Nicola Soranzo

Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

131 Tutorials

• FAIR Data, Workflows, and Research / Metadata ✍️
• FAIR Data, Workflows, and Research / FAIR and its Origins ✍️
• FAIR Data, Workflows, and Research / Data Registration ✍️
• FAIR Data, Workflows, and Research / Access ✍️
• FAIR Data, Workflows, and Research / Persistent Identifiers ✍️
• Development in Galaxy / Galaxy Webhooks 🧐
• Development in Galaxy / JavaScript plugins 🧐
• Development in Galaxy / Generic plugins 🧐
• Development in Galaxy / Data source integration 🧐
• Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
• Variant Analysis / Exome sequencing data analysis for diagnosing a genetic disease 🧐
• Variant Analysis / Calling variants in diploid systems ✍️ 🧐
• Variant Analysis / Calling variants in non-diploid systems 🧐
• Variant Analysis / From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis 🧐
• Variant Analysis / Mapping and molecular identification of phenotype-causing mutations 🧐
• Variant Analysis / Calling very rare variants 🧐
• Variant Analysis / Microbial Variant Calling 🧐
• Contributing to the Galaxy Training Material / Contributing with GitHub via its interface 🧐
• Contributing to the Galaxy Training Material / Generating PDF artefacts of the website 🧐
• Contributing to the Galaxy Training Material / Contributing to the Galaxy Training Network with GitHub 🧐
• Contributing to the Galaxy Training Material / Adding auto-generated video to your slides 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Contributing to the Galaxy Training Material / Including a new topic 🧐
• Contributing to the Galaxy Training Material / Updating diffs in admin training 🧐
• Contributing to the Galaxy Training Material / Tools, Data, and Workflows for tutorials 🧐
• Contributing to the Galaxy Training Material / Creating a new tutorial 🧐
• Contributing to the Galaxy Training Material / Creating Interactive Galaxy Tours 🧐
• Statistics and machine learning / Interval-Wise Testing for omics data 🧐
• Assembly / Making sense of a newly assembled genome 🧐
• Assembly / An Introduction to Genome Assembly 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Assembly / Unicycler Assembly 🧐
• Transcriptomics / 1: RNA-Seq reads to counts 🧐
• Transcriptomics / 3: RNA-seq genes to pathways 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis ✍️ 🧐
• Transcriptomics / Reference-based RNAseq data analysis (long) 🧐
• Transcriptomics / 2: RNA-seq counts to genes 🧐
• Transcriptomics / De novo transcriptome reconstruction with RNA-Seq 🧐
• Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
• Transcriptomics / CLIP-Seq data analysis from pre-processing to motif detection 🧐
• Transcriptomics / Differential abundance testing of small RNAs 🧐
• Transcriptomics / Network analysis with Heinz 🧐
• Transcriptomics / Visualization of RNA-Seq results with heatmap2 🧐
• Transcriptomics / Visualization of RNA-Seq results with Volcano Plot 🧐
• Teaching and Hosting Galaxy training / Running a workshop as an instructor 🧐
• Teaching and Hosting Galaxy training / Set up a Galaxy for Training 🧐
• Teaching and Hosting Galaxy training / Galaxy Admin Training 🧐
• Genome Annotation / Genome annotation with Maker 🧐
• Genome Annotation / Genome Annotation 🧐
• Genome Annotation / Genome annotation with Prokka 🧐
• Galaxy Server administration / Training Infrastructure as a Service (TIaaS) 🧐
• Galaxy Server administration / Performant Uploads with TUS 🧐
• Galaxy Server administration / Monitoring Galaxy and Pulsar with Sentry 🧐
• Galaxy Server administration / Reference Data with CVMFS 🧐
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 🧐
• Galaxy Server administration / Galaxy Database schema 🧐
• Galaxy Server administration / Distributed Object Storage 🧐
• Galaxy Server administration / Enable upload via FTP 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
• Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
• Galaxy Server administration / Connecting Galaxy to a compute cluster 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 📝 🧐
• Galaxy Server administration / Galaxy Monitoring with Reports 🧐
• Galaxy Server administration / Mapping Jobs to Destinations using TPV 🧐
• Galaxy Server administration / External Authentication ✍️ 🧐
• Galaxy Server administration / Reference Data with CVMFS without Ansible 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
• Galaxy Server administration / Automation with Jenkins 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Data Libraries 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Proteomics / Proteogenomics 3: Novel peptide analysis 🧐
• Proteomics / Secretome Prediction 🧐
• Proteomics / Protein FASTA Database Handling 🧐
• Proteomics / Peptide and Protein ID using SearchGUI and PeptideShaker 🧐
• Proteomics / Proteogenomics 1: Database Creation 🧐
• Proteomics / Label-free versus Labelled - How to Choose Your Quantitation Method 🧐
• Proteomics / Detection and quantitation of N-termini (degradomics) via N-TAILS 🧐
• Proteomics / Proteogenomics 2: Database Search 🧐
• Proteomics / Peptide and Protein Quantification via Stable Isotope Labelling (SIL) 🧐
• Proteomics / Peptide and Protein ID using OpenMS tools 🧐
• Proteomics / Metaproteomics tutorial 🧐
• Proteomics / Mass spectrometry imaging: Loading and exploring MSI data 🧐
• Single Cell / Pre-processing of Single-Cell RNA Data 🧐
• Single Cell / GO Enrichment Analysis on Single-Cell RNA-Seq Data 📝
• Single Cell / Clustering 3K PBMCs with Scanpy 🧐
• Single Cell / Understanding Barcodes 🧐
• Single Cell / Single-cell quality control with scater ✍️ 🧐
• Introduction to Galaxy Analyses / A short introduction to Galaxy ✍️ 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics ✍️ 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for everyone 🧐
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy 🧐
• Introduction to Galaxy Analyses / NGS data logistics 🧐
• Introduction to Galaxy Analyses / From peaks to genes ✍️ 🧐
• Introduction to Galaxy Analyses / IGV Introduction 🧐
• Epigenetics / Hi-C analysis of Drosophila melanogaster cells using HiCExplorer 🧐
• Epigenetics / Infinium Human Methylation BeadChip 🧐
• Epigenetics / Identification of the binding sites of the Estrogen receptor 🧐
• Epigenetics / DNA Methylation data analysis 🧐
• Epigenetics / Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🧐
• Epigenetics / ATAC-Seq data analysis 🧐
• Microbiome / Analyses of metagenomics data - The global picture 🧐
• Microbiome / 16S Microbial Analysis with mothur (extended) 🧐
• Ecology / RAD-Seq de-novo data analysis 🧐
• Ecology / RAD-Seq to construct genetic maps 🧐
• Ecology / RAD-Seq Reference-based data analysis 🧐
• Using Galaxy and Managing your Data / Creating, Editing and Importing Galaxy Workflows 🧐
• Using Galaxy and Managing your Data / Use Jupyter notebooks in Galaxy 🧐
• Using Galaxy and Managing your Data / Using dataset collections 🧐
• Using Galaxy and Managing your Data / Rule Based Uploader: Advanced 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 🧐
• Using Galaxy and Managing your Data / Extracting Workflows from Histories 🧐
• Sequence analysis / Quality Control 🧐
• Sequence analysis / Mapping 🧐
• Transcriptomics / Referenzbasierte RNA-Seq-Datenanalyse ✍️
• Introduction to Galaxy Analyses / Von Peaks zu Genen ✍️
• Transcriptomics / Análisis de datos RNA-Seq basados en referencias ✍️
• Introduction to Galaxy Analyses / De picos a genes ✍️
• Transcriptomics / Analisi dei dati RNA-Seq basata su riferimenti ✍️
• Introduction to Galaxy Analyses / Dai picchi ai geni ✍️

70 Slides

• Development in Galaxy / Galaxy from a developer point of view 🧐
• Development in Galaxy / Prerequisites for building software/conda packages 🧐
• Development in Galaxy / Tool development and integration into Galaxy ✍️ 🧐
• Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
• Development in Galaxy / Galaxy Webhooks 🧐
• Development in Galaxy / Tool Dependencies and Containers 🧐
• Development in Galaxy / Visualizations: JavaScript Plugins 🧐
• Development in Galaxy / Generic plugins 🧐
• Development in Galaxy / Galaxy Interactive Environments 🧐
• Development in Galaxy / Tool Dependencies and Conda ✍️ 🧐
• Development in Galaxy / Galaxy Interactive Tours 🧐
• Development in Galaxy / Scripting Galaxy using the API and BioBlend ✍️ 🧐
• Variant Analysis / Introduction to Variant analysis 🧐
• Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
• Contributing to the Galaxy Training Material / Creating Slides 🧐
• Contributing to the Galaxy Training Material / Overview of the Galaxy Training Material 🧐
• Assembly / An Introduction to Genome Assembly 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Assembly / Unicycler Assembly 🧐
• Transcriptomics / Visualization of RNA-Seq results with CummeRbund 🧐
• Transcriptomics / Introduction to Transcriptomics 🧐
• Genome Annotation / Genome annotation with Prokka 🧐
• Galaxy Server administration / Galaxy Troubleshooting 🧐
• Galaxy Server administration / Reference Genomes in Galaxy 🧐
• Galaxy Server administration / Gearing towards production 🧐
• Galaxy Server administration / Reference Data with CVMFS 🧐
• Galaxy Server administration / Storage Management 🧐
• Galaxy Server administration / uWSGI 🧐
• Galaxy Server administration / Galaxy Tool Management with Ephemeris ✍️ 🧐
• Galaxy Server administration / Galaxy Monitoring with gxadmin 🧐
• Galaxy Server administration / Terraform 🧐
• Galaxy Server administration / Server: Other 🧐
• Galaxy Server administration / Connecting Galaxy to a compute cluster ✍️ 🧐
• Galaxy Server administration / Ansible 🧐
• Galaxy Server administration / Galaxy Installation with Ansible 🧐
• Galaxy Server administration / External Authentication ✍️ 🧐
• Galaxy Server administration / Docker and Galaxy 🧐
• Galaxy Server administration / Galaxy on the Cloud 🧐
• Galaxy Server administration / Running Jobs on Remote Resources with Pulsar 🧐
• Galaxy Server administration / Advanced customisation of a Galaxy instance 🧐
• Galaxy Server administration / Empathy 🧐
• Galaxy Server administration / Galaxy from an administrator's point of view 🧐
• Galaxy Server administration / Galactic Database ✍️ 🧐
• Galaxy Server administration / User, Role, Group, Quota, and Authentication managment 🧐
• Galaxy Server administration / Galaxy Interactive Tools 🧐
• Galaxy Server administration / Server Maintenance: Cleanup, Backup, and Restoration 🧐
• Galaxy Server administration / Storage Management 🧐
• Galaxy Server administration / Controlling Galaxy with systemd or Supervisor 🧐
• Galaxy Server administration / Galaxy Monitoring with Telegraf and Grafana 🧐
• Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
• Introduction to Galaxy Analyses / A Short Introduction to Galaxy ✍️ 🧐
• Introduction to Galaxy Analyses / Introduction to Galaxy ✍️ 🧐
• Introduction to Galaxy Analyses / Options for using Galaxy ✍️ 🧐
• Epigenetics / Introduction to ChIP-Seq data analysis 🧐
• Epigenetics / Introduction to DNA Methylation data analysis 🧐
• Microbiome / Introduction to Microbiome Analysis 🧐
• Using Galaxy and Managing your Data / Getting data into Galaxy 🧐
• Sequence analysis / Quality Control 🧐
• Sequence analysis / Mapping 🧐
• Introduction to Galaxy Analyses / Una breve introducción a Galaxy ✍️

22 FAQs

• How do I know what I can do with a role? What variables are available?
• Contributing a Jupyter Notebook to the GTN
• Ändern des Datentyps ✍️
• Modifica del tipo di dato ✍️
• Changing the datatype
• Detecting the datatype (file format)
• Importar datos de una biblioteca de datos ✍️
• Importieren von Daten aus einer Datenbibliothek ✍️
• Importare i dati da una libreria di dati ✍️
• Importing data from a data library
• Importing data from repositories
• Cambiar el nombre de un conjunto de datos ✍️
• Umbenennen eines Datensatzes ✍️
• Rinominare un set di dati ✍️
• Renaming a dataset
• Para la creación de un historial nuevo ✍️
• Erstellen eines neuen Verlaufs ✍️
• Creare una nuova cronologia ✍️
• Creating a new history
• Créer un nouvel history
• Opening the workflow editor
• Extracting a workflow from your history

1 Event

• 2023 Galaxy Admin Training (Ghent) 🧑‍🏫

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GitHub Activity

github Issues Reported

103 Merged Pull Requests

See all of the github Pull Requests and github Commits by Nicola Soranzo.

• Add ELIXIR-STEERS grant
  template-and-tools
• Enable dependabot version updates for GitHub actions
  template-and-tools
• Fix ELIXIR-UK typos
  news
  Spocathon-HDR-ELIXIR
• Small fixes to the single-cell GO Enrichement tuto
  single-cell
  Spocathon-HDR-ELIXIR
• Fix ``create-env`` Make command
  template-and-tools
  Spocathon-HDR-ELIXIR

Reviewed 212 PRs

We love our community reviewing each other's work!

• Add setuptools pulsar requirement and drop amqp pin
  admin
• Fix following logs
  admin
• [GAT] Fix success check of tusd upload
  admin
• Bump aws-actions/configure-aws-credentials from 1 to 5
  template-and-tools
  dependencies
  github_actions
• Bump peaceiris/actions-gh-pages from 3 to 4
  template-and-tools
  dependencies
  github_actions

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