• Request Galaxy tools on a specific server
• Importing data from Sierra LIMS
• How can I get my container requiring jobs to run in a container?

📚 Tutorials

• Train and Test a Deep learning image classifier with Galaxy-Ludwig

🛠️ Workflows

• Ludwig - Image recognition model - MNIST

🖼️ Slides

• Intro to DataPLANT ARCs

📚 Tutorials

• DataPLANT ARCs

❓ Faqs

• Is there a certification available for the FAIR-by-Design Methodology?
• Can the FAIR-by-Design Methodology be used for FAIR development of other types of resources?
• Can this tutorial be adapted to other instructional development platforms?

📅 Events

• Workshop on high-throughput sequencing data analysis with Galaxy
• An introduction to High Performance Computing

📅 Events

• Single-cell and sPatial Omics | Collaboration Fest
• 🖖🏾 SPOC Write-a-thon

📅 Events

• 2024 Bioinformatics Bootcamp - The Open University

❓ Faqs

• Can I use a public Galaxy for my private data?

🎥 Recordings

• Recording of ERGA post-assembly QC

🎥 Recordings

• Recording of Deep Learning (Part 3) - Convolutional neural networks (CNN)

📚 Tutorials

• Getting your hands-on earth data

❓ Faqs

• Open History files in Integrated Genome Browser (IGB)
• Input Histories & Answer Keys

❓ Faqs

• Annotating Pre-requisites
• Using the new Contributions Annotation framework

📚 Tutorials

• Predicting EI+ mass spectra with QCxMS

🖼️ Slides

• Predicting EI+ mass spectra with QCxMS

🛠️ Workflows

• End-to-end EI+ mass spectra prediction workflow using QCxMS

🧑‍🏫 Contributors

• @zargham-ahmad
• @wverastegui
• @thanhleviet
• @SabrinaZander
• @paige-kulzer
• @Martin-Kuhl
• @Freymaurer
• @felicitas215
• @Sch-Da
• @CMR248
• @Brilator

🏢 Organisations

• @moffitt

📚 Tutorials

• Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2

🎥 Recordings

• Recording of Single-cell Formats and Resources
• Recording of Quality Control

🛠️ Workflows

• Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run'

🎥 Recordings

• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

🎥 Recordings

• Recording of Clustering 3K PBMCs with Scanpy

🎥 Recordings

• Recording of Identification of AMR genes in an assembled bacterial genome

🎥 Recordings

• Recording of Decontamination of a genome assembly
• Recording of Assembly of the mitochondrial genome from PacBio HiFi reads
• Recording of Building an amplicon sequence variant (ASV) table from 16S data using DADA2

❓ Faqs

• Using tutorial mode and the Case Study suite

📚 Tutorials

• GO Enrichment Analysis on Single-Cell RNA-Seq Data

🖼️ Slides

• GO Enrichment Analysis on Single-Cell RNA-Seq Data

🛠️ Workflows

• GO Enrichment Workflow

📚 Tutorials

• Ecoregionalization workflow tutorial

🎥 Recordings

• Recording of Galaxy Basics for genomics

🛠️ Workflows

• Ecoregionalization workflow

📚 Tutorials

• Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub

🎥 Recordings

• Recording of Making clinical datasets FAIR
• Recording of REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data
• Recording of Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub
• Recording of Chloroplast genome assembly
• Recording of Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
• Recording of Data management in Medicinal Chemistry
• Recording of Generating a single cell matrix using Alevin
• Recording of Importing files from public atlases

❓ Faqs

• Why is my tool erroring as 'Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.'

🎥 Recordings

• Recording of Long non-coding RNAs (lncRNAs) annotation with FEELnc

🎥 Recordings

• Recording of Understanding Galaxy history system
• Recording of Mapping

🎥 Recordings

• Recording of Visualization of RNA-Seq results with Volcano Plot

📚 Tutorials

• Decontamination of a genome assembly

🎥 Recordings

• Recording of Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data

🛠️ Workflows

• Assembly-decontamination-VGP9

📚 Tutorials

• Assembly of the mitochondrial genome from PacBio HiFi reads

🛠️ Workflows

• Mitogenome-Assembly-VGP0

🎥 Recordings

• Recording of Bacterial Genome Annotation

🧑‍🏫 Contributors

• @MennaGamal
• @trungN
• @tcollins2011
• @sujaikumar
• @paulocilasjr
• @mschatz
• @mhintze
• @meltemktn
• @mateeullah905
• @igormakunin
• @hfraser
• @hannahkimincompbio
• @GarethPrice-Aus
• @emmaustin20
• @DinithiRajapaksha
• @bethanmanley

🎥 Recordings

• Recording of Binning of metagenomic sequencing data

🎥 Recordings

• Recording of Fine tune large protein model (ProtTrans) using HuggingFace
• Recording of Classification in Machine Learning

📚 Tutorials

• Genome annotation with Helixer

🛠️ Workflows

• annotation_helixer

📅 Events

• From zero to hero with Python

📚 Tutorials

• Marine Omics identifying biosynthetic gene clusters

🛠️ Workflows

• Marine Omics identifying biosynthetic gene clusters

🎥 Recordings

• Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

🛤️ Learning pathways

• Proteogenomics

🎥 Recordings

• Recording of Calculating α and β diversity from microbiome taxonomic data

🛠️ Workflows

• WF5_Data_Interpretation_Worklow
• WF4_Quantitation_Workflow
• WF3_VERIFICATION_WORKFLOW
• WF2_Discovery-Workflow
• WF1_Database_Generation_Workflow

📚 Tutorials

• Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs)
• Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons

🎥 Recordings

• Recording of Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)

🛠️ Workflows

• Calculating diversity from microbiome taxonomic data

📚 Tutorials

• Calculating α and β diversity from microbiome taxonomic data

🎥 Recordings

• Recording of Quality and contamination control in bacterial isolate using Illumina MiSeq Data

🧑‍🏫 Contributors

• @tbrown91
• @RZ9082
• @natalie-wa
• @lybCNU
• @hujambo-dunia
• @dianichj
• @ahmedhamidawan

🏢 Organisations

• @mwk

🖼️ Slides

• Single-cell Formats and Resources

📰 News

• Galaxy Administrator Time Burden and Technology Usage

📰 News

• Simplifying GTN contribution with Google Forms

📅 Events

• BioNT Community Event & CarpentryConnect - Heidelberg 2024

📚 Tutorials

• Quality and contamination control in bacterial isolate using Illumina MiSeq Data

🛠️ Workflows

• Quality and contamination control in bacterial isolate using Illumina MiSeq Data

📰 News

• New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2

📅 Events

• EuroBioC2024 Carpentries workshops

📰 News

• Registration Open for BioNT Community Event & CarpentryConnect Heidelberg

📚 Tutorials

• Single-cell ATAC-seq standard processing with SnapATAC2

🛠️ Workflows

• Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2

📅 Events

• Workshop on high-throughput sequencing data analysis with Galaxy

🖼️ Slides

• Galaxy Administrator Time Burden and Technology Usage

📰 News

• So many new features! GTN 2023-2024 Updates

📅 Events

• Bioconductor Carpentries workshop: Analysis and Interpretation of Bulk RNA-Seq Data

📰 News

• 4th Mycobacterium tuberculosis complex NGS made easy

📅 Events

• Bioconductor North American conference (BioC2024)

📚 Tutorials

• Creating a Special Interest Group
• What's a Special Interest Group?

❓ Faqs

• How can I plan meetings across timezones?
• What is the Galaxy Governance Structure?
• How do I join the Galaxy Community Board?
• What's the Galaxy Community Board?

❓ Faqs

• Finding a material's PURL or Short URL

📅 Events

• A practical introduction to bioinformatics and RNA-seq using Galaxy

❓ Faqs

• Translations within the GTN

❓ Faqs

• Top level history controls
• History tagging
• Switching to an existing history
• History options
• Datasets versus collections
• Dataset snippet
• Dataset colors
• History annotation
• How to un-hide datasets?
• How to un-delete datasets?
• Manipulating multiple history datasets
• How to delete datasets?

🧑‍🏫 Contributors

• @CRHAD26
• @agCleo
• @achim-kit
• @CarolinLeister
• @isouyioul
• @domlgreen
• @korvoj
• @amisev1971
• @sonjafiliposka
• @StellaEggels
• @Rassine
• @Najatamk
• @Nilchia

💰 Grants

• @skills4eosc
• @nfdi4plants

🏢 Organisations

• @madland

❓ Faqs

• Creating a GTN FAQ

🎥 Recordings

• Recording of Clinical Metaproteomics 5: Data Interpretation
• Recording of Clinical Metaproteomics 3: Verification
• Recording of Clinical Metaproteomics 4: Quantitation
• Recording of Clinical Metaproteiomics 1: Database-Generation
• Recording of Clinical Metaproteomics 2: Discovery

📚 Tutorials

• Fine tune large protein model (ProtTrans) using HuggingFace

📰 News

• GTN Video Library 2.0: 107 hours of learning across 154 videos

❓ Faqs

• Recording a video tutorial
• Adding your recording to a tutorial or slide deck

📰 News

• From GTN Intern to Tutorial Author to Bioinformatician
• Phylogenetics tutorial takes researchers back to basics!

📰 News

• Open Call for Trainers for the Galaxy Training Academy

📅 Events

• Galaxy Training Academy 2024

🎥 Recordings

• Recording of M. tuberculosis Variant Analysis

🛠️ Workflows

• BY-COVID: Data Download

📰 News

• Celebrating the Milestone: 400 Tutorials on the Galaxy Training Network!
• New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2

📚 Tutorials

• Building an amplicon sequence variant (ASV) table from 16S data using DADA2

🛠️ Workflows

• Building an amplicon sequence variant (ASV) table from 16S data using DADA2

📰 News

• Standards compliant™ training news via RSS/Atom
• Integrating the Galaxy Training Network into the Tool Form

📅 Events

• FAIR data management in single-cell analysis

📰 News

• All GTN training data are now automatically mirrored via Onedata

📅 Events

• Mycobacterium tuberculosis complex NGS made easy

🧑‍🏫 Contributors

• @shwdey
• @matuskalas
• @linzyelton
• @lilianarutaihwa
• @bethlehem-adnew
• @arashghodousi
• @andrea-spitaleri
• @andreacabibbe
• @Allen13x

💰 Grants

• @edctp-eu

🛠️ Workflows

• Taxonomy Profiling and Visualization with Krona
• Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
• Allele-based Pathogen Identification

📅 Events

• Mycobacterium tuberculosis complex NGS made easy
• 2023 Galaxy Admin Training (Ghent)
• Admin Training @ GCC 2022: Online Training Day

❓ Faqs

• Creating a GTN Event

📰 News

• Introducing GTN Event Pages

🛠️ Workflows

• ml_regression

📰 News

• Open Galaxy Position at Galaxy Europe Team, University of Freiburg

📰 News

• Perfectly FAIR Training!

❓ Faqs

• Using Answer Key Histories

📚 Tutorials

• Phylogenetics - Back to basics

🖼️ Slides

• Phylogenetics - Back to Basics - Introduction
• Phylogenetics - Back to Basics - Multiple Sequence Alignment
• Phylogenetics - Back to Basics - Phylogenetic Networks
• Phylogenetics - Back to Basics - Building Trees
• Phylogenetics - Back to Basics - Terminology
• Phylogenetics - Back to Basics - Estimating trees from alignments

🛠️ Workflows

• Tree Building (imported from uploaded file)

🧑‍🏫 Contributors

• @yvesvdb
• @timonschlegel
• @sebastian-schaaf
• @s3by01
• @rwinand
• @prodromus
• @MariaTsayo
• @ksuderman
• @LonsBio
• @FilipposZ
• @ennovytje
• @angiolini
• @andrewr
• @awspolly

📰 News

• Open Galaxy Positions at Melbourne Bioinformatics

❓ Faqs

• Ensuring Workflows meet Best Practices

📚 Tutorials

• Screening assembled genomes for contamination using NCBI FCS

🛠️ Workflows

• NCBI Foreign Contamination Screen

📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat

🧑‍🏫 Contributors

• @nsjuty
• @clsiguret
• @B0r1sD

📰 News

• Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy

📚 Tutorials

• Pathway analysis with the MINERVA Platform

🛠️ Workflows

• mRNA-Seq BY-COVID Pipeline: Counts
• mRNA-Seq BY-COVID Pipeline: Analysis

📚 Tutorials

• FAIRification of an RNAseq dataset

📰 News

• New Learning Pathway for FAIR Data Management developed by ELIXIR-UK Data Stewardship Fellows and Experts

🛤️ Learning pathways

• FAIR Data Management

📚 Tutorials

• Persistent Identifiers
• FAIR and its Origins
• Access
• Data Registration
• Metadata

🛠️ Workflows

• Ocean's variables 2.0

📚 Tutorials

• Analyse Argo data

🛠️ Workflows

• Analyse Argo data

❓ Faqs

• View histories side-by-side
• View a list of all histories
• How to enable the Activity Bar

❓ Faqs

• Enhancing tabular dataset previews in reports/pages
• Making an element collapsible in a report

📰 News

• Cool URLs Don't Change, GTN URLs don't either.

📚 Tutorials

• QIIME 2 Moving Pictures

📚 Tutorials

• Creation of an interactive Galaxy tools table for your community

🛤️ Learning pathways

• Applying single-cell RNA-seq analysis
• Building training material in Galaxy

📚 Tutorials

• Adding and updating best practice metadata for Galaxy tools using the bio.tools registry

🛠️ Workflows

• ATAC-seq GTM

📰 News

• Lost in a topic? Try a Learning Pathway!

📚 Tutorials

• Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities
• Checking expected species and contamination in bacterial isolate

🛠️ Workflows

• Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available)
• Checking expected species and contamination in bacterial isolate

🧑‍🏫 Contributors

• @tvedtees
• @sitjart
• @saskia-lawson-tovey
• @SaimMomin12
• @proccaserra
• @Mehgan-E
• @lcooper
• @khens
• @kellsnow

📰 News

• GTN ❤️ GMOD

🛠️ Workflows

• Gene Cluster Product Similarity Search

📚 Tutorials

• Converting between common single cell data formats

🛠️ Workflows

• AnnData to SingleCellExperiment (SCE) conversion
• AnnData to Seurat conversion
• AnnData to Cell Data Set (CDS) conversion

🛤️ Learning pathways

• Clinical metaproteomics workflows within Galaxy

📚 Tutorials

• QIIME 2 Cancer Microbiome Intervention

📚 Tutorials

• Clinical Metaproteomics 5: Data Interpretation
• Clinical Metaproteomics 3: Verification
• Clinical Metaproteomics 4: Quantitation
• Clinical Metaproteiomics 1: Database-Generation
• Clinical Metaproteomics 2: Discovery

📚 Tutorials

• Creating high resolution images of Galaxy Workflows

📚 Tutorials

• Bacterial Genome Annotation

🛠️ Workflows

• Bacterial Genome Annotation

🧑‍🏫 Contributors

• @ThibaudGlinez
• @supernord
• @qchiujunhao
• @PatCapon39
• @asmasonomics

📰 News

• 🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket!

📰 News

• GTN in Discourse

📰 News

• Simplified GTN News submission via Google Form

📚 Tutorials

• Sentinel 5P data visualisation

🎥 Recordings

• Recording of Finding the muon stopping site with pymuon-suite in Galaxy

🛠️ Workflows

• Sentinel5 volcanic data

📚 Tutorials

• From NDVI data with OpenEO to time series visualisation with Holoviews

🛠️ Workflows

• NDVI with OpenEO
• NDVI with OpenEO

🛤️ Learning pathways

• Detection of AMR genes in bacterial genomes

📚 Tutorials

• Identification of AMR genes in an assembled bacterial genome

🛠️ Workflows

• mrsa AMR gene detection

📚 Tutorials

• Finding the muon stopping site with pymuon-suite in Galaxy
• Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS

🛠️ Workflows

• Finding the Muon Stopping Site: pymuon-suite in Galaxy

❓ Faqs

• Using data source tools with Pulsar

📰 News

• FAIR Data management in single cell analysis

📚 Tutorials

• Clean and manage Sanger sequences from raw files to aligned consensus
• Data management in Medicinal Chemistry

🛠️ Workflows

• Training Sanger sequences CHD8
• Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST
• Data management in Medicinal Chemistry workflow

🧑‍🏫 Contributors

• @PaulineSGN
• @martinwolst

🏢 Organisations

• @abromics

📰 News

• Galaxy Single-cell Community: Year in Review

📰 News

• GTN Helper Bots Connect the Galaxy

❓ Faqs

• Importing and Launching a WorkflowHub.eu Workflow
• Importing and Launching a Dockstore Workflow
• What is my.galaxy.training

📰 News

• User story: Where Galaxy meets medicinal chemistry

🛠️ Workflows

• EBI SCXA to AnnData (Scanpy) or Seurat Object

📚 Tutorials

• Converting NCBI Data to the AnnData Format

🛠️ Workflows

• NCBI to Anndata

📰 News

• Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows

🛠️ Workflows

• Intro_To_CNN_v1.0.11.0

📚 Tutorials

• Generating a single cell matrix using Alevin and combining datasets (bash + R)
• Inferring single cell trajectories with Scanpy

🛠️ Workflows

• Inferring Trajectories with Scanpy Tutorial Workflow

📚 Tutorials

• Binning of metagenomic sequencing data

🛠️ Workflows

• Clustering 3k PBMC with Scanpy

🧑‍🏫 Contributors

• @sanjaysrikakulam
• @PapXis
• @mbaardwijk
• @MattiHoch
• @mjostaszewski
• @burkemlou

📚 Tutorials

• Ocean's variables study

❓ Faqs

• How can I do analysis X? - Getting help

📚 Tutorials

• Ocean Data View (ODV)

❓ Faqs

• Import workflows from DockStore
• Upload datasets from GenomeArk
• Upload fasta datasets via links

📰 News

• GTN has left Twitter/X as of October
• Feedback: Easy slide recordings

📰 News

• Update: Workflow List now searches WorkflowHub.eu, advanced query syntax

🖼️ Slides

• Friends Don't Let Friends Make Bad Graphs

📚 Tutorials

• Importing files from public atlases

📚 Tutorials

• Ploting a Microbial Genome with Circos

🛠️ Workflows

• Circos for E. Coli

📚 Tutorials

• Course Builder

❓ Faqs

• Preparing materials for asynchronous learning: Tips
• Preparing materials for asynchronous learning: Self-Study
• Preparing materials for asynchronous learning: FAQs
• Preparing materials for asynchronous learning: CYOA

📚 Tutorials

• Sequence data submission to ENA

❓ Faqs

• Updating from 22.01 to 23.0 with Ansible

🧑‍🏫 Contributors

• @edmontosaurus
• @cxli233

📚 Tutorials

• Making clinical datasets FAIR

❓ Faqs

• What is a Learning Pathway?

🛠️ Workflows

• Infinium Human Methylation BeadChip

❓ Faqs

• Notebook-based tutorials can give different outputs

🛠️ Workflows

• Intro_To_RNN_v1_0_10_0
• Intro_To_FNN_v1_0_10_0

📰 News

• Single cell subdomain re-launch: Unified and feedback-driven

📚 Tutorials

• QGIS Web Feature Services

❓ Faqs

• How can I talk with other users?
• Use our Single Cell Omics Lab

📰 News

• New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets

🛤️ Learning pathways

• Introduction to Galaxy and Single Cell RNA Sequence analysis

📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat (R)

🧑‍🏫 Contributors

• @tuncK
• @kysrpex

💰 Grants

• @fairease
• @eurosciencegateway
• @elixir-uk-dash

❓ Faqs

• What licenses are used in the GTN?

❓ Faqs

• Debugging Memory Leaks

🛤️ Learning pathways

• Introductory SQL
• Introductory Python

📚 Tutorials

• FAIR Bioimage Metadata
• REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data

📚 Tutorials

• One protein along the UniProt page

🖼️ Slides

• Automated Cell Annotation

🧑‍🏫 Contributors

• @tb143
• @sonalhenson
• @smza
• @lisanna

💰 Grants

• @biont

📚 Tutorials

• Filter, plot and explore single-cell RNA-seq data with Scanpy (Python)

🧑‍🏫 Contributors

• @Laura190
• @kostrykin
• @katherine-d21

📰 News

• New Feature: GTN User Preferences

📚 Tutorials

• Scanpy Parameter Iterator

🛠️ Workflows

• Scanpy Parameter Iterator workflow full (imported from URL)

🛤️ Learning pathways

• Discovering Galaxy through climate analysis

🖼️ Slides

• Identification of non-canonical ORFs and their potential biological function

📚 Tutorials

• SARS-CoV-2 Viral Sample Alignment and Variant Visualization

❓ Faqs

• Quality Scores

🧑‍🏫 Contributors

• @SNG888

💰 Grants

• @ai4life

📰 News

• AI4Life teams up with GTN to enhance training resources

🛤️ Learning pathways

• Genome annotation for prokaryotes
• Genome annotation for eukaryotes
• Metagenomics data processing and analysis for microbiome
• From R to Machine Learning; an introductory course

📚 Tutorials

• ERGA post-assembly QC

🛠️ Workflows

• Post-assembly workflow

📰 News

• ELIXIR-UK Fellow Launches New FAIR Data Management Training

❓ Faqs

• Do the pipelines work with both isolates and direct from raw meat? or only isolate?
• Can we also use this workflow on Illumina raw reads?
• Can we use snippy pipeline instead for the phylogenetic analysis?
• Isn't it awkward to find so many humans sequences there, since we filter for them before?
• Is there a way to filter on the Kalimari database?
• From where can I import other genomes?
• For preprocessing part with host removal: Where do you find the abbreviations for each host species available (e.g. bos is cow, homo is human..)?
• What does `^.*Gallus|Homo|Bos.*$` mean?
• After sequencing with MinKNOW software, we get many fastq files, do these files need to be combined into one file before uploading or is it possible to upload them all at once?

📚 Tutorials

• Data visualisation Olympics - Visualization in R
• Data Manipulation Olympics - SQL
• Data Manipulation Olympics - JQ

❓ Faqs

• Converting the datatype of a collection
• Changing the datatype of a collection

🛠️ Workflows

• Filter, Plot and Explore Single-cell RNA-seq Data updated

📚 Tutorials

• Train-the-Trainer: putting it all together

📰 News

• New Feature: Pan-Galactic Tool Search

❓ Faqs

• Why host your materials with the GTN?

📰 News

• GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis

🧑‍🏫 Contributors

• @TanguyGen
• @robertmeller
• @nakucher
• @katherinecox
• @jtleek
• @hexhowells
• @ehumph
• @dechendb
• @cutsort
• @cansavvy
• @avahoffman

💰 Grants

• @nhgri-gdscn
• @nhgri-anvil
• @elixir-fair-data

📚 Tutorials

• FAIR Galaxy Training Material
• FAIR data management solutions
• FAIR in a nutshell

📚 Tutorials

• RO-Crate - Introduction

🎥 Recordings

• Recording of Understanding Galaxy history system
• Recording of Quality Control
• Recording of Pre-processing of 10X Single-Cell RNA Datasets
• Recording of 16S Microbial Analysis with mothur (short)

🛠️ Workflows

• Preprocessing of 10X scRNA-seq data

🖼️ Slides

• Contribute to the BioImage.IO models

🎥 Recordings

• Recording of Creating Galaxy tools from Conda Through Deployment
• Recording of Introduction to Genomics and Galaxy

🛤️ Learning pathways

• Train the Trainers

📚 Tutorials

• Genome-wide alternative splicing analysis

🎥 Recordings

• Recording of Metatranscriptomics analysis using microbiome RNA-seq data (short)
• Recording of Metatranscriptomics analysis using microbiome RNA-seq data

🛠️ Workflows

• GTN_differential_isoform_expression

🎥 Recordings

• Recording of Large genome assembly and polishing
• Recording of Taxonomic Profiling and Visualization of Metagenomic Data

🛠️ Workflows

• Trajectory analysis using Monocle3 - full tutorial workflow

📰 News

• New Galaxy training: Genome-wide alternative splicing analysis

📚 Tutorials

• RNA-seq Alignment with STAR
• Pox virus genome analysis from tiled-amplicon sequencing data

🎥 Recordings

• Recording of Reference-based RNA-Seq data analysis

🛠️ Workflows

• pox-virus-tiled-amplicon-ref-masking

🎥 Recordings

• Recording of Genome annotation with Funannotate
• Recording of Trio Analysis using Synthetic Datasets from RD-Connect GPAP

📰 News

• BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More

📚 Tutorials

• Submitting workflows to LifeMonitor
• Workflow Run RO-Crate Introduction
• RO-Crate in Python
• Best practices for workflows in GitHub repositories
• Exporting Workflow Run RO-Crates from Galaxy

🖼️ Slides

• Welcome to the BioImage Model Zoo

❓ Faqs

• Galaxy UI is slow
• Tool missing from Galaxy
• Debugging tool memory errors
• Debugging tool errors
• Blank page or no CSS/JavaScript
• Database Issues

🛠️ Workflows

• sort-and-change-case (imported from uploaded file)

🎥 Recordings

• Recording of Masking repeats with RepeatMasker
• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data
• Recording of Identification of the micro-organisms in a beer using Nanopore sequencing

🎥 Recordings

• Recording of Using dataset collections
• Recording of Combining single cell datasets after pre-processing

📚 Tutorials

• Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms)

🛠️ Workflows

• GC MS using XCMS

🛤️ Learning pathways

• Introduction to Galaxy and Ecological data analysis

📚 Tutorials

• Taxonomic Profiling and Visualization of Metagenomic Data

❓ Faqs

• Kraken2 and the k-mer approach for taxonomy classification

🛠️ Workflows

• Taxonomic Profiling and Visualization of Metagenomic Data

🎥 Recordings

• Recording of Assembly of metagenomic sequencing data

🎥 Recordings

• Recording of Galaxy Basics for everyone
• Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

🧑‍🏫 Contributors

• @npechl

💰 Grants

• @h2020-defend
• @fnso2019

📚 Tutorials

• Supervised Learning with Hyperdimensional Computing

❓ Faqs

• Pick the right Concatenate tool

📚 Tutorials

• Pre-processing of 10X Single-Cell ATAC-seq Datasets

🛠️ Workflows

• scATAC-seq FASTQ to Count Matrix
• scATAC-seq Count Matrix Filtering

📰 News

• New Feature: my.galaxy.training

📰 News

• New Feature: Click-to-run Workflows
• New Feature: GTN Rdoc
• New Feature: Persistent URLs (PURLs) / Shortlinks

📚 Tutorials

• Monitoring Galaxy and Pulsar with Sentry

🖼️ Slides

• BioImage Model Zoo: Advanced models in one-click

📚 Tutorials

• Customizing the look of Galaxy (Manual)
• Deploying a Beacon v1 in Galaxy
• Customizing the look of Galaxy
• Setting up Celery Workers for Galaxy
• Server Maintenance: Cleanup, Backup, and Restoration

❓ Faqs

• Mapping Jobs to Specific Storage By User
• Failing all jobs from a specific user
• Library Permission Issues
• Time to git commit
• Using Git With Ansible Vaults
• Opening a split screen in byobu
• How do I see what variables are set for a host?

🎥 Recordings

• Recording of RO-Crate - Introduction

📰 News

• New Feature: Learning Pathways!

🛤️ Learning pathways

• Introduction to Galaxy and Sequence analysis
• Admin Training Course

📚 Tutorials

• Sentinel 2 biodiversity

❓ Faqs

• Defining a Learning Pathway

🛠️ Workflows

• Sentinel 2 example

📚 Tutorials

• Inferring single cell trajectories with Monocle3 (R)

📚 Tutorials

• Obis marine indicators

🎥 Recordings

• Recording of Inferring single cell trajectories with Monocle3

🛠️ Workflows

• Marine Omics visualisation

🧑‍🏫 Contributors

• @stain
• @sophia120199
• @simleo
• @ptsefton
• @pauldg
• @kikkomep
• @kinow
• @ilveroluca
• @ElectronicBlueberry

💰 Grants

• @eosc-life
• @by-covid

📰 News

• New Feature: Trainer Directory! (Add yourself today!)

📚 Tutorials

• Production d'indicateurs champs de bloc

❓ Faqs

• Créer un nouvel history
• Importer via un lien
• Changer le type de données

📚 Tutorials

• Reference Data with Data Managers

📚 Tutorials

• Large genome assembly and polishing

❓ Faqs

• Import workflows from WorkflowHub
• Importing and launching a GTN workflow

🛠️ Workflows

• kmer counting - meryl - upgraded
• Trim and filter reads - fastp - upgraded
• Racon polish with long reads, x4 - upgraded
• Racon polish with Illumina reads (R1 only), x2 - upgraded
• Data QC - upgraded
• Combined workflows for large genome assembly - upgraded
• Assess genome quality - upgraded
• Assembly with Flye - upgraded
• Assembly polishing - upgraded

🧑‍🏫 Contributors

• @rlibouba
• @maximskorik
• @GitFab93
• @cfusterbarcelo
• @andrewsnelgrove

💰 Grants

• @CINECA-Project

🛠️ Workflows

• Gene-based Pathogen Identification

📚 Tutorials

• End-to-End Tissue Microarray Image Analysis with Galaxy-ME

🛠️ Workflows

• GTN_Exemplar_002_TMA_workflow

📰 News

• What are the most used tools in the GTN?

❓ Faqs

• Compatible Versions of Galaxy

📰 News

• GTN Celebrates Black History Month

🧑‍🏫 Contributors

• @vladvisan
• @paulzierep
• @alliecreason

📰 News

• New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

📚 Tutorials

• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition

🛠️ Workflows

• Nanopore Preprocessing

📚 Tutorials

• Removing the effects of the cell cycle

🛠️ Workflows

• Cell Cycle Regression Workflow

📰 News

• New Feature: Prometheus Metrics endpoint

📰 News

• New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic

📚 Tutorials

• Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution
• Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution
• Comparing inferred cell compositions using MuSiC deconvolution

🛠️ Workflows

• MuSiC-Deconvolution: Compare
• MuSiC-Deconvolution: Data generation | bulk | ESet
• MuSiC-Deconvolution: Data generation | sc | metadata
• MuSiC-Deconvolution: Data generation | sc | matrix + ESet

🛠️ Workflows

• gpu_jupytool

📚 Tutorials

• NCBI BLAST+ against the MAdLand

📰 News

• New GTN paper: "Galaxy Training: A powerful framework for teaching!"

📚 Tutorials

• Champs blocs indicators

🛠️ Workflows

• Champs blocs indicators

🛠️ Workflows

• workflow-generate-dataset-for-assembly-tutorial

🧑‍🏫 Contributors

• @mcharleston
• @GabrielaLopez
• @Camila-goclowski
• @adamtaranto

💰 Grants

• @elixir-converge

📚 Tutorials

• Assembly of metagenomic sequencing data

🛠️ Workflows

• Metagenomics assembly tutorial workflow

🧑‍🏫 Contributors

• @miRlyKayleigh
• @deeptivarshney

📰 News

• New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation!

📚 Tutorials

• Avian influenza viral strain analysis from gene segment sequencing data

📰 News

• New Topic: Single Cell Analysis!

❓ Faqs

• How do I know what protocol my data was sequenced with?

📚 Tutorials

• Python - Coding Style

❓ Faqs

• Creating a GTN News post

🧑‍🏫 Contributors

• @patrick-austin
• @leandro-liborio
• @joelvdavies
• @elichad
• @anish-mudaraddi

📚 Tutorials

• Visualize EBV cube data with Panoply netCDF viewer
• Cleaning GBIF data for the use in Ecology

🛠️ Workflows

• GBIF data Quality check and filtering workflow Feb-2020

📚 Tutorials

• Visualization of Climate Data using NetCDF xarray Map Plotting

❓ Faqs

• Importing data from remote files

🛠️ Workflows

• Xarray_Map_Plotting_Workflow

📚 Tutorials

• Preparing genomic data for phylogeny reconstruction

❓ Faqs

• How to set Data Privacy Features?

🛠️ Workflows

• preparing genomic data for phylogeny recostruction (GTN)

📚 Tutorials

• Python - Multiprocessing
• Python - Testing
• Virtual Environments For Software Development
• Python - Type annotations
• Conda Environments For Software Development
• Teaching Python

❓ Faqs

• Multipile similar tools available
• How to update account preferences?
• Can I create multiple Galaxy accounts?

❓ Faqs

• Beware of Cuts

📚 Tutorials

• Somatic Variant Discovery from WES Data Using Control-FREEC

🛠️ Workflows

• Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC

🧑‍🏫 Contributors

• @MarisaJL
• @d-salgado

📚 Tutorials

• Inferring single cell trajectories with Monocle3

🖼️ Slides

• Trajectory analysis

🛠️ Workflows

• Monocle3 workflow
• AnnData object to Monocle input files

📚 Tutorials

• Identification of the micro-organisms in a beer using Nanopore sequencing

❓ Faqs

• What is Taxonomy?
• FASTQ format

🛠️ Workflows

• Identification of the micro-organisms in a beer using Nanopore sequencing

📚 Tutorials

• Evaluating and ranking a set of pathways based on multiple metrics

🎥 Recordings

• Recording of Evaluating and ranking a set of pathways based on multiple metrics

🛠️ Workflows

• Pathway Analysis

📚 Tutorials

• Long non-coding RNAs (lncRNAs) annotation with FEELnc
• Design and plan session, course, materials
• Principles of learning and how they apply to training and teaching
• Motivation and Demotivation
• Training techniques to enhance learner participation and engagement
• Assessment and feedback in training and teachings
• Teaching experiences

🖼️ Slides

• Overview of the Galaxy Training Material for Instructors

❓ Faqs

• GTN Stats

🛠️ Workflows

• Long non-coding RNAs (lncRNAs) annotation with FEELnc

❓ Faqs

• Adding workflow tests with Planemo

📚 Tutorials

• Deploying Tailscale/Headscale for private mesh networking
• Deploying Wireguard for private mesh networking

❓ Faqs

• How does the GTN ensure accessibility?

📰 News

• New Tutorial: Data Manipulation

📚 Tutorials

• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin
• Combining single cell datasets after pre-processing
• Comparative gene analysis in unannotated genomes

❓ Faqs

• Why is Alevin is not working?

🛠️ Workflows

• Comparative gene analysis

❓ Faqs

• Contributing a Jupyter Notebook to the GTN

🧑‍🏫 Contributors

• @teresa-m
• @ppalagi
• @khaled196
• @hrukkudyr
• @allegravia

💰 Grants

• @epsrc-training-grant

🏢 Organisations

• @elixir-goblet-ttt

📚 Tutorials

• Genome Assembly Quality Control

🖼️ Slides

• Genome assembly quality control.

🛠️ Workflows

• Genome Assembly Quality Control

📚 Tutorials

• Refining Genome Annotations with Apollo (eukaryotes)

🧑‍🏫 Contributors

• @paulineauffret
• @chklopp

❓ Faqs

• Galaxy Admin Training Path

📚 Tutorials

• Functional annotation of protein sequences
• Data Manipulation Olympics

❓ Faqs

• Regular Expressions 101

🛠️ Workflows

• Functional annotation
• GTN Tutorial: Data manipulation Olympics - all steps and exercises

🖼️ Slides

• Galaxy and Celery

📚 Tutorials

• Writing Automated Tests for Galaxy

📚 Tutorials

• Variant Calling Workflow

📚 Tutorials

• How I learned to stop worrying and love the systemd
• Version Control with Git

🎥 Recordings

• Recording of Using Workflow Parameters
• Recording of Workflow Reports

❓ Faqs

• Flatten a list of list of paired datasets into a list of paired datasets

🧑‍🏫 Contributors

• @mira-miracoli
• @CameronFRWatson

📚 Tutorials

• Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools
• Scripting Galaxy using the API and BioBlend

🎥 Recordings

• Recording of Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools

🛠️ Workflows

• RetroSynthesis

📚 Tutorials

• Basics of using Git from the Command Line

❓ Faqs

• How many mules?
• Customising the welcome page
• Is YAML sensitive to True/true/False/false
• How do I know what I can do with a role? What variables are available?
• What is the difference between the roles with `role:` prefix and without?
• Error: "skipping: no hosts matched"
• What if you forget `--diff`?
• Define once, reference many times
• Variable connection

📰 News

• New Tutorial: Workflow Reports

📚 Tutorials

• Workflow Reports
• GTN Metadata

🛠️ Workflows

• GTN Training: Workflow Reports
• GTN Training: Workflow Reports - Galaxy 101 For Everyone

🧑‍🏫 Contributors

• @wee-snufkin
• @Quickbeasts51429

📰 News

• GTN Metadata Schemas

📚 Tutorials

• Adding Quizzes to your Tutorial
• Trio Analysis using Synthetic Datasets from RD-Connect GPAP

🛠️ Workflows

• Trio Analysis Tutorial

📚 Tutorials

• Designing plasmids encoding predicted pathways by using the BASIC assembly method

🛠️ Workflows

• Genetic Design (BASIC Assembly)

🎥 Recordings

• Recording of Designing plasmids encoding predicted pathways by using the BASIC assembly method

❓ Faqs

• Quotas for datasets and histories
• Working with deleted datasets

🧑‍🏫 Contributors

• @Sofokli5
• @chensy96
• @brigidagallone

📚 Tutorials

• Python - Introductory Graduation
• Python - Subprocess
• Python - Basic Types & Type Conversion
• Python - Flow Control
• Python - Loops
• Python - Math
• Python - Globbing
• Python - Files & CSV
• Python - Functions
• Python - Argparse
• Python - Try & Except
• Python - Lists & Strings & Dictionaries

🛠️ Workflows

• QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN

❓ Faqs

• Tool doesn't recognize input datasets
• Understanding 'canceled by admin' or cluster failure error messages

❓ Faqs

• Understanding ValueError error messages
• Understanding walltime error messages
• Understanding 'exceeds memory allocation' error messages
• Understanding input error messages
• Mismatched Chromosome identifiers and how to avoid them
• Ways to use Galaxy
• Working with very large fastq datasets
• Working with very large fasta datasets
• Understanding Datatypes
• Working with GFF GFT GTF2 GFF3 reference annotation
• Finding BAM dataset identifiers
• Troubleshooting Custom Genome fasta

❓ Faqs

• Sorting Reference Genome
• How to hide datasets?

❓ Faqs

• Where is the tool help?

❓ Faqs

• How to use Custom Reference Genomes?
• Directly obtaining UCSC sourced *genome* identifiers

❓ Faqs

• How do I create an account on a public Galaxy instance?
• Finding and working with "Histories shared with me"
• Best practices for loading fastq data into Galaxy

❓ Faqs

• Purging datasets
• Extended Help for Differential Expression Analysis Tools
• NCBI SRA sourced fastq data
• How do `fastq.gz` datasets relate to the `.fastqsanger` datatype metadata assignment?
• Data retrieval with “NCBI SRA Tools” (fastq-dump)
• Using compressed fastq data as tool inputs
• Does your account usage quota seem incorrect?
• How to find and correct tool errors related to Metadata?

❓ Faqs

• How to format fastq data for tools that require .fastqsanger format?
• Identifying and formatting Tabular Datasets
• Incomplete Dataset Download
• How can I reduce quota usage while still retaining prior work (data, tools, methods)?
• Sorting Tools
• How can I upload data using EBI-SRA?
• How can I load data?
• Datasets not downloading at all
• Downloading datasets using command line
• Unsharing unwanted histories

📰 News

• New Tutorial Feature: Choose Your Own Tutorial

❓ Faqs

• Find all Histories and purge (aka permanently delete)

📚 Tutorials

• A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy
• Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data

❓ Faqs

• Reporting usage problems, security issues, and bugs
• Transfer entire histories from one Galaxy server to another
• Moving datasets between Galaxy servers
• Finding Datasets

❓ Faqs

• Forgot Password

❓ Faqs

• Changing acount email or password

❓ Faqs

• Different dataset icons and their usage

❓ Faqs

• Finding Histories
• Downloading histories
• Downloading datasets

🧑‍🏫 Contributors

• @samanthaanjei
• @Nurzhamalyrys
• @JasperO98
• @beachyesh
• @AnomalyCodes

❓ Faqs

• Understanding job statuses
• Will my jobs keep running?

❓ Faqs

• TB Variant Report crashes (with an error about KeyError: 'protein')

📚 Tutorials

• Tree thinking for tuberculosis evolution and epidemiology
• Identifying tuberculosis transmission links: from SNPs to transmission clusters

🛠️ Workflows

• Mtb phylogeny
• From VCFs to SNP distance matrix
• From Fastqs to VCFs and BAMs
• From BAMs to drug resistance prediction with TB-profiler

📰 News

• New Tutorial: VGP assembly pipeline

🎥 Recordings

• Recording of Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

❓ Faqs

• Using IGV with Galaxy

🎥 Recordings

• Recording of Creating Galaxy tools from Conda Through Deployment
• Recording of Performant Uploads with TUS

🎥 Recordings

• Recording of Introduction to CRISPR screen analysis
• Recording of CRISPR screen analysis

🖼️ Slides

• Introduction to CRISPR screen analysis

🛠️ Workflows

• Analysis using MDAnalysis

🎥 Recordings

• Recording of Genome annotation with Funannotate
• Recording of Masking repeats with RepeatMasker
• Recording of Pangeo Notebook in Galaxy - Introduction to Xarray
• Recording of Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
• Recording of Biodiversity data exploration
• Recording of Metabarcoding/eDNA through Obitools
• Recording of Compute and analyze biodiversity metrics with PAMPA toolsuite

❓ Faqs

• Why do we have a variant mapping file when it is not being used in the workflow?
• How many search engines can you use in SearchGUI?
• What kind of variants are seen in the output?
• The workflows contain several Query tabular for text manipulation, is there a tutorial for that?
• Can I use these workflows on datasets generated from our laboratory?
• Example histories for the proteogenomics tutorials
• In the MVP platform, is it possible to view the genomic location of all the peptides?
• Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference?
• Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools?

📚 Tutorials

• Galaxy Interactive Tools

❓ Faqs

• Downloading the files from the NCBI server fails or takes too long.
• The UMAP Plots errors out sometimes?
• UCSC import: what should my file look like?
• Viewing tool logs (`stdout` and `stderr`)
• Organizing the tool panel
• Do I have to run the tools in the order of the tutorial?
• Does MaxQuant in Galaxy support TMT, iTRAQ, etc.?
• Is it possible to subsample some samples if you have more reads?
• MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups?
• What is a SNP?
• How many proteins can be identified and quantified in shotgun proteomics?
• My snippy is running for a very long time. Is this normal?
• Additional resources to learn more about proteomic data analysis
• Are Barcodes always on R1 and Sequence data on R2?
• Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results?
• For the “quantitation method” what is the default if I just leave it as “None”? Label free?
• Can we polish the assembly with long reads too?
• Running more than one round of Pilon polishing
• When I get a warning for base per sequence content, what should I do?
• Does MaxQuant give as output possibility the PSMs and PEPs?
• What does it mean to normalize the LFQ intensities?
• MultiQC error for your FastQC reports?
• If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide).
• Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant.
• When can you use (or cannot use) Match between runs in MaxQuant?
• JBrowse is taking a long time to complete?
• The input for a tool is not listed in the dropdown
• Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools?
• Changing the heatmap colours
• What is Gene Ontology (GO)?
• Where can I read more about Quality Control of data?
• What is the principle of an enrichment analysis?
• FASTQ files: `fastq` vs `fastqsanger` vs ..
• Compressed FASTQ files, (`*.gz`)
• Do we need a contaminant FASTA for MQ in galaxy?
• The Build tissue-specific expression dataset tool (step one) exits with an error code.
• What is the advantage of breaking down protein to peptides before mass spec?
• In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library?
• Why does my assembly graph in Bandage look different to the one pictured in the tutorial?
• AnnData Import/ AnnData Manipulate not working?
• Is it possible to use alternative tools to those proposed in the tutorial?
• Automatically trim adapters (without providing custom sequences)
• It says I already have an account when registering for ecology.usegalaxy.eu

📚 Tutorials

• Performant Uploads with TUS
• Biodiversity data exploration

🎥 Recordings

• Recording of Galaxy Installation with Ansible

❓ Faqs

• How to read a Diff
• Using tutorial mode

🛠️ Workflows

• Workflow 'Biodiversity data exploration tuto'

🧑‍🏫 Contributors

• @tduigou
• @sylviamahara
• @plushz
• @msozzoni
• @Melkeb
• @Marie59
• @kenza12
• @jfaulon
• @jbmihoub
• @ioanagry
• @guillaume-gricourt
• @garimavs
• @GaloGS
• @dpelletier
• @dbrites
• @cstritt
• @breakthewall
• @bernandez

📚 Tutorials

• Metabarcoding/eDNA through Obitools

❓ Faqs

• Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library?
• Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data?
• Changing the tool version
• Can this ASaiM workflow be used for single-end data?
• When I try to run a Selenium test, I get an error
• Is the ToolFactory a complete replacement for manual tool building?
• On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc.
• On Scanpy PlotEmbed, the tool is failing
• Only one Planemo test runs at a time. Why doesn't the server allow more than one at once?
• I cannot run client tests because yarn is not installed.
• Can we use the ASaiM-MT workflow on multiple input files at the same time?
• Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed?
• First job I submitted remains grey or running for a long time - is it broken?
• Where can I get planemo?
• What file/data formats are defined for I/O in Galaxy?
• My Scanpy FindMarkers step is giving me an empty table
• Why do we use FASTQ interlacer and not the FASTQ joiner?
• `docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory`
• My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ?
• I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
• I want to use a collection for outputs but it always passes the test even when the script fails. Why?
• The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda?
• Why is Alevin is not working?
• What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library?
• If a Tool is Missing
• Are these data free to use and download?
• Contacting Galaxy Administrators
• Where do I get more support?
• What should I do special if on usegalaxy.be?
• Can I use alternative tools for the Quantification step?
• Why don't the aligned read files have quality scores?
• When will aligned read objects be available for other data types?
• Where can I find the full listing and description of the columns in each metadata table?
• Where can I find example queries for use in the cloud and elsewhere?
• Do you have resources to help me get started working in the cloud?
• What information should I include when reporting a problem?
• My jobs aren't running!

🛠️ Workflows

• Workflow constructed from history 'Tuto Obitools'

📚 Tutorials

• Pangeo Notebook in Galaxy - Introduction to Xarray
• Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools

🖼️ Slides

• The Pangeo ecosystem
• Pangeo ecosystem 101 for everyone

🛠️ Workflows

• Pangeo Jupyter Notebook
• GTN 'Pangeo 101 for everyone - Xarray'

📚 Tutorials

• Protein target prediction of a bioactive ligand with Align-it and ePharmaLib

🛠️ Workflows

• Zauberkugel

📚 Tutorials

• Bulk RNA Deconvolution with MuSiC

🛠️ Workflows

• MuSiC Workflow

🧑‍🏫 Contributors

• @onorvez
• @neoformit
• @Lain-inrae
• @fboyer
• @ecoissac
• @aurelienmoumbock

📰 News

• New Feature: Automatic RMarkdown

❓ Faqs

• Learning with RMarkdown in RStudio
• Knitting RMarkdown documents in RStudio

🎥 Recordings

• Recording of Image classification in Galaxy with fruit 360 dataset

🖼️ Slides

• Galaxy workflows in Dockstore

🧑‍🏫 Contributors

• @rabernat
• @pickettbd
• @gf777
• @BasileGoussard
• @abueg

📰 News

• Support for annotating Funding Agencies
• GTN Smörgåsbord 2: Tapas Edition

📚 Tutorials

• Mass spectrometry: LC-MS data processing

📰 News

• New FAQs: How does the GTN stay FAIR and Collaborative
• New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate

📚 Tutorials

• Image classification in Galaxy with fruit 360 dataset

🖼️ Slides

• Image classification in Galaxy with fruit 360 dataset

❓ Faqs

• How does the GTN ensure our training materials are FAIR?
• How does the GTN implement the "Ten simple rules for collaborative lesson development"

🛠️ Workflows

• fruit_360

🧑‍🏫 Contributors

• @coverbeck
• @bethsheets
• @avani-k

🖼️ Slides

• An introduction to get started in genome assembly and annotation

📚 Tutorials

• Genome assembly using PacBio data
• Genome annotation with Funannotate
• Masking repeats with RepeatMasker

🛠️ Workflows

• Genome Assembly using PacBio data
• RepeatMasker
• Funannotate

📰 News

• New Feature: GTN Video Library

❓ Faqs

• I’m using the same training data, tools, and parameters as the tutorial, but I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why?
• In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean?
• RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'?
• Is it possible to visualize the RNA STAR bam file using the JBrowse tool?
• When is the "infer experiment" tool used in practice?
• Could I use a different p-adj value for filtering differentially expressed genes?
• The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts?

📚 Tutorials

• Make & Snakemake

❓ Faqs

• What other methods are available to study the functional state of the microbiome within Galaxy?
• I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset?
• Which search algorithms are recommended for searching the metaproteomics data?
• Can I use these workflows on datasets generated from our laboratory?
• Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
• What software tools are available to determine taxonomic composition from mass spectrometry data?
• I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches?
• How does one convert RAW files to MGF peak lists within Galaxy?
• How does one compare metaproteomics measurements from two experimental conditions?
• Are UMIs not actually unique?
• I got slightly different numbers than were in the tutorial
• My jobs are not running / I cannot see the history overview menu
• My Galaxy looks different than in the tutorial/video
• UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone?
• I can’t find the “Analyze Data” button

❓ Faqs

• Which version of SearchGUI and PeptideShaker shall I use for this tutorial?

❓ Faqs

• Why do we only consider highly variable genes?
• Can RNA-seq techniques be applied to scRNA-seq?
• What exactly is a ‘Gene profile’?
• Why do we do dimension reduction and then clustering? Why not just cluster on the actual data?
• Why is amplification more of an issue in scRNA-seq than RNA-seq?

📰 News

• New Feature: GTN API with OpenAPI 3 specification

📚 Tutorials

• Plotting in Python
• Advanced Python
• Introduction to Python

🧑‍🏫 Contributors

• @twishigulati
• @suchitrathapa
• @stephanierobin
• @lleroi
• @IrelCM
• @alexcorm
• @alaaelghamry

❓ Faqs

• Undeleting history

📚 Tutorials

• dplyr & tidyverse for data processing

❓ Faqs

• Extraer un flujo de trabajo de tu historial
• Compartiendo un historial
• Uso del cuaderno de apuntes para ver varios conjuntos de datos

🖼️ Slides

• Una breve introducción a Galaxy
• Una introducción al análisis de datos scRNA-seq
• Introducción al análisis de datos de scRNA-seq

📚 Tutorials

• CRISPR screen analysis

🛠️ Workflows

• Workflow constructed from history 'CRISPR tutorial Kenji'

📰 News

• New Topic: Data Science Survival Kit
• Attention Contributors: GTN Performance Enhancements

📚 Tutorials

• SQL with Python
• Introduction to SQL
• SQL Educational Game - Murder Mystery
• Advanced SQL
• SQL with R

🛠️ Workflows

• CLM-FATES_ ALP1 simulation (5 years)
• Climate 101

📚 Tutorials

• Filtrado, representación y exploración de secuenciación de ARN de células únicas

❓ Faqs

• Para volver a ejecutar una herramienta
• Importación por medio de enlaces
• Cambiar el tipo de datos

🧑‍🏫 Contributors

• @themudo
• @Shorla
• @saritadc
• @saramorsy
• @sandygudie
• @robertmand
• @rahmot
• @otatadeabigail
• @NUKnightLab
• @myles-bilong
• @millen2223
• @mariipia10
• @lgallegovillar
• @lamouresparus
• @kenjifujihara
• @jrr-cpt
• @gatwirival
• @Ezichi-Fav
• @dirowa
• @davelopez
• @Chinonyemildred
• @bfranicevic
• @ajadi-abiola
• @AfiDede

📚 Tutorials

• CLI Educational Game - Bashcrawl
• CLI basics
• Advanced CLI in Galaxy

❓ Faqs

• Open a Terminal in Jupyter

📰 News

• Got a minute? Take our survey about Galaxy for training and have your say!

📰 News

• New Feature: Automatic Jupyter Notebooks

🖼️ Slides

• Una Breve Introducción a Galaxy

❓ Faqs

• Why not use Excel?

❓ Faqs

• Cambiando el nombre de un historial
• Para la creación de un historial nuevo

🧑‍🏫 Contributors

• @npalopoli
• @mcmaniou

🏢 Organisations

• @carpentries

📚 Tutorials

• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin

📚 Tutorials

• How to reproduce published Galaxy analyses

🛠️ Workflows

• GTN Training: Galaxy 101 For Everyone

📚 Tutorials

• MaxQuant and MSstats for the analysis of TMT data

🛠️ Workflows

• MaxQuant MSstatsTMT Training

📚 Tutorials

• Submitting sequence data to ENA

🖼️ Slides

• Submitting SARS-CoV-2 sequences to ENA

🛠️ Workflows

• GTN_ENA_upload_workflow

🎥 Recordings

• Recording of Using dataset collections
• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

📚 Tutorials

• Removal of human reads from SARS-CoV-2 sequencing data

❓ Faqs

• Upload fastqsanger datasets via links

🛠️ Workflows

• GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data

🧑‍🏫 Contributors

• @roncoronimiguel
• @KlemensFroehlich

📰 News

• New Feature: a feedback page to aggregate and display feedback answers

📰 News

• Accessibility Improvements

🎥 Recordings

• Recording of Whole transcriptome analysis of Arabidopsis thaliana

🎥 Recordings

• Recording of Galaxy Basics for genomics

📰 News

• New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

📚 Tutorials

• Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

❓ Faqs

• Importing a workflow using the search
• Importing a history
• Upload many files (>10) via FTP
• Upload few files (1-10)

🎥 Recordings

• Recording of Use Apptainer containers for running Galaxy jobs
• Recording of Galaxy Tool Management with Ephemeris
• Recording of Galaxy Tool Management with Ephemeris
• Recording of Running Jobs on Remote Resources with Pulsar
• Recording of Galaxy Installation with Ansible

❓ Faqs

• Troubleshooting errors

📰 News

• New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R

📰 News

• New Tutorial: GitPod for contributing to the GTN

🎥 Recordings

• Recording of EncyclopeDIA

📚 Tutorials

• Running the GTN website online using GitPod

❓ Faqs

• How to Contribute to Galaxy

📚 Tutorials

• EncyclopeDIA

🛠️ Workflows

• EncyclopeDIA-GTN

📚 Tutorials

• Enable upload via FTP

📚 Tutorials

• Creating Galaxy tools from Conda Through Deployment
• Debugging Galaxy

📚 Tutorials

• Visualization of RNA-Seq results with Volcano Plot in R

❓ Faqs

• Annotate a workflow

🛠️ Workflows

• Retrieve climate data from Copernicus

❓ Faqs

• Make a workflow public

📚 Tutorials

• Contributing a New Feature to Galaxy Core
• Upgrading Galaxy
• Automating Galaxy workflows using the command line

🛠️ Workflows

• vcf2lineage

📚 Tutorials

• Updating diffs in admin training

❓ Faqs

• Got lost along the way?

📰 News

• New Tutorial: Genome Annotation with Apollo

📚 Tutorials

• Refining Genome Annotations with Apollo (prokaryotes)
• Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

🖼️ Slides

• Refining Genome Annotations with Apollo

🛠️ Workflows

• Apollo Load Test
• VGP assembly: training workflow

🖼️ Slides

• Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2

❓ Faqs

• Which isobaric labeled quantification methods does MaxQuant in Galaxy support?
• Including custom modifications into MaxQuant in Galaxy?
• Do I need to create collections to run MaxQuant analysis or can I use single sample inputs?

🖼️ Slides

• Feedforward neural networks (FNN) Deep Learning - Part 1

📰 News

• Oh no, it changed! Quick, to the archive menu.

🧑‍🏫 Contributors

• @xtrojak
• @OlegZharkov
• @davebx

📚 Tutorials

• SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis

🖼️ Slides

• Recurrent neural networks (RNN) Deep Learning - Part 2

❓ Faqs

• Viewing a workflow report

📚 Tutorials

• ToolFactory: Generating Tools From More Complex Scripts
• ToolFactory: Generating Tools From Simple Scripts

🖼️ Slides

• Introduction to the ToolFactory tutorial.

📰 News

• New Feature: Easy Abbreviation
• Contributing to BioBlend as a developer

📚 Tutorials

• Contributing to BioBlend as a developer

📚 Tutorials

• Introduction to Machine Learning using R

📰 News

• ¿Hablas español?: The first curated tutorial in Spanish!

📚 Tutorials

• Breve introducción a Galaxy - en español

🖼️ Slides

• Convolutional neural networks (CNN) Deep Learning - Part 3

🎥 Recordings

• Recording of Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2
• Recording of SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis

📚 Tutorials

• PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis

🛠️ Workflows

• papaa@0.1.9_PI3K_OG_model_tutorial

🧑‍🏫 Contributors

• @rikeshi
• @pclo
• @RareSeas
• @mboudet
• @jontrow
• @EngyNasr
• @assuntad23
• @ales-ibt

📚 Tutorials

• Deep Learning (Part 1) - Feedforward neural networks (FNN)

🎥 Recordings

• Recording of Whole transcriptome analysis of Arabidopsis thaliana

📚 Tutorials

• Deep Learning (Part 3) - Convolutional neural networks (CNN)

🖼️ Slides

• Whole transcriptome analysis of Arabidopsis thaliana

📰 News

• New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana

📚 Tutorials

• Whole transcriptome analysis of Arabidopsis thaliana
• Analysis of plant scRNA-Seq Data with Scanpy

🖼️ Slides

• Introduction to ATAC-Seq data analysis

🛠️ Workflows

• Plant bulk RNA-Seq workflow
• scRNA Plant Analysis

📚 Tutorials

• Inferring single cell trajectories with Scanpy (Python)

📰 News

• New Feature: Video Player

📚 Tutorials

• Text-mining with the SimText toolset

❓ Faqs

• Open interactive tool

🛠️ Workflows

• Simtext training workflow

📰 News

• New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy

📰 News

• New Feature: FAQs
• New Tutorials: Genome assembly of a MRSA genome

📚 Tutorials

• Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
• Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
• Filter, plot and explore single-cell RNA-seq data with Scanpy

❓ Faqs

• Nanopore sequencing
• Illumina MiSeq sequencing
• Running a workflow
• Renaming workflow outputs
• Setting parameters at run-time
• Importing a workflow
• Hiding intermediate steps
• Extracting a workflow from your history
• Opening the workflow editor
• Creating a new workflow
• Add Mapped reads track to IGV from Galaxy
• Add genome and annotations to IGV from Galaxy
• How can I create a tutorial skeleton from a Galaxy workflow?
• Select multiple datasets
• Selecting a dataset collection as input
• Re-running a tool
• Getting your API key
• Where can I read more about this analysis?
• How do I use this material?
• Where can I run the hands-on tutorials?
• Where do I start?
• How can I get help?
• Stop RStudio
• Launch RStudio
• Launch JupyterLab
• Where do I start?
• How do I get help?
• What Galaxy instance should I use for my training?
• What are the best practices for teaching with Galaxy?
• Install tools via the Admin UI
• Which icons are available to use in my tutorial?
• Searching your history
• Renaming a history
• Creating a new history
• Copy a dataset between histories
• What are the tutorials for?
• Sustainability of the training-material and metadata
• How is the content licensed?
• How can I cite the GTN?
• What audiences are the tutorials for?
• How can I advertise the training materials on my posters?
• What is this website?
• What is Galaxy?
• Are there any upcoming events focused on Galaxy Training?
• Using the Window Manager to view multiple datasets
• Renaming a dataset
• Importing via links
• Importing data from a data library
• Detecting the datatype (file format)
• Creating a new file
• Converting the file format
• Changing database/build (dbkey)
• Changing the datatype
• Adding a tag
• How can I create new content without dealing with git?
• How can I test an Interactive Tour?
• How can I report mistakes or errors?
• What can I do to help the project?
• How can I give feedback?
• How can I fix mistakes or expand an existing tutorial using the GitHub interface?
• How can I contribute in "advanced" mode?
• How can I get started with contributing?
• Thanks!
• Renaming a collection
• Creating a paired collection
• Creating a dataset collection
• Adding a tag to a collection
• Running Ansible on your remote machine
• Results may vary
• Adding a custom database/build (dbkey)
• Operating system compatibility
• How can I adapt this tutorial to my own data?
• Sharing your History

🛠️ Workflows

• Genome Assembly of MRSA using Illumina MiSeq Data
• CS3_Filter, Plot and Explore Single-cell RNA-seq Data

📰 News

• Galaxy Community Conference 2021
• Next GTN CoFest May 20, 2021
• New Tutorial: Object tracking using CellProfiler

🎥 Recordings

• Recording of Understanding Barcodes
• Recording of Pre-processing of 10X Single-Cell RNA Datasets
• Recording of Clustering 3K PBMCs with Scanpy

📰 News

• Galaxy 21.01 released!
• Report on the GTN Smörgåsbord event

📚 Tutorials

• Object tracking using CellProfiler

🛠️ Workflows

• CP_object_tracking_example

📰 News

• New Feature: Automatic Slides-to-video conversion

🎥 Recordings

• Recording of Bulk RNA Deconvolution with MuSiC

📚 Tutorials

• Generating a single cell matrix using Alevin

🛠️ Workflows

• Combining datasets after pre-processing
• Generating a single cell matrix using Alevin

📰 News

• Galaxy Admin Training Success

🧑‍🏫 Contributors

• @sunyi000
• @mgramm1
• @dlalgroup