Weekly Updates

📰 News

• GTN's Gift for 2024 (December 19, 2024)
• 🖖🏾Galaxy SPOC Community: Year in Review (December 18, 2024)
• Organizing GTA2025: Give us feedback and your availability! (December 17, 2024)

📅 Events

• Galaxy at SURF Research Cloud workshop (December 18, 2024)
• Code & Collaborate: The FAIRytale of Software Development (December 18, 2024)

📚 Tutorials

• Creating community content (December 20, 2024)
• Galaxy usage on SURF Research Cloud (December 18, 2024)
• Pulsar usage on SURF Research Cloud (December 18, 2024)

❓ Faqs

• How do I add a news feed to a Matrix channel? (December 20, 2024)
• How do I find the Maintainer Home pages? (December 20, 2024)
• How do I find the Community Home pages? (December 20, 2024)
• How can I add my SIG meetings to the Galaxy Community Activities calendar? (December 20, 2024)

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📚 Tutorials

• Data submission using ENA upload Tool (December 13, 2024)
• Building the LORIS LLR6 PanCancer Model Using PyCaret (December 13, 2024)

❓ Faqs

• Slow incremental builds (December 13, 2024)
• What is an Architectural Decision Record (ADR)? (December 13, 2024)
• GTN Architectural Decision Record Template (December 13, 2024)
• GTN ADR: Why Jekyll and not another Static Site Generator (SSG) (December 13, 2024)
• GTN ADR: Image Storage (December 13, 2024)

🛠️ Workflows

• scRNA Plant Analysis (December 13, 2024)
• Ludwig - Image recognition model - MNIST (December 13, 2024)

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📰 News

• SPOC CoFest 2024: How did it go? (December 06, 2024)
• Credit where it's due: GTN Reviewers in the spotlight (December 02, 2024)

🛤️ Learning pathways

• Tool development for a nice & shiny subdomain (December 04, 2024)

📚 Tutorials

• Overview of the Galaxy OMERO-suite - Upload images and metadata in OMERO using Galaxy (December 04, 2024)
• Make your tools available on your subdomain (December 03, 2024)

🖼️ Slides

• An earth-system RO-Crate (December 02, 2024)

❓ Faqs

• How do I add my community to the Galaxy CoDex? (December 05, 2024)
• Syncing your Fork of the GTN (December 04, 2024)
• Updating the default branch from master to main (December 04, 2024)
• Forking the GTN repository (December 04, 2024)

🛠️ Workflows

• Seurat Filter, Plot and Exlore tutorial (December 05, 2024)

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📰 News

• New Tutorial: Tracking of mitochondria and capturing mitoflashes (November 29, 2024)

📅 Events

• 🖖🏾 SPOC II: the Write-a-Than (November 26, 2024)

📚 Tutorials

• Updating tool versions in a tutorial (November 29, 2024)
• Create a subdomain for your community on UseGalaxy.eu (November 27, 2024)

🧑‍🏫 Contributors

• @yuliiaorlova (December 01, 2024)
• @Swathi266 (December 01, 2024)
• @mirelaminkova (December 01, 2024)
• @GokceOGUZ (December 01, 2024)
• @dometto (December 01, 2024)
• @adairama (December 01, 2024)
• @adya29 (December 01, 2024)

💰 Grants

• @nfdi4bioimage (December 01, 2024)

🏢 Organisations

• @dfg (December 01, 2024)

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📚 Tutorials

• Tracking of mitochondria and capturing mitoflashes (November 20, 2024)

🛠️ Workflows

• Capturing mitoflashes (November 20, 2024)

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📅 Events

• Galaxy at Congresso Brasileiro de Biologia Evolutiva (November 12, 2024)

📚 Tutorials

• Running the GTN website online using GitHub CodeSpaces (November 11, 2024)

❓ Faqs

• Add Toolshed category to a tool (November 13, 2024)

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📚 Tutorials

• Alternative Celery Deployment for Galaxy (November 07, 2024)
• Single Cell Publication - Data Analysis (November 07, 2024)
• Single Cell Publication - Data Plotting (November 07, 2024)

❓ Faqs

• Supporting Tutorial Mode (GTN-in-Galaxy) in a tutorial (November 07, 2024)

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🛤️ Learning pathways

• Applying single-cell RNA-seq analysis in Coding Environments (October 30, 2024)

📚 Tutorials

• Train and Test a Deep learning image classifier with Galaxy-Ludwig (October 28, 2024)

❓ Faqs

• Why isn't my history updating? (October 30, 2024)
• Using answer key histories (October 30, 2024)
• Request Galaxy tools on a specific server (October 30, 2024)
• Importing data from Sierra LIMS (October 30, 2024)
• How can I get my container requiring jobs to run in a container? (October 30, 2024)

🛠️ Workflows

• Ludwig - Image recognition model - MNIST (October 28, 2024)

🧑‍🏫 Contributors

• @rmassei (November 01, 2024)

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📚 Tutorials

• DataPLANT ARCs (October 22, 2024)

🖼️ Slides

• Intro to DataPLANT ARCs (October 24, 2024)

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📅 Events

• Workshop on high-throughput sequencing data analysis with Galaxy (October 15, 2024)
• An introduction to High Performance Computing (October 15, 2024)

❓ Faqs

• Is there a certification available for the FAIR-by-Design Methodology? (October 17, 2024)
• Can the FAIR-by-Design Methodology be used for FAIR development of other types of resources? (October 17, 2024)
• Can this tutorial be adapted to other instructional development platforms? (October 17, 2024)

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📅 Events

• Single-cell and sPatial Omics | Collaboration Fest (October 11, 2024)
• 🖖🏾 SPOC Write-a-thon (October 11, 2024)
• 2024 Bioinformatics Bootcamp - The Open University (October 10, 2024)

❓ Faqs

• Can I use a public Galaxy for my private data? (October 08, 2024)

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📚 Tutorials

• Getting your hands-on earth data (October 04, 2024)
• Predicting EI+ mass spectra with QCxMS (October 01, 2024)
• Identifying Mycorrhizal Fungi from ITS2 sequencing using LotuS2 (September 30, 2024)

🖼️ Slides

• Predicting EI+ mass spectra with QCxMS (October 01, 2024)

🎥 Recordings

• Recording of ERGA post-assembly QC (October 06, 2024)
• Recording of Deep Learning (Part 3) - Convolutional neural networks (CNN) (October 05, 2024)
• Recording of Single-cell Formats and Resources (September 30, 2024)
• Recording of Quality Control (September 30, 2024)

❓ Faqs

• Open History files in Integrated Genome Browser (IGB) (October 04, 2024)
• Input Histories & Answer Keys (October 04, 2024)
• Annotating Pre-requisites (October 02, 2024)
• Using the new Contributions Annotation framework (October 02, 2024)

🛠️ Workflows

• End-to-end EI+ mass spectra prediction workflow using QCxMS (October 01, 2024)
• Workflow for Identifying MF from ITS2 sequencing using LotuS2 - tutorial example run' (September 30, 2024)

🧑‍🏫 Contributors

• @zargham-ahmad (October 01, 2024)
• @wverastegui (October 01, 2024)
• @thanhleviet (October 01, 2024)
• @SabrinaZander (October 01, 2024)
• @paige-kulzer (October 01, 2024)
• @Martin-Kuhl (October 01, 2024)
• @Freymaurer (October 01, 2024)
• @felicitas215 (October 01, 2024)
• @Sch-Da (October 01, 2024)
• @CMR248 (October 01, 2024)
• @Brilator (October 01, 2024)

🏢 Organisations

• @moffitt (October 01, 2024)

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🎥 Recordings

• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (September 27, 2024)
• Recording of Clustering 3K PBMCs with Scanpy (September 26, 2024)
• Recording of Identification of AMR genes in an assembled bacterial genome (September 24, 2024)

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📚 Tutorials

• GO Enrichment Analysis on Single-Cell RNA-Seq Data (September 17, 2024)
• Ecoregionalization workflow tutorial (September 16, 2024)

🖼️ Slides

• GO Enrichment Analysis on Single-Cell RNA-Seq Data (September 17, 2024)

🎥 Recordings

• Recording of Decontamination of a genome assembly (September 20, 2024)
• Recording of Assembly of the mitochondrial genome from PacBio HiFi reads (September 20, 2024)
• Recording of Building an amplicon sequence variant (ASV) table from 16S data using DADA2 (September 20, 2024)
• Recording of Galaxy Basics for genomics (September 16, 2024)

❓ Faqs

• Using tutorial mode and the Case Study suite (September 18, 2024)

🛠️ Workflows

• GO Enrichment Workflow (September 17, 2024)
• Ecoregionalization workflow (September 16, 2024)

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📚 Tutorials

• Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub (September 13, 2024)

🎥 Recordings

• Recording of Making clinical datasets FAIR (September 12, 2024)
• Recording of REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data (September 12, 2024)
• Recording of Introduction to Data Management Plan (DMP) for Peatland Research and PeatDataHub (September 12, 2024)
• Recording of Chloroplast genome assembly (September 12, 2024)
• Recording of Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data (September 12, 2024)
• Recording of Data management in Medicinal Chemistry (September 12, 2024)
• Recording of Generating a single cell matrix using Alevin (September 12, 2024)
• Recording of Importing files from public atlases (September 12, 2024)
• Recording of Long non-coding RNAs (lncRNAs) annotation with FEELnc (September 11, 2024)

❓ Faqs

• Why is my tool erroring as 'Above error raised while reading key '/layers' of type <class 'h5py._hl.group.Group'> from /.' (September 12, 2024)

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📚 Tutorials

• Decontamination of a genome assembly (September 04, 2024)
• Assembly of the mitochondrial genome from PacBio HiFi reads (September 03, 2024)

🎥 Recordings

• Recording of Understanding Galaxy history system (September 07, 2024)
• Recording of Mapping (September 07, 2024)
• Recording of Visualization of RNA-Seq results with Volcano Plot (September 06, 2024)
• Recording of Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data (September 04, 2024)
• Recording of Bacterial Genome Annotation (September 02, 2024)

🛠️ Workflows

• Assembly-decontamination-VGP9 (September 04, 2024)
• Mitogenome-Assembly-VGP0 (September 03, 2024)

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🎥 Recordings

• Recording of Binning of metagenomic sequencing data (August 30, 2024)
• Recording of Fine tune large protein model (ProtTrans) using HuggingFace (August 29, 2024)
• Recording of Classification in Machine Learning (August 29, 2024)

🧑‍🏫 Contributors

• @MennaGamal (September 01, 2024)
• @trungN (September 01, 2024)
• @tcollins2011 (September 01, 2024)
• @sujaikumar (September 01, 2024)
• @paulocilasjr (September 01, 2024)
• @mschatz (September 01, 2024)
• @mhintze (September 01, 2024)
• @meltemktn (September 01, 2024)
• @mateeullah905 (September 01, 2024)
• @igormakunin (September 01, 2024)
• @hfraser (September 01, 2024)
• @hannahkimincompbio (September 01, 2024)
• @GarethPrice-Aus (September 01, 2024)
• @emmaustin20 (September 01, 2024)
• @DinithiRajapaksha (September 01, 2024)
• @bethanmanley (September 01, 2024)

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📅 Events

• From zero to hero with Python (August 20, 2024)

📚 Tutorials

• Genome annotation with Helixer (August 21, 2024)
• Marine Omics identifying biosynthetic gene clusters (August 19, 2024)

🛠️ Workflows

• annotation_helixer (August 21, 2024)
• Marine Omics identifying biosynthetic gene clusters (August 19, 2024)

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🎥 Recordings

• Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition (August 16, 2024)

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🛤️ Learning pathways

• Proteogenomics (August 09, 2024)

📚 Tutorials

• Querying the University of Bradford GDC Beacon Database for Copy Number Variants (CNVs) (August 06, 2024)
• Working with Beacon V2: A Comprehensive Guide to Creating, Uploading, and Searching for Variants with Beacons (August 06, 2024)

🎥 Recordings

• Recording of Calculating α and β diversity from microbiome taxonomic data (August 08, 2024)
• Recording of Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) (August 06, 2024)

🛠️ Workflows

• WF5_Data_Interpretation_Worklow (August 08, 2024)
• WF4_Quantitation_Workflow (August 08, 2024)
• WF3_VERIFICATION_WORKFLOW (August 08, 2024)
• WF2_Discovery-Workflow (August 08, 2024)
• WF1_Database_Generation_Workflow (August 08, 2024)
• Calculating diversity from microbiome taxonomic data (August 06, 2024)

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📚 Tutorials

• Calculating α and β diversity from microbiome taxonomic data (August 01, 2024)

🎥 Recordings

• Recording of Quality and contamination control in bacterial isolate using Illumina MiSeq Data (August 01, 2024)

🧑‍🏫 Contributors

• @tbrown91 (August 01, 2024)
• @RZ9082 (August 01, 2024)
• @natalie-wa (August 01, 2024)
• @lybCNU (August 01, 2024)
• @hujambo-dunia (August 01, 2024)
• @dianichj (August 01, 2024)
• @ahmedhamidawan (August 01, 2024)

🏢 Organisations

• @mwk (August 01, 2024)

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📰 News

• Galaxy Administrator Time Burden and Technology Usage (July 22, 2024)

🖼️ Slides

• Single-cell Formats and Resources (July 26, 2024)

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📰 News

• Simplifying GTN contribution with Google Forms (July 17, 2024)

📅 Events

• BioNT Community Event & CarpentryConnect - Heidelberg 2024 (July 15, 2024)

📚 Tutorials

• Quality and contamination control in bacterial isolate using Illumina MiSeq Data (July 15, 2024)

🛠️ Workflows

• Quality and contamination control in bacterial isolate using Illumina MiSeq Data (July 15, 2024)

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📰 News

• New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2 (July 12, 2024)
• Registration Open for BioNT Community Event & CarpentryConnect Heidelberg (July 11, 2024)
• So many new features! GTN 2023-2024 Updates (July 09, 2024)
• 4th Mycobacterium tuberculosis complex NGS made easy (July 08, 2024)

📅 Events

• EuroBioC2024 Carpentries workshops (July 12, 2024)
• Workshop on high-throughput sequencing data analysis with Galaxy (July 10, 2024)
• Bioconductor Carpentries workshop: Analysis and Interpretation of Bulk RNA-Seq Data (July 09, 2024)
• Bioconductor North American conference (BioC2024) (July 08, 2024)

📚 Tutorials

• Single-cell ATAC-seq standard processing with SnapATAC2 (July 11, 2024)
• Creating a Special Interest Group (July 08, 2024)
• What's a Special Interest Group? (July 08, 2024)

🖼️ Slides

• Galaxy Administrator Time Burden and Technology Usage (July 10, 2024)

❓ Faqs

• How can I plan meetings across timezones? (July 08, 2024)
• What is the Galaxy Governance Structure? (July 08, 2024)
• How do I join the Galaxy Community Board? (July 08, 2024)
• What's the Galaxy Community Board? (July 08, 2024)

🛠️ Workflows

• Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 (July 11, 2024)

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📅 Events

• A practical introduction to bioinformatics and RNA-seq using Galaxy (July 03, 2024)

❓ Faqs

• Finding a material's PURL or Short URL (July 04, 2024)
• Translations within the GTN (July 03, 2024)
• Top level history controls (July 02, 2024)
• History tagging (July 02, 2024)
• Switching to an existing history (July 02, 2024)
• History options (July 02, 2024)
• Datasets versus collections (July 02, 2024)
• Dataset snippet (July 02, 2024)
• Dataset colors (July 02, 2024)
• History annotation (July 02, 2024)
• How to un-hide datasets? (July 02, 2024)
• How to un-delete datasets? (July 02, 2024)
• Manipulating multiple history datasets (July 02, 2024)
• How to delete datasets? (July 02, 2024)

🧑‍🏫 Contributors

• @CRHAD26 (July 01, 2024)
• @agCleo (July 01, 2024)
• @achim-kit (July 01, 2024)
• @CarolinLeister (July 01, 2024)
• @isouyioul (July 01, 2024)
• @domlgreen (July 01, 2024)
• @korvoj (July 01, 2024)
• @amisev1971 (July 01, 2024)
• @sonjafiliposka (July 01, 2024)
• @StellaEggels (July 01, 2024)
• @Rassine (July 01, 2024)
• @Najatamk (July 01, 2024)
• @Nilchia (July 01, 2024)

💰 Grants

• @skills4eosc (July 01, 2024)
• @nfdi4plants (July 01, 2024)

🏢 Organisations

• @madland (July 01, 2024)

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❓ Faqs

• Creating a GTN FAQ (June 26, 2024)

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📚 Tutorials

• Fine tune large protein model (ProtTrans) using HuggingFace (June 17, 2024)

🎥 Recordings

• Recording of Clinical Metaproteomics 5: Data Interpretation (June 21, 2024)
• Recording of Clinical Metaproteomics 3: Verification (June 21, 2024)
• Recording of Clinical Metaproteomics 4: Quantitation (June 21, 2024)
• Recording of Clinical Metaproteiomics 1: Database-Generation (June 21, 2024)
• Recording of Clinical Metaproteomics 2: Discovery (June 21, 2024)

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📰 News

• GTN Video Library 2.0: 107 hours of learning across 154 videos (June 14, 2024)
• From GTN Intern to Tutorial Author to Bioinformatician (June 13, 2024)
• Phylogenetics tutorial takes researchers back to basics! (June 13, 2024)
• Open Call for Trainers for the Galaxy Training Academy (June 11, 2024)

📅 Events

• Galaxy Training Academy 2024 (June 11, 2024)

🎥 Recordings

• Recording of M. tuberculosis Variant Analysis (June 11, 2024)

❓ Faqs

• Recording a video tutorial (June 14, 2024)
• Adding your recording to a tutorial or slide deck (June 14, 2024)

🛠️ Workflows

• BY-COVID: Data Download (June 11, 2024)

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📰 News

• Celebrating the Milestone: 400 Tutorials on the Galaxy Training Network! (June 06, 2024)
• New Galaxy training: Building an amplicon sequence variant (ASV) table from 16S data using DADA2 (June 06, 2024)
• Standards compliant™ training news via RSS/Atom (June 04, 2024)
• Integrating the Galaxy Training Network into the Tool Form (June 04, 2024)
• All GTN training data are now automatically mirrored via Onedata (June 03, 2024)

📅 Events

• FAIR data management in single-cell analysis (June 04, 2024)
• Mycobacterium tuberculosis complex NGS made easy (June 03, 2024)

📚 Tutorials

• Building an amplicon sequence variant (ASV) table from 16S data using DADA2 (June 05, 2024)

🛠️ Workflows

• Building an amplicon sequence variant (ASV) table from 16S data using DADA2 (June 05, 2024)

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🛠️ Workflows

• Taxonomy Profiling and Visualization with Krona (May 29, 2024)
• Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation (May 29, 2024)
• Allele-based Pathogen Identification (May 29, 2024)

🧑‍🏫 Contributors

• @shwdey (June 01, 2024)
• @matuskalas (June 01, 2024)
• @linzyelton (June 01, 2024)
• @lilianarutaihwa (June 01, 2024)
• @bethlehem-adnew (June 01, 2024)
• @arashghodousi (June 01, 2024)
• @andrea-spitaleri (June 01, 2024)
• @andreacabibbe (June 01, 2024)
• @Allen13x (June 01, 2024)

💰 Grants

• @edctp-eu (June 01, 2024)

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📰 News

• Introducing GTN Event Pages (May 22, 2024)

📅 Events

• Mycobacterium tuberculosis complex NGS made easy (May 23, 2024)
• 2023 Galaxy Admin Training (Ghent) (May 23, 2024)
• Admin Training @ GCC 2022: Online Training Day (May 23, 2024)

❓ Faqs

• Creating a GTN Event (May 23, 2024)

🛠️ Workflows

• ml_regression (May 21, 2024)

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📰 News

• Open Galaxy Position at Galaxy Europe Team, University of Freiburg (May 15, 2024)
• Perfectly FAIR Training! (May 13, 2024)

❓ Faqs

• Using Answer Key Histories (May 13, 2024)

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📚 Tutorials

• Phylogenetics - Back to basics (May 10, 2024)

🖼️ Slides

• Phylogenetics - Back to Basics - Introduction (May 10, 2024)
• Phylogenetics - Back to Basics - Multiple Sequence Alignment (May 10, 2024)
• Phylogenetics - Back to Basics - Phylogenetic Networks (May 10, 2024)
• Phylogenetics - Back to Basics - Building Trees (May 10, 2024)
• Phylogenetics - Back to Basics - Terminology (May 10, 2024)
• Phylogenetics - Back to Basics - Estimating trees from alignments (May 10, 2024)

🛠️ Workflows

• Tree Building (imported from uploaded file) (May 10, 2024)

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🧑‍🏫 Contributors

• @yvesvdb (May 01, 2024)
• @timonschlegel (May 01, 2024)
• @sebastian-schaaf (May 01, 2024)
• @s3by01 (May 01, 2024)
• @rwinand (May 01, 2024)
• @prodromus (May 01, 2024)
• @MariaTsayo (May 01, 2024)
• @ksuderman (May 01, 2024)
• @LonsBio (May 01, 2024)
• @FilipposZ (May 01, 2024)
• @ennovytje (May 01, 2024)
• @angiolini (May 01, 2024)
• @andrewr (May 01, 2024)
• @awspolly (May 01, 2024)

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📰 News

• Open Galaxy Positions at Melbourne Bioinformatics (April 24, 2024)

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📚 Tutorials

• Screening assembled genomes for contamination using NCBI FCS (April 16, 2024)

❓ Faqs

• Ensuring Workflows meet Best Practices (April 17, 2024)

🛠️ Workflows

• NCBI Foreign Contamination Screen (April 16, 2024)

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📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat (April 09, 2024)

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🧑‍🏫 Contributors

• @nsjuty (April 01, 2024)
• @clsiguret (April 01, 2024)
• @B0r1sD (April 01, 2024)

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📰 News

• Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy (March 28, 2024)
• New Learning Pathway for FAIR Data Management developed by ELIXIR-UK Data Stewardship Fellows and Experts (March 26, 2024)

🛤️ Learning pathways

• FAIR Data Management (March 26, 2024)

📚 Tutorials

• Pathway analysis with the MINERVA Platform (March 28, 2024)
• FAIRification of an RNAseq dataset (March 27, 2024)
• Persistent Identifiers (March 26, 2024)
• FAIR and its Origins (March 26, 2024)
• Access (March 26, 2024)
• Data Registration (March 26, 2024)
• Metadata (March 26, 2024)

🛠️ Workflows

• mRNA-Seq BY-COVID Pipeline: Counts (March 28, 2024)
• mRNA-Seq BY-COVID Pipeline: Analysis (March 28, 2024)
• Ocean's variables 2.0 (March 25, 2024)

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📰 News

• Cool URLs Don't Change, GTN URLs don't either. (March 18, 2024)

📚 Tutorials

• Analyse Argo data (March 24, 2024)

❓ Faqs

• View histories side-by-side (March 21, 2024)
• View a list of all histories (March 21, 2024)
• How to enable the Activity Bar (March 21, 2024)
• Enhancing tabular dataset previews in reports/pages (March 19, 2024)
• Making an element collapsible in a report (March 19, 2024)

🛠️ Workflows

• Analyse Argo data (March 24, 2024)

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📚 Tutorials

• QIIME 2 Moving Pictures (March 14, 2024)
• Creation of an interactive Galaxy tools table for your community (March 13, 2024)

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📰 News

• Lost in a topic? Try a Learning Pathway! (March 04, 2024)

🛤️ Learning pathways

• Applying single-cell RNA-seq analysis (March 07, 2024)
• Building training material in Galaxy (March 07, 2024)

📚 Tutorials

• Adding and updating best practice metadata for Galaxy tools using the bio.tools registry (March 06, 2024)
• Creating metadata using Ecological Metadata Language (EML) standard with EML Assembly Line functionalities (March 04, 2024)
• Checking expected species and contamination in bacterial isolate (March 04, 2024)

🛠️ Workflows

• ATAC-seq GTM (March 06, 2024)
• Genome Assembly of MRSA using Oxford Nanopore MinION (and Illumina data if available) (March 04, 2024)
• Checking expected species and contamination in bacterial isolate (March 04, 2024)

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📰 News

• GTN ❤️ GMOD (February 29, 2024)

🧑‍🏫 Contributors

• @tvedtees (March 01, 2024)
• @sitjart (March 01, 2024)
• @saskia-lawson-tovey (March 01, 2024)
• @SaimMomin12 (March 01, 2024)
• @proccaserra (March 01, 2024)
• @Mehgan-E (March 01, 2024)
• @lcooper (March 01, 2024)
• @khens (March 01, 2024)
• @kellsnow (March 01, 2024)

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🛠️ Workflows

• Gene Cluster Product Similarity Search (February 21, 2024)

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🛤️ Learning pathways

• Clinical metaproteomics workflows within Galaxy (February 12, 2024)

📚 Tutorials

• Converting between common single cell data formats (February 13, 2024)
• QIIME 2 Cancer Microbiome Intervention (February 12, 2024)

🛠️ Workflows

• AnnData to SingleCellExperiment (SCE) conversion (February 13, 2024)
• AnnData to Seurat conversion (February 13, 2024)
• AnnData to Cell Data Set (CDS) conversion (February 13, 2024)

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📚 Tutorials

• Clinical Metaproteomics 5: Data Interpretation (February 06, 2024)
• Clinical Metaproteomics 3: Verification (February 06, 2024)
• Clinical Metaproteomics 4: Quantitation (February 06, 2024)
• Clinical Metaproteiomics 1: Database-Generation (February 06, 2024)
• Clinical Metaproteomics 2: Discovery (February 06, 2024)
• Creating high resolution images of Galaxy Workflows (February 05, 2024)

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📰 News

• 🪐📲 Hosting Galaxy at the Edge: Directly in Your Pocket! (January 31, 2024)
• GTN in Discourse (January 30, 2024)
• Simplified GTN News submission via Google Form (January 29, 2024)

📚 Tutorials

• Bacterial Genome Annotation (February 01, 2024)

🛠️ Workflows

• Bacterial Genome Annotation (February 01, 2024)

🧑‍🏫 Contributors

• @ThibaudGlinez (February 01, 2024)
• @supernord (February 01, 2024)
• @qchiujunhao (February 01, 2024)
• @PatCapon39 (February 01, 2024)
• @asmasonomics (February 01, 2024)

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🛤️ Learning pathways

• Detection of AMR genes in bacterial genomes (January 23, 2024)

📚 Tutorials

• Sentinel 5P data visualisation (January 26, 2024)
• From NDVI data with OpenEO to time series visualisation with Holoviews (January 24, 2024)
• Identification of AMR genes in an assembled bacterial genome (January 23, 2024)
• Finding the muon stopping site with pymuon-suite in Galaxy (January 22, 2024)
• Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS (January 22, 2024)

🎥 Recordings

• Recording of Finding the muon stopping site with pymuon-suite in Galaxy (January 26, 2024)

🛠️ Workflows

• Sentinel5 volcanic data (January 26, 2024)
• NDVI with OpenEO (January 24, 2024)
• NDVI with OpenEO (January 24, 2024)
• mrsa AMR gene detection (January 23, 2024)
• Finding the Muon Stopping Site: pymuon-suite in Galaxy (January 22, 2024)

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📰 News

• FAIR Data management in single cell analysis (January 17, 2024)

❓ Faqs

• Using data source tools with Pulsar (January 19, 2024)

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📚 Tutorials

• Clean and manage Sanger sequences from raw files to aligned consensus (January 08, 2024)
• Data management in Medicinal Chemistry (January 08, 2024)

🛠️ Workflows

• Training Sanger sequences CHD8 (January 08, 2024)
• Sanger1 : From AB1 to aligned consensus and primers fasta + BLAST (January 08, 2024)
• Data management in Medicinal Chemistry workflow (January 08, 2024)

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🧑‍🏫 Contributors

• @PaulineSGN (January 01, 2024)
• @martinwolst (January 01, 2024)

🏢 Organisations

• @abromics (January 01, 2024)

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📰 News

• Galaxy Single-cell Community: Year in Review (December 22, 2023)
• GTN Helper Bots Connect the Galaxy (December 20, 2023)
• User story: Where Galaxy meets medicinal chemistry (December 18, 2023)

❓ Faqs

• Importing and Launching a WorkflowHub.eu Workflow (December 19, 2023)
• Importing and Launching a Dockstore Workflow (December 19, 2023)
• What is my.galaxy.training (December 19, 2023)

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📰 News

• Tutorial Feature: Easier launching of WorkflowHub & Dockstore Workflows (December 12, 2023)

📚 Tutorials

• Converting NCBI Data to the AnnData Format (December 13, 2023)

🛠️ Workflows

• EBI SCXA to AnnData (Scanpy) or Seurat Object (December 14, 2023)
• NCBI to Anndata (December 13, 2023)
• Intro_To_CNN_v1.0.11.0 (December 11, 2023)

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📚 Tutorials

• Generating a single cell matrix using Alevin and combining datasets (bash + R) (December 08, 2023)
• Inferring single cell trajectories with Scanpy (December 08, 2023)
• Binning of metagenomic sequencing data (December 05, 2023)

🛠️ Workflows

• Inferring Trajectories with Scanpy Tutorial Workflow (December 08, 2023)
• Clustering 3k PBMC with Scanpy (December 05, 2023)

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📚 Tutorials

• Ocean's variables study (November 29, 2023)
• Ocean Data View (ODV) (November 27, 2023)

❓ Faqs

• How can I do analysis X? - Getting help (November 28, 2023)
• Import workflows from DockStore (November 27, 2023)
• Upload datasets from GenomeArk (November 27, 2023)
• Upload fasta datasets via links (November 27, 2023)

🧑‍🏫 Contributors

• @sanjaysrikakulam (December 01, 2023)
• @PapXis (December 01, 2023)
• @mbaardwijk (December 01, 2023)
• @MattiHoch (December 01, 2023)
• @mjostaszewski (December 01, 2023)
• @burkemlou (December 01, 2023)

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📰 News

• GTN has left Twitter/X as of October (November 21, 2023)
• Feedback: Easy slide recordings (November 21, 2023)
• Update: Workflow List now searches WorkflowHub.eu, advanced query syntax (November 20, 2023)

🖼️ Slides

• Friends Don't Let Friends Make Bad Graphs (November 20, 2023)

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📚 Tutorials

• Importing files from public atlases (November 14, 2023)

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📚 Tutorials

• Ploting a Microbial Genome with Circos (November 08, 2023)

🛠️ Workflows

• Circos for E. Coli (November 08, 2023)

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📚 Tutorials

• Course Builder (November 02, 2023)
• Sequence data submission to ENA (November 01, 2023)

❓ Faqs

• Preparing materials for asynchronous learning: Tips (November 02, 2023)
• Preparing materials for asynchronous learning: Self-Study (November 02, 2023)
• Preparing materials for asynchronous learning: FAQs (November 02, 2023)
• Preparing materials for asynchronous learning: CYOA (November 02, 2023)
• Updating from 22.01 to 23.0 with Ansible (November 01, 2023)

🧑‍🏫 Contributors

• @edmontosaurus (November 01, 2023)
• @cxli233 (November 01, 2023)

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📚 Tutorials

• Making clinical datasets FAIR (October 24, 2023)

❓ Faqs

• What is a Learning Pathway? (October 23, 2023)

🛠️ Workflows

• Infinium Human Methylation BeadChip (October 23, 2023)

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❓ Faqs

• Notebook-based tutorials can give different outputs (October 17, 2023)

🛠️ Workflows

• Intro_To_RNN_v1_0_10_0 (October 17, 2023)
• Intro_To_FNN_v1_0_10_0 (October 17, 2023)

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📰 News

• Single cell subdomain re-launch: Unified and feedback-driven (October 12, 2023)

📚 Tutorials

• QGIS Web Feature Services (October 11, 2023)

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📰 News

• New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets (October 05, 2023)

🛤️ Learning pathways

• Introduction to Galaxy and Single Cell RNA Sequence analysis (October 04, 2023)

📚 Tutorials

• Filter, plot, and explore single cell RNA-seq data with Seurat (R) (October 02, 2023)

❓ Faqs

• How can I talk with other users? (October 08, 2023)
• Use our Single Cell Omics Lab (October 08, 2023)

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❓ Faqs

• What licenses are used in the GTN? (September 28, 2023)

🧑‍🏫 Contributors

• @tuncK (October 01, 2023)
• @kysrpex (October 01, 2023)

💰 Grants

• @fairease (October 01, 2023)
• @eurosciencegateway (October 01, 2023)
• @elixir-uk-dash (October 01, 2023)

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❓ Faqs

• Debugging Memory Leaks (September 22, 2023)

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🛤️ Learning pathways

• Introductory SQL (September 13, 2023)
• Introductory Python (September 13, 2023)

📚 Tutorials

• FAIR Bioimage Metadata (September 13, 2023)
• REMBI - Recommended Metadata for Biological Images – metadata guidelines for bioimaging data (September 13, 2023)

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📚 Tutorials

• One protein along the UniProt page (September 07, 2023)

🖼️ Slides

• Automated Cell Annotation (September 04, 2023)

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🧑‍🏫 Contributors

• @tb143 (September 01, 2023)
• @sonalhenson (September 01, 2023)
• @smza (September 01, 2023)
• @lisanna (September 01, 2023)

💰 Grants

• @biont (September 01, 2023)

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📚 Tutorials

• Filter, plot and explore single-cell RNA-seq data with Scanpy (Python) (August 25, 2023)

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🧑‍🏫 Contributors

• @Laura190 (August 01, 2023)
• @kostrykin (August 01, 2023)
• @katherine-d21 (August 01, 2023)

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📰 News

• New Feature: GTN User Preferences (July 20, 2023)

📚 Tutorials

• Scanpy Parameter Iterator (July 19, 2023)

🛠️ Workflows

• Scanpy Parameter Iterator workflow full (imported from URL) (July 19, 2023)

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🛤️ Learning pathways

• Discovering Galaxy through climate analysis (July 13, 2023)

📚 Tutorials

• SARS-CoV-2 Viral Sample Alignment and Variant Visualization (July 10, 2023)

🖼️ Slides

• Identification of non-canonical ORFs and their potential biological function (July 11, 2023)

❓ Faqs

• Quality Scores (July 10, 2023)

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📰 News

• AI4Life teams up with GTN to enhance training resources (June 27, 2023)

🛤️ Learning pathways

• Genome annotation for prokaryotes (June 27, 2023)
• Genome annotation for eukaryotes (June 27, 2023)
• Metagenomics data processing and analysis for microbiome (June 27, 2023)
• From R to Machine Learning; an introductory course (June 27, 2023)

🧑‍🏫 Contributors

• @SNG888 (July 01, 2023)

💰 Grants

• @ai4life (July 01, 2023)

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📰 News

• ELIXIR-UK Fellow Launches New FAIR Data Management Training (June 21, 2023)

📚 Tutorials

• ERGA post-assembly QC (June 23, 2023)

❓ Faqs

• Do the pipelines work with both isolates and direct from raw meat? or only isolate? (June 21, 2023)
• Can we also use this workflow on Illumina raw reads? (June 21, 2023)
• Can we use snippy pipeline instead for the phylogenetic analysis? (June 21, 2023)
• Isn't it awkward to find so many humans sequences there, since we filter for them before? (June 21, 2023)
• Is there a way to filter on the Kalimari database? (June 21, 2023)
• From where can I import other genomes? (June 21, 2023)
• 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..)? (June 21, 2023)
• What does `^.*Gallus|Homo|Bos.*$` mean? (June 21, 2023)
• 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? (June 21, 2023)

🛠️ Workflows

• Post-assembly workflow (June 23, 2023)

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📚 Tutorials

• Data visualisation Olympics - Visualization in R (June 16, 2023)
• Data Manipulation Olympics - SQL (June 16, 2023)
• Data Manipulation Olympics - JQ (June 16, 2023)
• Train-the-Trainer: putting it all together (June 12, 2023)

❓ Faqs

• Converting the datatype of a collection (June 15, 2023)
• Changing the datatype of a collection (June 15, 2023)

🛠️ Workflows

• Filter, Plot and Explore Single-cell RNA-seq Data updated (June 13, 2023)

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📰 News

• New Feature: Pan-Galactic Tool Search (June 07, 2023)

❓ Faqs

• Why host your materials with the GTN? (June 07, 2023)

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📰 News

• GTN Celebrates Pride Month: Alan Hart & M. Tuberculosis (June 01, 2023)

📚 Tutorials

• FAIR Galaxy Training Material (May 30, 2023)
• FAIR data management solutions (May 30, 2023)
• FAIR in a nutshell (May 30, 2023)

🧑‍🏫 Contributors

• @TanguyGen (June 01, 2023)
• @robertmeller (June 01, 2023)
• @nakucher (June 01, 2023)
• @katherinecox (June 01, 2023)
• @jtleek (June 01, 2023)
• @hexhowells (June 01, 2023)
• @ehumph (June 01, 2023)
• @dechendb (June 01, 2023)
• @cutsort (June 01, 2023)
• @cansavvy (June 01, 2023)
• @avahoffman (June 01, 2023)

💰 Grants

• @nhgri-gdscn (June 01, 2023)
• @nhgri-anvil (June 01, 2023)
• @elixir-fair-data (June 01, 2023)

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📚 Tutorials

• RO-Crate - Introduction (May 23, 2023)

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📰 News

• New Galaxy training: Genome-wide alternative splicing analysis (May 15, 2023)

🛤️ Learning pathways

• Train the Trainers (May 17, 2023)

📚 Tutorials

• Genome-wide alternative splicing analysis (May 17, 2023)
• RNA-seq Alignment with STAR (May 15, 2023)
• Pox virus genome analysis from tiled-amplicon sequencing data (May 15, 2023)

🖼️ Slides

• Contribute to the BioImage.IO models (May 18, 2023)

🎥 Recordings

• Recording of Understanding Galaxy history system (May 19, 2023)
• Recording of Quality Control (May 19, 2023)
• Recording of Pre-processing of 10X Single-Cell RNA Datasets (May 19, 2023)
• Recording of 16S Microbial Analysis with mothur (short) (May 19, 2023)
• Recording of Creating Galaxy tools from Conda Through Deployment (May 18, 2023)
• Recording of Introduction to Genomics and Galaxy (May 18, 2023)
• Recording of Metatranscriptomics analysis using microbiome RNA-seq data (short) (May 17, 2023)
• Recording of Metatranscriptomics analysis using microbiome RNA-seq data (May 17, 2023)
• Recording of Large genome assembly and polishing (May 16, 2023)
• Recording of Taxonomic Profiling and Visualization of Metagenomic Data (May 16, 2023)
• Recording of Reference-based RNA-Seq data analysis (May 15, 2023)

🛠️ Workflows

• Preprocessing of 10X scRNA-seq data (May 19, 2023)
• GTN_differential_isoform_expression (May 17, 2023)
• Trajectory analysis using Monocle3 - full tutorial workflow (May 16, 2023)
• pox-virus-tiled-amplicon-ref-masking (May 15, 2023)

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📰 News

• BY-COVID and RO-Crate collaboration brings new topic: FAIR Data, Workflows & More (May 11, 2023)

📚 Tutorials

• Submitting workflows to LifeMonitor (May 11, 2023)
• Workflow Run RO-Crate Introduction (May 11, 2023)
• RO-Crate in Python (May 11, 2023)
• Best practices for workflows in GitHub repositories (May 11, 2023)
• Exporting Workflow Run RO-Crates from Galaxy (May 11, 2023)
• Mass spectrometry: GC-MS data processing (with XCMS, RAMClustR, RIAssigner, and matchms) (May 08, 2023)

🖼️ Slides

• Welcome to the BioImage Model Zoo (May 11, 2023)

🎥 Recordings

• Recording of Genome annotation with Funannotate (May 12, 2023)
• Recording of Trio Analysis using Synthetic Datasets from RD-Connect GPAP (May 12, 2023)
• Recording of Masking repeats with RepeatMasker (May 10, 2023)
• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (May 10, 2023)
• Recording of Identification of the micro-organisms in a beer using Nanopore sequencing (May 10, 2023)
• Recording of Using dataset collections (May 09, 2023)
• Recording of Combining single cell datasets after pre-processing (May 09, 2023)

❓ Faqs

• Galaxy UI is slow (May 11, 2023)
• Tool missing from Galaxy (May 11, 2023)
• Debugging tool memory errors (May 11, 2023)
• Debugging tool errors (May 11, 2023)
• Blank page or no CSS/JavaScript (May 11, 2023)
• Database Issues (May 11, 2023)

🛠️ Workflows

• sort-and-change-case (imported from uploaded file) (May 11, 2023)
• GC MS using XCMS (May 08, 2023)

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🛤️ Learning pathways

• Introduction to Galaxy and Ecological data analysis (May 03, 2023)

📚 Tutorials

• Taxonomic Profiling and Visualization of Metagenomic Data (May 03, 2023)

🎥 Recordings

• Recording of Assembly of metagenomic sequencing data (May 02, 2023)
• Recording of Galaxy Basics for everyone (May 01, 2023)
• Recording of Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition (May 01, 2023)

❓ Faqs

• Kraken2 and the k-mer approach for taxonomy classification (May 03, 2023)

🛠️ Workflows

• Taxonomic Profiling and Visualization of Metagenomic Data (May 03, 2023)

🧑‍🏫 Contributors

• @npechl (May 01, 2023)

💰 Grants

• @h2020-defend (May 01, 2023)
• @fnso2019 (May 01, 2023)

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📚 Tutorials

• Supervised Learning with Hyperdimensional Computing (April 28, 2023)
• Pre-processing of 10X Single-Cell ATAC-seq Datasets (April 24, 2023)

❓ Faqs

• Pick the right Concatenate tool (April 28, 2023)

🛠️ Workflows

• scATAC-seq FASTQ to Count Matrix (April 24, 2023)
• scATAC-seq Count Matrix Filtering (April 24, 2023)

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📰 News

• New Feature: my.galaxy.training (April 20, 2023)
• New Feature: Click-to-run Workflows (April 19, 2023)
• New Feature: GTN Rdoc (April 19, 2023)
• New Feature: Persistent URLs (PURLs) / Shortlinks (April 19, 2023)

📚 Tutorials

• Monitoring Galaxy and Pulsar with Sentry (April 19, 2023)

🖼️ Slides

• BioImage Model Zoo: Advanced models in one-click (April 18, 2023)

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📰 News

• New Feature: Learning Pathways! (April 13, 2023)

🛤️ Learning pathways

• Introduction to Galaxy and Sequence analysis (April 13, 2023)
• Admin Training Course (April 13, 2023)

📚 Tutorials

• Customizing the look of Galaxy (Manual) (April 16, 2023)
• Deploying a Beacon v1 in Galaxy (April 16, 2023)
• Customizing the look of Galaxy (April 16, 2023)
• Setting up Celery Workers for Galaxy (April 16, 2023)
• Server Maintenance: Cleanup, Backup, and Restoration (April 16, 2023)
• Sentinel 2 biodiversity (April 13, 2023)
• Inferring single cell trajectories with Monocle3 (R) (April 12, 2023)
• Obis marine indicators (April 11, 2023)

🎥 Recordings

• Recording of RO-Crate - Introduction (April 14, 2023)
• Recording of Inferring single cell trajectories with Monocle3 (April 11, 2023)

❓ Faqs

• Mapping Jobs to Specific Storage By User (April 16, 2023)
• Failing all jobs from a specific user (April 16, 2023)
• Library Permission Issues (April 16, 2023)
• Time to git commit (April 16, 2023)
• Using Git With Ansible Vaults (April 16, 2023)
• Opening a split screen in byobu (April 16, 2023)
• How do I see what variables are set for a host? (April 16, 2023)
• Defining a Learning Pathway (April 13, 2023)

🛠️ Workflows

• Sentinel 2 example (April 13, 2023)
• Marine Omics visualisation (April 11, 2023)

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🧑‍🏫 Contributors

• @stain (April 01, 2023)
• @sophia120199 (April 01, 2023)
• @simleo (April 01, 2023)
• @ptsefton (April 01, 2023)
• @pauldg (April 01, 2023)
• @kikkomep (April 01, 2023)
• @kinow (April 01, 2023)
• @ilveroluca (April 01, 2023)
• @ElectronicBlueberry (April 01, 2023)

💰 Grants

• @eosc-life (April 01, 2023)
• @by-covid (April 01, 2023)

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📰 News

• New Feature: Trainer Directory! (Add yourself today!) (March 21, 2023)

📚 Tutorials

• Production d'indicateurs champs de bloc (March 21, 2023)

❓ Faqs

• Créer un nouvel history (March 21, 2023)
• Importer via un lien (March 21, 2023)
• Changer le type de données (March 21, 2023)

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📚 Tutorials

• Reference Data with Data Managers (March 17, 2023)

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📚 Tutorials

• Large genome assembly and polishing (March 06, 2023)

❓ Faqs

• Import workflows from WorkflowHub (March 06, 2023)
• Importing and launching a GTN workflow (March 06, 2023)

🛠️ Workflows

• kmer counting - meryl - upgraded (March 06, 2023)
• Trim and filter reads - fastp - upgraded (March 06, 2023)
• Racon polish with long reads, x4 - upgraded (March 06, 2023)
• Racon polish with Illumina reads (R1 only), x2 - upgraded (March 06, 2023)
• Data QC - upgraded (March 06, 2023)
• Combined workflows for large genome assembly - upgraded (March 06, 2023)
• Assess genome quality - upgraded (March 06, 2023)
• Assembly with Flye - upgraded (March 06, 2023)
• Assembly polishing - upgraded (March 06, 2023)

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🧑‍🏫 Contributors

• @rlibouba (March 01, 2023)
• @maximskorik (March 01, 2023)
• @GitFab93 (March 01, 2023)
• @cfusterbarcelo (March 01, 2023)
• @andrewsnelgrove (March 01, 2023)

💰 Grants

• @CINECA-Project (March 01, 2023)

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🛠️ Workflows

• Gene-based Pathogen Identification (February 23, 2023)

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📚 Tutorials

• End-to-End Tissue Microarray Image Analysis with Galaxy-ME (February 14, 2023)

🛠️ Workflows

• GTN_Exemplar_002_TMA_workflow (February 14, 2023)

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📰 News

• What are the most used tools in the GTN? (February 08, 2023)

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📰 News

• GTN Celebrates Black History Month (February 02, 2023)

❓ Faqs

• Compatible Versions of Galaxy (February 03, 2023)

🧑‍🏫 Contributors

• @vladvisan (February 01, 2023)
• @paulzierep (February 01, 2023)
• @alliecreason (February 01, 2023)

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📰 News

• New Tutorial: Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition (January 26, 2023)
• New Feature: Prometheus Metrics endpoint (January 24, 2023)
• New GTN Feature Tag-based Topics enables new SARS-CoV-2 topic (January 23, 2023)

📚 Tutorials

• Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition (January 26, 2023)
• Removing the effects of the cell cycle (January 25, 2023)

🛠️ Workflows

• Nanopore Preprocessing (January 26, 2023)
• Cell Cycle Regression Workflow (January 25, 2023)

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📚 Tutorials

• Bulk matrix to ESet | Creating the bulk RNA-seq dataset for deconvolution (January 20, 2023)
• Matrix Exchange Format to ESet | Creating a single-cell RNA-seq reference dataset for deconvolution (January 20, 2023)
• Comparing inferred cell compositions using MuSiC deconvolution (January 20, 2023)
• NCBI BLAST+ against the MAdLand (January 16, 2023)

🛠️ Workflows

• MuSiC-Deconvolution: Compare (January 20, 2023)
• MuSiC-Deconvolution: Data generation | bulk | ESet (January 20, 2023)
• MuSiC-Deconvolution: Data generation | sc | metadata (January 20, 2023)
• MuSiC-Deconvolution: Data generation | sc | matrix + ESet (January 20, 2023)
• gpu_jupytool (January 18, 2023)

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📰 News

• New GTN paper: "Galaxy Training: A powerful framework for teaching!" (January 10, 2023)

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📚 Tutorials

• Champs blocs indicators (January 04, 2023)

🛠️ Workflows

• Champs blocs indicators (January 04, 2023)
• workflow-generate-dataset-for-assembly-tutorial (January 02, 2023)

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🧑‍🏫 Contributors

• @mcharleston (January 01, 2023)
• @GabrielaLopez (January 01, 2023)
• @Camila-goclowski (January 01, 2023)
• @adamtaranto (January 01, 2023)

💰 Grants

• @elixir-converge (January 01, 2023)

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📚 Tutorials

• Assembly of metagenomic sequencing data (December 05, 2022)

🛠️ Workflows

• Metagenomics assembly tutorial workflow (December 05, 2022)

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📰 News

• New Tutorial Suite: Deconvolution with MuSiC, from public data to disease interrogation! (November 29, 2022)

🧑‍🏫 Contributors

• @miRlyKayleigh (December 01, 2022)
• @deeptivarshney (December 01, 2022)

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📚 Tutorials

• Avian influenza viral strain analysis from gene segment sequencing data (November 21, 2022)

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📰 News

• New Topic: Single Cell Analysis! (November 18, 2022)

❓ Faqs

• How do I know what protocol my data was sequenced with? (November 18, 2022)

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📚 Tutorials

• Python - Coding Style (November 03, 2022)

❓ Faqs

• Creating a GTN News post (November 01, 2022)

🧑‍🏫 Contributors

• @patrick-austin (November 01, 2022)
• @leandro-liborio (November 01, 2022)
• @joelvdavies (November 01, 2022)
• @elichad (November 01, 2022)
• @anish-mudaraddi (November 01, 2022)

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📚 Tutorials

• Visualize EBV cube data with Panoply netCDF viewer (October 28, 2022)
• Cleaning GBIF data for the use in Ecology (October 28, 2022)
• Visualization of Climate Data using NetCDF xarray Map Plotting (October 26, 2022)

❓ Faqs

• Importing data from remote files (October 26, 2022)

🛠️ Workflows

• GBIF data Quality check and filtering workflow Feb-2020 (October 28, 2022)
• Xarray_Map_Plotting_Workflow (October 26, 2022)

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📚 Tutorials

• Preparing genomic data for phylogeny reconstruction (October 21, 2022)
• Python - Multiprocessing (October 19, 2022)
• Python - Testing (October 19, 2022)
• Virtual Environments For Software Development (October 19, 2022)
• Python - Type annotations (October 19, 2022)
• Conda Environments For Software Development (October 19, 2022)
• Teaching Python (October 19, 2022)

❓ Faqs

• How to set Data Privacy Features? (October 21, 2022)
• Multipile similar tools available (October 19, 2022)
• How to update account preferences? (October 19, 2022)
• Can I create multiple Galaxy accounts? (October 19, 2022)
• Beware of Cuts (October 18, 2022)

🛠️ Workflows

• preparing genomic data for phylogeny recostruction (GTN) (October 21, 2022)

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📚 Tutorials

• Somatic Variant Discovery from WES Data Using Control-FREEC (October 05, 2022)

🛠️ Workflows

• Somatic-Variant-Discovery-from-WES-Data-Using-Control-FREEC (October 05, 2022)

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📚 Tutorials

• Inferring single cell trajectories with Monocle3 (September 30, 2022)
• Identification of the micro-organisms in a beer using Nanopore sequencing (September 29, 2022)
• Evaluating and ranking a set of pathways based on multiple metrics (September 26, 2022)

🖼️ Slides

• Trajectory analysis (September 30, 2022)

🎥 Recordings

• Recording of Evaluating and ranking a set of pathways based on multiple metrics (September 26, 2022)

❓ Faqs

• What is Taxonomy? (September 29, 2022)
• FASTQ format (September 29, 2022)

🛠️ Workflows

• Monocle3 workflow (September 30, 2022)
• AnnData object to Monocle input files (September 30, 2022)
• Identification of the micro-organisms in a beer using Nanopore sequencing (September 29, 2022)
• Pathway Analysis (September 26, 2022)

🧑‍🏫 Contributors

• @MarisaJL (October 01, 2022)
• @d-salgado (October 01, 2022)

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📚 Tutorials

• Long non-coding RNAs (lncRNAs) annotation with FEELnc (September 23, 2022)
• Design and plan session, course, materials (September 23, 2022)
• Principles of learning and how they apply to training and teaching (September 23, 2022)
• Motivation and Demotivation (September 23, 2022)
• Training techniques to enhance learner participation and engagement (September 23, 2022)
• Assessment and feedback in training and teachings (September 23, 2022)
• Teaching experiences (September 23, 2022)
• Deploying Tailscale/Headscale for private mesh networking (September 21, 2022)
• Deploying Wireguard for private mesh networking (September 21, 2022)

🖼️ Slides

• Overview of the Galaxy Training Material for Instructors (September 23, 2022)

❓ Faqs

• GTN Stats (September 23, 2022)
• Adding workflow tests with Planemo (September 22, 2022)

🛠️ Workflows

• Long non-coding RNAs (lncRNAs) annotation with FEELnc (September 23, 2022)

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❓ Faqs

• How does the GTN ensure accessibility? (September 12, 2022)

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📰 News

• New Tutorial: Data Manipulation (September 11, 2022)

📚 Tutorials

• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin (September 08, 2022)
• Combining single cell datasets after pre-processing (September 08, 2022)
• Comparative gene analysis in unannotated genomes (September 08, 2022)

❓ Faqs

• Why is Alevin is not working? (September 08, 2022)

🛠️ Workflows

• Comparative gene analysis (September 08, 2022)

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❓ Faqs

• Contributing a Jupyter Notebook to the GTN (September 01, 2022)

🧑‍🏫 Contributors

• @teresa-m (September 01, 2022)
• @ppalagi (September 01, 2022)
• @khaled196 (September 01, 2022)
• @hrukkudyr (September 01, 2022)
• @allegravia (September 01, 2022)

💰 Grants

• @epsrc-training-grant (September 01, 2022)

🏢 Organisations

• @elixir-goblet-ttt (September 01, 2022)

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📚 Tutorials

• Genome Assembly Quality Control (August 26, 2022)
• Refining Genome Annotations with Apollo (eukaryotes) (August 22, 2022)

🖼️ Slides

• Genome assembly quality control. (August 26, 2022)

🛠️ Workflows

• Genome Assembly Quality Control (August 26, 2022)

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🧑‍🏫 Contributors

• @paulineauffret (August 01, 2022)
• @chklopp (August 01, 2022)

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📚 Tutorials

• Functional annotation of protein sequences (July 20, 2022)
• Data Manipulation Olympics (July 20, 2022)

❓ Faqs

• Galaxy Admin Training Path (July 22, 2022)
• Regular Expressions 101 (July 20, 2022)

🛠️ Workflows

• Functional annotation (July 20, 2022)
• GTN Tutorial: Data manipulation Olympics - all steps and exercises (July 20, 2022)

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📚 Tutorials

• Writing Automated Tests for Galaxy (July 15, 2022)

🖼️ Slides

• Galaxy and Celery (July 16, 2022)

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📚 Tutorials

• Variant Calling Workflow (July 07, 2022)
• How I learned to stop worrying and love the systemd (July 06, 2022)
• Version Control with Git (July 06, 2022)

🎥 Recordings

• Recording of Using Workflow Parameters (July 06, 2022)
• Recording of Workflow Reports (July 06, 2022)

❓ Faqs

• Flatten a list of list of paired datasets into a list of paired datasets (July 06, 2022)

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🧑‍🏫 Contributors

• @mira-miracoli (July 01, 2022)
• @CameronFRWatson (July 01, 2022)

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📚 Tutorials

• Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools (June 23, 2022)
• Scripting Galaxy using the API and BioBlend (June 23, 2022)

🎥 Recordings

• Recording of Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools (June 23, 2022)

🛠️ Workflows

• RetroSynthesis (June 23, 2022)

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📚 Tutorials

• Basics of using Git from the Command Line (June 16, 2022)

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❓ Faqs

• How many mules? (June 07, 2022)
• Customising the welcome page (June 07, 2022)
• Is YAML sensitive to True/true/False/false (June 07, 2022)
• How do I know what I can do with a role? What variables are available? (June 07, 2022)
• What is the difference between the roles with `role:` prefix and without? (June 07, 2022)
• Error: "skipping: no hosts matched" (June 07, 2022)
• What if you forget `--diff`? (June 07, 2022)
• Define once, reference many times (June 07, 2022)
• Variable connection (June 07, 2022)

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📰 News

• New Tutorial: Workflow Reports (June 02, 2022)

📚 Tutorials

• Workflow Reports (June 02, 2022)
• GTN Metadata (June 02, 2022)

🛠️ Workflows

• GTN Training: Workflow Reports (June 02, 2022)
• GTN Training: Workflow Reports - Galaxy 101 For Everyone (June 02, 2022)

🧑‍🏫 Contributors

• @wee-snufkin (June 01, 2022)
• @Quickbeasts51429 (June 01, 2022)

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📰 News

• GTN Metadata Schemas (May 20, 2022)

📚 Tutorials

• Adding Quizzes to your Tutorial (May 19, 2022)
• Trio Analysis using Synthetic Datasets from RD-Connect GPAP (May 19, 2022)

🛠️ Workflows

• Trio Analysis Tutorial (May 19, 2022)

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📚 Tutorials

• Designing plasmids encoding predicted pathways by using the BASIC assembly method (May 12, 2022)

🎥 Recordings

• Recording of Designing plasmids encoding predicted pathways by using the BASIC assembly method (May 11, 2022)

🛠️ Workflows

• Genetic Design (BASIC Assembly) (May 12, 2022)

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❓ Faqs

• Quotas for datasets and histories (May 06, 2022)
• Working with deleted datasets (May 06, 2022)

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📚 Tutorials

• Python - Introductory Graduation (April 25, 2022)
• Python - Subprocess (April 25, 2022)
• Python - Basic Types & Type Conversion (April 25, 2022)
• Python - Flow Control (April 25, 2022)
• Python - Loops (April 25, 2022)
• Python - Math (April 25, 2022)
• Python - Globbing (April 25, 2022)
• Python - Files & CSV (April 25, 2022)
• Python - Functions (April 25, 2022)
• Python - Argparse (April 25, 2022)
• Python - Try & Except (April 25, 2022)
• Python - Lists & Strings & Dictionaries (April 25, 2022)

🛠️ Workflows

• QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN (April 25, 2022)

🧑‍🏫 Contributors

• @Sofokli5 (May 01, 2022)
• @chensy96 (May 01, 2022)
• @brigidagallone (May 01, 2022)

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❓ Faqs

• Tool doesn't recognize input datasets (April 23, 2022)
• Understanding 'canceled by admin' or cluster failure error messages (April 23, 2022)
• Understanding ValueError error messages (April 22, 2022)
• Understanding walltime error messages (April 22, 2022)
• Understanding 'exceeds memory allocation' error messages (April 22, 2022)
• Understanding input error messages (April 22, 2022)
• Mismatched Chromosome identifiers and how to avoid them (April 22, 2022)
• Ways to use Galaxy (April 22, 2022)
• Working with very large fastq datasets (April 22, 2022)
• Working with very large fasta datasets (April 22, 2022)
• Understanding Datatypes (April 22, 2022)
• Working with GFF GFT GTF2 GFF3 reference annotation (April 22, 2022)
• Finding BAM dataset identifiers (April 22, 2022)
• Troubleshooting Custom Genome fasta (April 22, 2022)
• Sorting Reference Genome (April 19, 2022)
• How to hide datasets? (April 19, 2022)
• Where is the tool help? (April 18, 2022)

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📰 News

• New Tutorial Feature: Choose Your Own Tutorial (April 12, 2022)

❓ Faqs

• How to use Custom Reference Genomes? (April 17, 2022)
• Directly obtaining UCSC sourced *genome* identifiers (April 17, 2022)
• How do I create an account on a public Galaxy instance? (April 15, 2022)
• Finding and working with "Histories shared with me" (April 15, 2022)
• Best practices for loading fastq data into Galaxy (April 15, 2022)
• Purging datasets (April 14, 2022)
• Extended Help for Differential Expression Analysis Tools (April 14, 2022)
• NCBI SRA sourced fastq data (April 14, 2022)
• How do `fastq.gz` datasets relate to the `.fastqsanger` datatype metadata assignment? (April 14, 2022)
• Data retrieval with “NCBI SRA Tools” (fastq-dump) (April 14, 2022)
• Using compressed fastq data as tool inputs (April 14, 2022)
• Does your account usage quota seem incorrect? (April 14, 2022)
• How to find and correct tool errors related to Metadata? (April 14, 2022)
• How to format fastq data for tools that require .fastqsanger format? (April 13, 2022)
• Identifying and formatting Tabular Datasets (April 13, 2022)
• Incomplete Dataset Download (April 13, 2022)
• How can I reduce quota usage while still retaining prior work (data, tools, methods)? (April 13, 2022)
• Sorting Tools (April 13, 2022)
• How can I upload data using EBI-SRA? (April 13, 2022)
• How can I load data? (April 13, 2022)
• Datasets not downloading at all (April 13, 2022)
• Downloading datasets using command line (April 13, 2022)
• Unsharing unwanted histories (April 13, 2022)
• Find all Histories and purge (aka permanently delete) (April 12, 2022)

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📚 Tutorials

• A Docker-based interactive Jupyterlab powered by GPU for artificial intelligence in Galaxy (April 06, 2022)
• Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data (April 06, 2022)

❓ Faqs

• Reporting usage problems, security issues, and bugs (April 06, 2022)
• Transfer entire histories from one Galaxy server to another (April 06, 2022)
• Moving datasets between Galaxy servers (April 06, 2022)
• Finding Datasets (April 06, 2022)
• Forgot Password (April 05, 2022)
• Changing acount email or password (April 04, 2022)

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❓ Faqs

• Different dataset icons and their usage (April 02, 2022)
• Finding Histories (April 01, 2022)
• Downloading histories (April 01, 2022)
• Downloading datasets (April 01, 2022)
• Understanding job statuses (March 30, 2022)
• Will my jobs keep running? (March 30, 2022)

🧑‍🏫 Contributors

• @samanthaanjei (April 01, 2022)
• @Nurzhamalyrys (April 01, 2022)
• @JasperO98 (April 01, 2022)
• @beachyesh (April 01, 2022)
• @AnomalyCodes (April 01, 2022)

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📰 News

• New Tutorial: VGP assembly pipeline (March 14, 2022)

📚 Tutorials

• Tree thinking for tuberculosis evolution and epidemiology (March 16, 2022)
• Identifying tuberculosis transmission links: from SNPs to transmission clusters (March 16, 2022)

❓ Faqs

• TB Variant Report crashes (with an error about KeyError: 'protein') (March 17, 2022)

🛠️ Workflows

• Mtb phylogeny (March 16, 2022)
• From VCFs to SNP distance matrix (March 16, 2022)
• From Fastqs to VCFs and BAMs (March 16, 2022)
• From BAMs to drug resistance prediction with TB-profiler (March 16, 2022)

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🖼️ Slides

• Introduction to CRISPR screen analysis (March 07, 2022)

🎥 Recordings

• Recording of Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step (March 13, 2022)
• Recording of Creating Galaxy tools from Conda Through Deployment (March 11, 2022)
• Recording of Performant Uploads with TUS (March 11, 2022)
• Recording of Introduction to CRISPR screen analysis (March 10, 2022)
• Recording of CRISPR screen analysis (March 10, 2022)

❓ Faqs

• Using IGV with Galaxy (March 13, 2022)

🛠️ Workflows

• Analysis using MDAnalysis (March 07, 2022)

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📚 Tutorials

• Galaxy Interactive Tools (March 02, 2022)
• Performant Uploads with TUS (March 01, 2022)
• Biodiversity data exploration (March 01, 2022)
• Metabarcoding/eDNA through Obitools (February 28, 2022)

🎥 Recordings

• Recording of Genome annotation with Funannotate (March 03, 2022)
• Recording of Masking repeats with RepeatMasker (March 03, 2022)
• Recording of Pangeo Notebook in Galaxy - Introduction to Xarray (March 03, 2022)
• Recording of Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools (March 03, 2022)
• Recording of Biodiversity data exploration (March 03, 2022)
• Recording of Metabarcoding/eDNA through Obitools (March 03, 2022)
• Recording of Compute and analyze biodiversity metrics with PAMPA toolsuite (March 03, 2022)
• Recording of Galaxy Installation with Ansible (March 01, 2022)

❓ Faqs

• Why do we have a variant mapping file when it is not being used in the workflow? (March 03, 2022)
• How many search engines can you use in SearchGUI? (March 03, 2022)
• What kind of variants are seen in the output? (March 03, 2022)
• The workflows contain several Query tabular for text manipulation, is there a tutorial for that? (March 03, 2022)
• Can I use these workflows on datasets generated from our laboratory? (March 03, 2022)
• Example histories for the proteogenomics tutorials (March 03, 2022)
• In the MVP platform, is it possible to view the genomic location of all the peptides? (March 03, 2022)
• Why do we change the chromosome names in the Ensembl GTF to match the UCSC genome reference? (March 03, 2022)
• Is it possible to replace the existing alignment tools such as HISAT and Freebayes with other tools? (March 03, 2022)
• Downloading the files from the NCBI server fails or takes too long. (March 02, 2022)
• The UMAP Plots errors out sometimes? (March 02, 2022)
• UCSC import: what should my file look like? (March 02, 2022)
• Viewing tool logs (`stdout` and `stderr`) (March 02, 2022)
• Organizing the tool panel (March 02, 2022)
• Do I have to run the tools in the order of the tutorial? (March 02, 2022)
• Does MaxQuant in Galaxy support TMT, iTRAQ, etc.? (March 02, 2022)
• Is it possible to subsample some samples if you have more reads? (March 02, 2022)
• MSStats: what does ‘compare groups = yes’ mean? And the comparison matrix to define the contrast between the 2 groups? (March 02, 2022)
• What is a SNP? (March 02, 2022)
• How many proteins can be identified and quantified in shotgun proteomics? (March 02, 2022)
• My snippy is running for a very long time. Is this normal? (March 02, 2022)
• Additional resources to learn more about proteomic data analysis (March 02, 2022)
• Are Barcodes always on R1 and Sequence data on R2? (March 02, 2022)
• Why does the query `SRR11772204 OR SRR11597145 OR SRR11667145` in the Run Selector not return any results? (March 02, 2022)
• For the “quantitation method” what is the default if I just leave it as “None”? Label free? (March 02, 2022)
• Can we polish the assembly with long reads too? (March 02, 2022)
• Running more than one round of Pilon polishing (March 02, 2022)
• When I get a warning for base per sequence content, what should I do? (March 02, 2022)
• Does MaxQuant give as output possibility the PSMs and PEPs? (March 02, 2022)
• What does it mean to normalize the LFQ intensities? (March 02, 2022)
• MultiQC error for your FastQC reports? (March 02, 2022)
• If you use a mqpar file, can you include modifications that are not in the Galaxy version? For instance, propionamide (Cys alkylation by acrylamide). (March 02, 2022)
• Do you need to merge the databases? Because you can select multiple fasta files in MaxQuant. (March 02, 2022)
• When can you use (or cannot use) Match between runs in MaxQuant? (March 02, 2022)
• JBrowse is taking a long time to complete? (March 02, 2022)
• The input for a tool is not listed in the dropdown (March 02, 2022)
• Most tools seem to have options for assembly using long and short reads, what are the pros and cons of the different tools? (March 02, 2022)
• Changing the heatmap colours (March 02, 2022)
• What is Gene Ontology (GO)? (March 02, 2022)
• Where can I read more about Quality Control of data? (March 02, 2022)
• What is the principle of an enrichment analysis? (March 02, 2022)
• FASTQ files: `fastq` vs `fastqsanger` vs .. (March 02, 2022)
• Compressed FASTQ files, (`*.gz`) (March 02, 2022)
• Do we need a contaminant FASTA for MQ in galaxy? (March 02, 2022)
• The Build tissue-specific expression dataset tool (step one) exits with an error code. (March 02, 2022)
• What is the advantage of breaking down protein to peptides before mass spec? (March 02, 2022)
• In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library? (March 02, 2022)
• Why does my assembly graph in Bandage look different to the one pictured in the tutorial? (March 02, 2022)
• AnnData Import/ AnnData Manipulate not working? (March 02, 2022)
• Is it possible to use alternative tools to those proposed in the tutorial? (March 02, 2022)
• Automatically trim adapters (without providing custom sequences) (March 02, 2022)
• It says I already have an account when registering for ecology.usegalaxy.eu (March 02, 2022)
• How to read a Diff (March 01, 2022)
• Using tutorial mode (March 01, 2022)
• Can EncyclopeDIA be run on a DIA-MS dataset without a spectral library? (February 28, 2022)
• Why don't we perform the V-Search dereplication step of ASaiM for metatrascriptomic data? (February 28, 2022)
• Changing the tool version (February 28, 2022)
• Can this ASaiM workflow be used for single-end data? (February 28, 2022)
• When I try to run a Selenium test, I get an error (February 28, 2022)
• Is the ToolFactory a complete replacement for manual tool building? (February 28, 2022)
• On the Scanpy PlotEmbed step, my object doesn’t have Il2ra or Cd8b1 or Cd8a etc. (February 28, 2022)
• On Scanpy PlotEmbed, the tool is failing (February 28, 2022)
• Only one Planemo test runs at a time. Why doesn't the server allow more than one at once? (February 28, 2022)
• I cannot run client tests because yarn is not installed. (February 28, 2022)
• Can we use the ASaiM-MT workflow on multiple input files at the same time? (February 28, 2022)
• Why do I need that big (~5GB!) complicated Docker thing - can I just install the ToolFactory into our local galaxy server from the toolshed? (February 28, 2022)
• First job I submitted remains grey or running for a long time - is it broken? (February 28, 2022)
• Where can I get planemo? (February 28, 2022)
• What file/data formats are defined for I/O in Galaxy? (February 28, 2022)
• My Scanpy FindMarkers step is giving me an empty table (February 28, 2022)
• Why do we use FASTQ interlacer and not the FASTQ joiner? (February 28, 2022)
• `docker-compose up` fails with error `/usr/bin/start.sh: line 133: /galaxy/.venv/bin/uwsgi: No such file or directory` (February 28, 2022)
• My Rscript tool generates a strange R error on STDOUT about an invalid operation on a closure called 'args' ? (February 28, 2022)
• I get a different number of transcripts with a significant change in gene expression between the G1E and megakaryocyte cellular states. Why? (February 28, 2022)
• I want to use a collection for outputs but it always passes the test even when the script fails. Why? (February 28, 2022)
• The folder `recipes/belerophon/` and the file `meta.yaml` already exist in bioconda? (February 28, 2022)
• Why is Alevin is not working? (February 28, 2022)
• What advantages does a Chromatogram Library have over a DDA-generated library or predicted spectral library? (February 28, 2022)
• If a Tool is Missing (February 28, 2022)
• Are these data free to use and download? (February 28, 2022)
• Contacting Galaxy Administrators (February 28, 2022)
• Where do I get more support? (February 28, 2022)
• What should I do special if on usegalaxy.be? (February 28, 2022)
• Can I use alternative tools for the Quantification step? (February 28, 2022)
• Why don't the aligned read files have quality scores? (February 28, 2022)
• When will aligned read objects be available for other data types? (February 28, 2022)
• Where can I find the full listing and description of the columns in each metadata table? (February 28, 2022)
• Where can I find example queries for use in the cloud and elsewhere? (February 28, 2022)
• Do you have resources to help me get started working in the cloud? (February 28, 2022)
• What information should I include when reporting a problem? (February 28, 2022)
• My jobs aren't running! (February 28, 2022)

🛠️ Workflows

• Workflow 'Biodiversity data exploration tuto' (March 01, 2022)
• Workflow constructed from history 'Tuto Obitools' (February 28, 2022)

🧑‍🏫 Contributors

• @tduigou (March 01, 2022)
• @sylviamahara (March 01, 2022)
• @plushz (March 01, 2022)
• @msozzoni (March 01, 2022)
• @Melkeb (March 01, 2022)
• @Marie59 (March 01, 2022)
• @kenza12 (March 01, 2022)
• @jfaulon (March 01, 2022)
• @jbmihoub (March 01, 2022)
• @ioanagry (March 01, 2022)
• @guillaume-gricourt (March 01, 2022)
• @garimavs (March 01, 2022)
• @GaloGS (March 01, 2022)
• @dpelletier (March 01, 2022)
• @dbrites (March 01, 2022)
• @cstritt (March 01, 2022)
• @breakthewall (March 01, 2022)
• @bernandez (March 01, 2022)

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📚 Tutorials

• Pangeo Notebook in Galaxy - Introduction to Xarray (February 18, 2022)
• Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools (February 18, 2022)
• Protein target prediction of a bioactive ligand with Align-it and ePharmaLib (February 15, 2022)

🖼️ Slides

• The Pangeo ecosystem (February 18, 2022)
• Pangeo ecosystem 101 for everyone (February 18, 2022)

🛠️ Workflows

• Pangeo Jupyter Notebook (February 18, 2022)
• GTN 'Pangeo 101 for everyone - Xarray' (February 18, 2022)
• Zauberkugel (February 15, 2022)

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📚 Tutorials

• Bulk RNA Deconvolution with MuSiC (February 11, 2022)

🛠️ Workflows

• MuSiC Workflow (February 11, 2022)

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🧑‍🏫 Contributors

• @onorvez (February 01, 2022)
• @neoformit (February 01, 2022)
• @Lain-inrae (February 01, 2022)
• @fboyer (February 01, 2022)
• @ecoissac (February 01, 2022)
• @aurelienmoumbock (February 01, 2022)

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📰 News

• New Feature: Automatic RMarkdown (January 28, 2022)

❓ Faqs

• Learning with RMarkdown in RStudio (January 27, 2022)
• Knitting RMarkdown documents in RStudio (January 27, 2022)

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🎥 Recordings

• Recording of Image classification in Galaxy with fruit 360 dataset (January 19, 2022)

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🖼️ Slides

• Galaxy workflows in Dockstore (January 14, 2022)

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🧑‍🏫 Contributors

• @rabernat (January 01, 2022)
• @pickettbd (January 01, 2022)
• @gf777 (January 01, 2022)
• @BasileGoussard (January 01, 2022)
• @abueg (January 01, 2022)

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📰 News

• Support for annotating Funding Agencies (December 14, 2021)
• GTN Smörgåsbord 2: Tapas Edition (December 14, 2021)

📚 Tutorials

• Mass spectrometry: LC-MS data processing (December 14, 2021)

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📰 News

• New FAQs: How does the GTN stay FAIR and Collaborative (December 01, 2021)
• New Tutorials: PacBio data QC and Genome Assembly, and Genome Annotation with Funannotate (December 01, 2021)

📚 Tutorials

• Image classification in Galaxy with fruit 360 dataset (December 01, 2021)
• Genome assembly using PacBio data (November 29, 2021)
• Genome annotation with Funannotate (November 29, 2021)
• Masking repeats with RepeatMasker (November 29, 2021)

🖼️ Slides

• Image classification in Galaxy with fruit 360 dataset (December 01, 2021)
• An introduction to get started in genome assembly and annotation (November 30, 2021)

❓ Faqs

• How does the GTN ensure our training materials are FAIR? (December 01, 2021)
• How does the GTN implement the "Ten simple rules for collaborative lesson development" (December 01, 2021)

🛠️ Workflows

• fruit_360 (December 01, 2021)
• Genome Assembly using PacBio data (November 29, 2021)
• RepeatMasker (November 29, 2021)
• Funannotate (November 29, 2021)

🧑‍🏫 Contributors

• @coverbeck (December 01, 2021)
• @bethsheets (December 01, 2021)
• @avani-k (December 01, 2021)

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📰 News

• New Feature: GTN Video Library (November 23, 2021)

❓ 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? (November 22, 2021)
• In 'infer experiments' I get unequal numbers, but in the IGV it looks like it is unstranded. What does this mean? (November 22, 2021)
• RNAstar: Why do we set 36 for 'Length of the genomic sequence around annotated junctions'? (November 22, 2021)
• Is it possible to visualize the RNA STAR bam file using the JBrowse tool? (November 22, 2021)
• When is the "infer experiment" tool used in practice? (November 22, 2021)
• Could I use a different p-adj value for filtering differentially expressed genes? (November 22, 2021)
• The tutorial uses the normalised count table for visualisation. What about using VST normalised counts or rlog normalised counts? (November 22, 2021)

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📚 Tutorials

• Make & Snakemake (November 18, 2021)

❓ Faqs

• What other methods are available to study the functional state of the microbiome within Galaxy? (November 17, 2021)
• I have a really large search database, what search strategies do you recommend for searching my mass spectrometry dataset? (November 17, 2021)
• Which search algorithms are recommended for searching the metaproteomics data? (November 17, 2021)
• Can I use these workflows on datasets generated from our laboratory? (November 17, 2021)
• Why do we do dimension reduction and then clustering? Why not just cluster on the actual data? (November 17, 2021)
• What software tools are available to determine taxonomic composition from mass spectrometry data? (November 17, 2021)
• I have FASTQ files from metagenomics or metatranscriptomics datasets? How can I convert them into a protein FASTA file for metaproteomics searches? (November 17, 2021)
• How does one convert RAW files to MGF peak lists within Galaxy? (November 17, 2021)
• How does one compare metaproteomics measurements from two experimental conditions? (November 17, 2021)
• Are UMIs not actually unique? (November 17, 2021)
• I got slightly different numbers than were in the tutorial (November 17, 2021)
• My jobs are not running / I cannot see the history overview menu (November 17, 2021)
• My Galaxy looks different than in the tutorial/video (November 17, 2021)
• UCSC - I fetched data from a remote website but now I’m logged out of Galaxy and my data is gone? (November 17, 2021)
• I can’t find the “Analyze Data” button (November 17, 2021)

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📰 News

• New Feature: GTN API with OpenAPI 3 specification (November 10, 2021)

📚 Tutorials

• Plotting in Python (November 08, 2021)
• Advanced Python (November 08, 2021)
• Introduction to Python (November 08, 2021)

❓ Faqs

• Which version of SearchGUI and PeptideShaker shall I use for this tutorial? (November 14, 2021)
• Why do we only consider highly variable genes? (November 11, 2021)
• Can RNA-seq techniques be applied to scRNA-seq? (November 11, 2021)
• What exactly is a ‘Gene profile’? (November 11, 2021)
• Why do we do dimension reduction and then clustering? Why not just cluster on the actual data? (November 11, 2021)
• Why is amplification more of an issue in scRNA-seq than RNA-seq? (November 11, 2021)

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🧑‍🏫 Contributors

• @twishigulati (November 01, 2021)
• @suchitrathapa (November 01, 2021)
• @stephanierobin (November 01, 2021)
• @lleroi (November 01, 2021)
• @IrelCM (November 01, 2021)
• @alexcorm (November 01, 2021)
• @alaaelghamry (November 01, 2021)

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❓ Faqs

• Undeleting history (October 25, 2021)

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📚 Tutorials

• dplyr & tidyverse for data processing (October 20, 2021)

🖼️ Slides

• Una breve introducción a Galaxy (October 19, 2021)
• Una introducción al análisis de datos scRNA-seq (October 19, 2021)
• Introducción al análisis de datos de scRNA-seq (October 19, 2021)

❓ Faqs

• Extraer un flujo de trabajo de tu historial (October 20, 2021)
• Compartiendo un historial (October 20, 2021)
• Uso del cuaderno de apuntes para ver varios conjuntos de datos (October 20, 2021)

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📰 News

• New Topic: Data Science Survival Kit (October 12, 2021)
• Attention Contributors: GTN Performance Enhancements (October 12, 2021)

📚 Tutorials

• CRISPR screen analysis (October 15, 2021)
• SQL with Python (October 11, 2021)
• Introduction to SQL (October 11, 2021)
• SQL Educational Game - Murder Mystery (October 11, 2021)
• Advanced SQL (October 11, 2021)
• SQL with R (October 11, 2021)

🛠️ Workflows

• Workflow constructed from history 'CRISPR tutorial Kenji' (October 15, 2021)
• CLM-FATES_ ALP1 simulation (5 years) (October 11, 2021)
• Climate 101 (October 11, 2021)

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📚 Tutorials

• Filtrado, representación y exploración de secuenciación de ARN de células únicas (October 07, 2021)

❓ Faqs

• Para volver a ejecutar una herramienta (October 06, 2021)
• Importación por medio de enlaces (October 06, 2021)
• Cambiar el tipo de datos (October 06, 2021)

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📰 News

• Got a minute? Take our survey about Galaxy for training and have your say! (September 29, 2021)

📚 Tutorials

• CLI Educational Game - Bashcrawl (September 30, 2021)
• CLI basics (September 30, 2021)
• Advanced CLI in Galaxy (September 30, 2021)

❓ Faqs

• Open a Terminal in Jupyter (September 30, 2021)

🧑‍🏫 Contributors

• @themudo (October 01, 2021)
• @Shorla (October 01, 2021)
• @saritadc (October 01, 2021)
• @saramorsy (October 01, 2021)
• @sandygudie (October 01, 2021)
• @robertmand (October 01, 2021)
• @rahmot (October 01, 2021)
• @otatadeabigail (October 01, 2021)
• @NUKnightLab (October 01, 2021)
• @myles-bilong (October 01, 2021)
• @millen2223 (October 01, 2021)
• @mariipia10 (October 01, 2021)
• @lgallegovillar (October 01, 2021)
• @lamouresparus (October 01, 2021)
• @kenjifujihara (October 01, 2021)
• @jrr-cpt (October 01, 2021)
• @gatwirival (October 01, 2021)
• @Ezichi-Fav (October 01, 2021)
• @dirowa (October 01, 2021)
• @davelopez (October 01, 2021)
• @Chinonyemildred (October 01, 2021)
• @bfranicevic (October 01, 2021)
• @ajadi-abiola (October 01, 2021)
• @AfiDede (October 01, 2021)

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📰 News

• New Feature: Automatic Jupyter Notebooks (September 24, 2021)

🖼️ Slides

• Una Breve Introducción a Galaxy (September 21, 2021)

❓ Faqs

• Why not use Excel? (September 21, 2021)

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📚 Tutorials

• Generación de una matriz de datos de secuenciación de ARN de células únicas utilizando Alevin (August 31, 2021)

❓ Faqs

• Cambiando el nombre de un historial (September 02, 2021)
• Para la creación de un historial nuevo (September 02, 2021)

🧑‍🏫 Contributors

• @npalopoli (September 01, 2021)
• @mcmaniou (September 01, 2021)

🏢 Organisations

• @carpentries (September 01, 2021)

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📚 Tutorials

• How to reproduce published Galaxy analyses (August 25, 2021)

🛠️ Workflows

• GTN Training: Galaxy 101 For Everyone (August 25, 2021)

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📚 Tutorials

• MaxQuant and MSstats for the analysis of TMT data (August 13, 2021)
• Submitting sequence data to ENA (August 10, 2021)

🖼️ Slides

• Submitting SARS-CoV-2 sequences to ENA (August 10, 2021)

🎥 Recordings

• Recording of Using dataset collections (August 09, 2021)
• Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (August 09, 2021)

🛠️ Workflows

• MaxQuant MSstatsTMT Training (August 13, 2021)
• GTN_ENA_upload_workflow (August 10, 2021)

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📚 Tutorials

• Removal of human reads from SARS-CoV-2 sequencing data (August 04, 2021)

❓ Faqs

• Upload fastqsanger datasets via links (August 04, 2021)

🛠️ Workflows

• GTN - Sequence Analyses - Removal of human reads from SARS-CoV-2 sequencing data (August 04, 2021)

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📰 News

• New Feature: a feedback page to aggregate and display feedback answers (July 28, 2021)
• Accessibility Improvements (July 27, 2021)

🧑‍🏫 Contributors

• @roncoronimiguel (August 01, 2021)
• @KlemensFroehlich (August 01, 2021)

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🎥 Recordings

• Recording of Whole transcriptome analysis of Arabidopsis thaliana (July 25, 2021)
• Recording of Galaxy Basics for genomics (July 21, 2021)

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📰 News

• New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (June 30, 2021)

📚 Tutorials

• Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data (June 30, 2021)

🎥 Recordings

• Recording of Use Apptainer containers for running Galaxy jobs (June 28, 2021)
• Recording of Galaxy Tool Management with Ephemeris (June 28, 2021)
• Recording of Galaxy Tool Management with Ephemeris (June 28, 2021)
• Recording of Running Jobs on Remote Resources with Pulsar (June 28, 2021)
• Recording of Galaxy Installation with Ansible (June 28, 2021)

❓ Faqs

• Importing a workflow using the search (June 30, 2021)
• Importing a history (June 30, 2021)
• Upload many files (>10) via FTP (June 30, 2021)
• Upload few files (1-10) (June 30, 2021)
• Troubleshooting errors (June 28, 2021)

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📰 News

• New Tutorial: Visualization of RNA-Seq results with Volcano Plot in R (June 26, 2021)
• New Tutorial: GitPod for contributing to the GTN (June 25, 2021)

📚 Tutorials

• Running the GTN website online using GitPod (June 24, 2021)
• EncyclopeDIA (June 21, 2021)

🎥 Recordings

• Recording of EncyclopeDIA (June 25, 2021)

❓ Faqs

• How to Contribute to Galaxy (June 24, 2021)

🛠️ Workflows

• EncyclopeDIA-GTN (June 21, 2021)

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📚 Tutorials

• Enable upload via FTP (June 18, 2021)
• Creating Galaxy tools from Conda Through Deployment (June 15, 2021)
• Debugging Galaxy (June 15, 2021)
• Visualization of RNA-Seq results with Volcano Plot in R (June 14, 2021)

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📚 Tutorials

• Contributing a New Feature to Galaxy Core (June 08, 2021)
• Upgrading Galaxy (June 08, 2021)
• Automating Galaxy workflows using the command line (June 08, 2021)
• Updating diffs in admin training (June 07, 2021)

❓ Faqs

• Annotate a workflow (June 11, 2021)
• Make a workflow public (June 10, 2021)
• Got lost along the way? (June 07, 2021)

🛠️ Workflows

• Retrieve climate data from Copernicus (June 11, 2021)
• vcf2lineage (June 08, 2021)

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📰 News

• New Tutorial: Genome Annotation with Apollo (June 04, 2021)
• Oh no, it changed! Quick, to the archive menu. (June 01, 2021)

📚 Tutorials

• Refining Genome Annotations with Apollo (prokaryotes) (June 04, 2021)
• Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step (June 04, 2021)
• SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (May 31, 2021)

🖼️ Slides

• Refining Genome Annotations with Apollo (June 04, 2021)
• Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2 (June 03, 2021)
• Feedforward neural networks (FNN) Deep Learning - Part 1 (June 02, 2021)
• Recurrent neural networks (RNN) Deep Learning - Part 2 (May 31, 2021)

❓ Faqs

• Which isobaric labeled quantification methods does MaxQuant in Galaxy support? (June 03, 2021)
• Including custom modifications into MaxQuant in Galaxy? (June 03, 2021)
• Do I need to create collections to run MaxQuant analysis or can I use single sample inputs? (June 03, 2021)
• Viewing a workflow report (May 31, 2021)

🛠️ Workflows

• Apollo Load Test (June 04, 2021)
• VGP assembly: training workflow (June 04, 2021)

🧑‍🏫 Contributors

• @xtrojak (June 01, 2021)
• @OlegZharkov (June 01, 2021)
• @davebx (June 01, 2021)

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📰 News

• New Feature: Easy Abbreviation (May 25, 2021)
• Contributing to BioBlend as a developer (May 25, 2021)

📚 Tutorials

• ToolFactory: Generating Tools From More Complex Scripts (May 26, 2021)
• ToolFactory: Generating Tools From Simple Scripts (May 26, 2021)
• Contributing to BioBlend as a developer (May 25, 2021)

🖼️ Slides

• Introduction to the ToolFactory tutorial. (May 26, 2021)

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📰 News

• ¿Hablas español?: The first curated tutorial in Spanish! (May 20, 2021)

📚 Tutorials

• Introduction to Machine Learning using R (May 21, 2021)
• Breve introducción a Galaxy - en español (May 20, 2021)

🖼️ Slides

• Convolutional neural networks (CNN) Deep Learning - Part 3 (May 19, 2021)

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🎥 Recordings

• Recording of Introduction to SRA Aligned Read Format and Cloud Metadata for SARS-CoV-2 (May 15, 2021)
• Recording of SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis (May 15, 2021)

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📚 Tutorials

• PAPAA PI3K_OG: PanCancer Aberrant Pathway Activity Analysis (May 06, 2021)

🛠️ Workflows

• papaa@0.1.9_PI3K_OG_model_tutorial (May 06, 2021)

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📚 Tutorials

• Deep Learning (Part 1) - Feedforward neural networks (FNN) (April 28, 2021)

🧑‍🏫 Contributors

• @rikeshi (May 01, 2021)
• @pclo (May 01, 2021)
• @RareSeas (May 01, 2021)
• @mboudet (May 01, 2021)
• @jontrow (May 01, 2021)
• @EngyNasr (May 01, 2021)
• @assuntad23 (May 01, 2021)
• @ales-ibt (May 01, 2021)

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📚 Tutorials

• Deep Learning (Part 3) - Convolutional neural networks (CNN) (April 19, 2021)

🎥 Recordings

• Recording of Whole transcriptome analysis of Arabidopsis thaliana (April 20, 2021)

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🖼️ Slides

• Whole transcriptome analysis of Arabidopsis thaliana (April 16, 2021)

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📰 News

• New Tutorials: Whole transcriptome analysis of Arabidopsis thaliana (April 10, 2021)
• New Feature: Video Player (April 06, 2021)

📚 Tutorials

• Whole transcriptome analysis of Arabidopsis thaliana (April 08, 2021)
• Analysis of plant scRNA-Seq Data with Scanpy (April 08, 2021)
• Inferring single cell trajectories with Scanpy (Python) (April 07, 2021)
• Text-mining with the SimText toolset (April 05, 2021)

🖼️ Slides

• Introduction to ATAC-Seq data analysis (April 08, 2021)

❓ Faqs

• Open interactive tool (April 05, 2021)

🛠️ Workflows

• Plant bulk RNA-Seq workflow (April 08, 2021)
• scRNA Plant Analysis (April 08, 2021)
• Simtext training workflow (April 05, 2021)

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📰 News

• New Tutorial: Downstream Single-cell RNA Plant analysis with ScanPy (March 30, 2021)

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📰 News

• New Feature: FAQs (March 24, 2021)
• New Tutorials: Genome assembly of a MRSA genome (March 24, 2021)

📚 Tutorials

• Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) (March 24, 2021)
• Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data (March 24, 2021)
• Filter, plot and explore single-cell RNA-seq data with Scanpy (March 24, 2021)

❓ Faqs

• Nanopore sequencing (March 24, 2021)
• Illumina MiSeq sequencing (March 24, 2021)
• Running a workflow (March 24, 2021)
• Renaming workflow outputs (March 24, 2021)
• Setting parameters at run-time (March 24, 2021)
• Importing a workflow (March 24, 2021)
• Hiding intermediate steps (March 24, 2021)
• Extracting a workflow from your history (March 24, 2021)
• Opening the workflow editor (March 24, 2021)
• Creating a new workflow (March 24, 2021)
• Add Mapped reads track to IGV from Galaxy (March 24, 2021)
• Add genome and annotations to IGV from Galaxy (March 24, 2021)
• How can I create a tutorial skeleton from a Galaxy workflow? (March 24, 2021)
• Select multiple datasets (March 24, 2021)
• Selecting a dataset collection as input (March 24, 2021)
• Re-running a tool (March 24, 2021)
• Getting your API key (March 24, 2021)
• Where can I read more about this analysis? (March 24, 2021)
• How do I use this material? (March 24, 2021)
• Where can I run the hands-on tutorials? (March 24, 2021)
• Where do I start? (March 24, 2021)
• How can I get help? (March 24, 2021)
• Stop RStudio (March 24, 2021)
• Launch RStudio (March 24, 2021)
• Launch JupyterLab (March 24, 2021)
• Where do I start? (March 24, 2021)
• How do I get help? (March 24, 2021)
• What Galaxy instance should I use for my training? (March 24, 2021)
• What are the best practices for teaching with Galaxy? (March 24, 2021)
• Install tools via the Admin UI (March 24, 2021)
• Which icons are available to use in my tutorial? (March 24, 2021)
• Searching your history (March 24, 2021)
• Renaming a history (March 24, 2021)
• Creating a new history (March 24, 2021)
• Copy a dataset between histories (March 24, 2021)
• What are the tutorials for? (March 24, 2021)
• Sustainability of the training-material and metadata (March 24, 2021)
• How is the content licensed? (March 24, 2021)
• How can I cite the GTN? (March 24, 2021)
• What audiences are the tutorials for? (March 24, 2021)
• How can I advertise the training materials on my posters? (March 24, 2021)
• What is this website? (March 24, 2021)
• What is Galaxy? (March 24, 2021)
• Are there any upcoming events focused on Galaxy Training? (March 24, 2021)
• Using the Window Manager to view multiple datasets (March 24, 2021)
• Renaming a dataset (March 24, 2021)
• Importing via links (March 24, 2021)
• Importing data from a data library (March 24, 2021)
• Detecting the datatype (file format) (March 24, 2021)
• Creating a new file (March 24, 2021)
• Converting the file format (March 24, 2021)
• Changing database/build (dbkey) (March 24, 2021)
• Changing the datatype (March 24, 2021)
• Adding a tag (March 24, 2021)
• How can I create new content without dealing with git? (March 24, 2021)
• How can I test an Interactive Tour? (March 24, 2021)
• How can I report mistakes or errors? (March 24, 2021)
• What can I do to help the project? (March 24, 2021)
• How can I give feedback? (March 24, 2021)
• How can I fix mistakes or expand an existing tutorial using the GitHub interface? (March 24, 2021)
• How can I contribute in "advanced" mode? (March 24, 2021)
• How can I get started with contributing? (March 24, 2021)
• Thanks! (March 24, 2021)
• Renaming a collection (March 24, 2021)
• Creating a paired collection (March 24, 2021)
• Creating a dataset collection (March 24, 2021)
• Adding a tag to a collection (March 24, 2021)
• Running Ansible on your remote machine (March 24, 2021)
• Results may vary (March 24, 2021)
• Adding a custom database/build (dbkey) (March 24, 2021)
• Operating system compatibility (March 24, 2021)
• How can I adapt this tutorial to my own data? (March 24, 2021)
• Sharing your History (March 24, 2021)

🛠️ Workflows

• Genome Assembly of MRSA using Illumina MiSeq Data (March 24, 2021)
• CS3_Filter, Plot and Explore Single-cell RNA-seq Data (March 24, 2021)

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📰 News

• Galaxy Community Conference 2021 (March 18, 2021)
• Next GTN CoFest May 20, 2021 (March 18, 2021)
• New Tutorial: Object tracking using CellProfiler (March 18, 2021)
• Galaxy 21.01 released! (March 17, 2021)
• Report on the GTN Smörgåsbord event (March 17, 2021)
• New Feature: Automatic Slides-to-video conversion (March 16, 2021)

📚 Tutorials

• Object tracking using CellProfiler (March 17, 2021)

🎥 Recordings

• Recording of Understanding Barcodes (March 18, 2021)
• Recording of Pre-processing of 10X Single-Cell RNA Datasets (March 18, 2021)
• Recording of Clustering 3K PBMCs with Scanpy (March 18, 2021)

🛠️ Workflows

• CP_object_tracking_example (March 17, 2021)

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🎥 Recordings

• Recording of Bulk RNA Deconvolution with MuSiC (March 08, 2021)

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📰 News

• Galaxy Admin Training Success (March 01, 2021)

📚 Tutorials

• Generating a single cell matrix using Alevin (March 03, 2021)

🛠️ Workflows

• Combining datasets after pre-processing (March 03, 2021)
• Generating a single cell matrix using Alevin (March 03, 2021)

🧑‍🏫 Contributors

• @sunyi000 (March 01, 2021)
• @mgramm1 (March 01, 2021)
• @dlalgroup (March 01, 2021)

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📚 Tutorials

• Deep Learning (Part 2) - Recurrent neural networks (RNN) (February 23, 2021)

🛠️ Workflows

• Compute and analyze biodiversity metrics with PAMPA toolsuite (February 24, 2021)

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📚 Tutorials

• MaxQuant and MSstats for the analysis of label-free data (February 17, 2021)

🎥 Recordings

• Recording of Creating Galaxy tools from Conda Through Deployment (February 15, 2021)
• Recording of ToolFactory: Generating Tools From More Complex Scripts (February 15, 2021)
• Recording of RNA Seq Counts to Viz in R (February 15, 2021)
• Recording of Visualization of RNA-Seq results with Volcano Plot in R (February 15, 2021)
• Recording of R basics in Galaxy (February 15, 2021)
• Recording of Advanced R in Galaxy (February 15, 2021)
• Recording of Running the GTN website online using GitPod (February 15, 2021)
• Recording of Introduction to Machine Learning using R (February 15, 2021)
• Recording of Inferring single cell trajectories with Scanpy (Python) (February 15, 2021)
• Recording of Upgrading Galaxy (February 15, 2021)
• Recording of Training Infrastructure as a Service (TIaaS) (February 15, 2021)
• Recording of Mapping Jobs to Destinations using TPV (February 15, 2021)
• Recording of Use Apptainer containers for running Galaxy jobs (February 15, 2021)
• Recording of Rule Based Uploader: Advanced (February 15, 2021)
• Recording of Rule Based Uploader (February 15, 2021)
• Recording of ToolFactory: Generating Tools From Simple Scripts (February 15, 2021)
• Recording of Introduction to Transcriptomics (February 15, 2021)
• Recording of Creating Slides (February 15, 2021)
• Recording of Introduction to proteomics, protein identification, quantification and statistical modelling (February 15, 2021)
• Recording of An introduction to scRNA-seq data analysis (February 15, 2021)
• Recording of Connecting Galaxy to a compute cluster (February 15, 2021)
• Recording of Connecting Galaxy to a compute cluster (February 15, 2021)
• Recording of Galaxy Tool Management with Ephemeris (February 15, 2021)
• Recording of User, Role, Group, Quota, and Authentication managment (February 15, 2021)
• Recording of Galaxy Monitoring with Telegraf and Grafana (February 15, 2021)
• Recording of Galaxy Monitoring with Telegraf and Grafana (February 15, 2021)
• Recording of Storage Management (February 15, 2021)
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• Recording of Ansible (February 15, 2021)
• Recording of Ansible (February 15, 2021)
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• Recording of Running Jobs on Remote Resources with Pulsar (February 15, 2021)
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• Recording of Reference Data with CVMFS (February 15, 2021)
• Recording of Galaxy Interactive Tools (February 15, 2021)
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• Recording of Introduction to Microbiome Analysis (February 15, 2021)
• Recording of Galaxy Basics for everyone (February 15, 2021)
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• Recording of Introduction to Genomics and Galaxy (February 15, 2021)
• Recording of Refining Genome Annotations with Apollo (February 15, 2021)
• Recording of Refining Genome Annotations with Apollo (prokaryotes) (February 15, 2021)
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• Recording of From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis (February 15, 2021)
• Recording of Whole transcriptome analysis of Arabidopsis thaliana (February 15, 2021)
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• Recording of De novo transcriptome reconstruction with RNA-Seq (February 15, 2021)
• Recording of Creating a new tutorial (February 15, 2021)
• Recording of Annotating a protein list identified by LC-MS/MS experiments (February 15, 2021)
• Recording of Proteogenomics 1: Database Creation (February 15, 2021)
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• Recording of MaxQuant and MSstats for the analysis of label-free data (February 15, 2021)
• Recording of Proteogenomics 2: Database Search (February 15, 2021)
• Recording of Introduction to ATAC-Seq data analysis (February 15, 2021)
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• Recording of Deep Learning (Part 3) - Convolutional neural networks (CNN) (February 15, 2021)
• Recording of Quality Control (February 15, 2021)
• Recording of Quality Control (February 15, 2021)
• Recording of Mapping (February 15, 2021)
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• Recording of Functionally Assembled Terrestrial Ecosystem Simulator (FATES) (February 15, 2021)
• Recording of Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads (February 15, 2021)
• Recording of Chloroplast genome assembly (February 15, 2021)
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• Recording of Generating a single cell matrix using Alevin (February 15, 2021)
• Recording of Analysis of plant scRNA-Seq Data with Scanpy (February 15, 2021)
• Recording of Combining single cell datasets after pre-processing (February 15, 2021)
• Recording of Filter, plot and explore single-cell RNA-seq data with Scanpy (February 15, 2021)
• Recording of Circos (February 15, 2021)
• Recording of Visualisation with Circos (February 15, 2021)
• Recording of Automating Galaxy workflows using the command line (February 15, 2021)
• Recording of 16S Microbial Analysis with mothur (short) (February 15, 2021)
• Recording of Antibiotic resistance detection (February 15, 2021)
• Recording of Metatranscriptomics analysis using microbiome RNA-seq data (short) (February 15, 2021)
• Recording of Metatranscriptomics analysis using microbiome RNA-seq data (February 15, 2021)
• Recording of Reference-based RNA-Seq data analysis (February 15, 2021)
• Recording of An Introduction to Genome Assembly (February 15, 2021)
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• Adding auto-generated video to your slides (October 20, 2020)

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• Metatranscriptomics analysis using microbiome RNA-seq data (short) (February 13, 2020)
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• Workflow 3: Functional Information (quick) (February 13, 2020)
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• Visualisations in Galaxy (January 10, 2020)
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• Annotating a protein list identified by LC-MS/MS experiments (September 12, 2019)
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• ProteoRE ProteomeAnnotation Tutorial (release 2.0) (September 12, 2019)
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• ATAC-seq GTM (September 02, 2019)

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• Analyse HeLa fluorescence siRNA screen (August 13, 2019)
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• Regional GAM (July 04, 2019)
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• Galaxy Installation on Kubernetes (July 02, 2019)
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• Essential genes detection with Transposon insertion sequencing (July 02, 2019)
• Mass spectrometry: LC-MS analysis (July 02, 2019)

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• Essential genes detection with Transposon insertion sequencing (July 02, 2019)

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• Visualization Of RNA-Seq Results With Volcano Plot (July 07, 2019)
• Regional GAM Workflow (July 04, 2019)
• Tutorial regionalGAM Complete Multispecies (July 04, 2019)
• Phenology "stacked" Visualization Creation (July 04, 2019)
• Abundance Index "stacked" Visualization Creation (July 04, 2019)
• Workflow Constructed From History 'imported: testpourGCC' (July 02, 2019)

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• Exome Seq Training Pre-Mapped W Cached Ref (June 26, 2019)
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• Workshop Kickoff (June 04, 2019)

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• NAMD MD From CHARMM GUI (June 03, 2019)
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• 16S Microbial Analysis with mothur (short) (May 13, 2019)

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• Introduction to Genome Annotation (May 13, 2019)

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• Workflow 5: OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] (May 13, 2019)
• Workflow 4: Mock OTU Clustering [Galaxy Training: 16S Microbial Analysis With Mothur] (May 13, 2019)
• Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur] (May 13, 2019)
• Workflow 2: Data Cleaning And Chimera Removal [Galaxy Training: 16S Microbial Analysis With Mothur] (May 13, 2019)
• Workflow 1: Quality Control [Galaxy Training: 16S Microbial Analysis With Mothur] (May 13, 2019)

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• Name tags for following complex histories (April 08, 2019)

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• Identification of somatic and germline variants from tumor and normal sample pairs (March 13, 2019)

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