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PhenoMeNal: accessing metabolomics workflows in Galaxy

• beginner
Metabolomics Chemical biology Galaxy
Video

A common framework for designing portable federated pipelines

•• intermediate
Data architecture, analysis and design data access federated data analysis
Installation instructions, Manual

How to use Common Workflow Language

• beginner
Workflows commonwl common workflow language CWL eLearning EeLP
Recorded webinar, Slidedeck

Europe PMC API workshop: Part two

API Literature search Literature database search Europe PMC Annotations
Online material, Recording, hands-on tutorial

MaBoSS: a tool for modelling biological systems

• beginner
Mathematical modelling cancer Signalling boolean modelling logical modelling
Recorded webinar

Exploring metabolite metabolism using the Enzyme Portal

Enzymes Metabolomics
Training materials, Video

GA4GH Passports and ELIXIR AAI

•• intermediate
AAI GA4GH Passports Auhtorisation
Video

Status Update Code of Conduct: Teaming up & Talking about it

•• intermediate
GDPR Healthcare research data harmonization
Webinar

EBI Metagenomics: analysing and exploring metagenomics data

Metagenomics MGnify Sequence Analysis Microbiology
e-learning

2024 highlights: A year of on-demand training

Bioinformatics Introduction
Video

Useful ontologies for harmonizing cohort data

• beginner
Data integration and warehousing Data management Ontology and terminology Ontologies Cohort data data annotation
Video

Applying data standards to the harmonization of COVID-19 datasets from different sources

• beginner
Data integration and warehousing Data integration Standards Standardised vocabulary data harmonization Ontologies
Video

Annotating data using next generation biobanking ontology (NGBO)

• beginner
Data integration and warehousing Ontology and terminology Standards Ontologies Data Integration data harmonization Standardised vocabulary
Video

FAIR software tools

• beginner
Software engineering FAIR software tools Software
Video

Making cohort data FAIR

• beginner
Data integration and warehousing Data management FAIR data Cohort data Ontologies Standards
Video

Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?

• beginner
Data management FAIR data Health data Open science
Video

Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects

•• intermediate
Data architecture, analysis and design Cloud computing Data analysis Standards Translational research
Series of videos

CINECA discovery service catalog

•• intermediate
Cohort data Standards federated data analysis Beacon queries
Tutorial

MGnify quick tour

Metagenomics Sequence analysis MGnify Microbiology
e-learning

Structural volume data

Electron microscopy Protein structure analysis Structural biology Structural bioinformatics Segmentation Volume matching
Recorded webinar

Discovering scientific evidence using Europe PMC SciLite annotation
Life Sciences Literature Database

Finding the data behind research publications with Europe PMC

Biomedical Literature Data links databases External links
Life Sciences Literature Database

Discovering scientific evidence using Europe PMC SciLite annotation

Biomedical Literature Annotations Literature search SciLite Protein structure viewer Chemical viewer
Course materials

Managing a Bioinformatics Core Facility: CABANA Virtual Workshop Handbook
Recorded webinar

Annotate your proteins with the UniProt Functional Annotation system UniFire

Proteins Function analysis
Webinar

Preprint discovery 101: Tips & tricks for authors and readers

Europe PMC, Preprints
e-learning

The International Mouse Phenotyping Consortium: Finding phenotypes for your gene of interest

Genotype and phenotype Model organisms Gene function Mouse models IMPC Mammalian Phenotype Ontology Mouse knockouts CRISPR
e-learning

Workflows: Combining tools for data analysis

Workflows Galaxy NextFlow SnakeMake EOSC-Life
Webinar

Integrating publications into bioinformatics analysis

Europe PMC REST API Bioinformatic analysis
e-learning

Methods in bioinformatics: Biological data analysis and interpretation

Networks

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PhenoMeNal: accessing metabolomics workflows in Galaxy

A common framework for designing portable federated pipelines

How to use Common Workflow Language

Europe PMC API workshop: Part two

MaBoSS: a tool for modelling biological systems

Exploring metabolite metabolism using the Enzyme Portal

GA4GH Passports and ELIXIR AAI

Status Update Code of Conduct: Teaming up & Talking about it

EBI Metagenomics: analysing and exploring metagenomics data

2024 highlights: A year of on-demand training

Useful ontologies for harmonizing cohort data

Applying data standards to the harmonization of COVID-19 datasets from different sources

Annotating data using next generation biobanking ontology (NGBO)

FAIR software tools

Making cohort data FAIR

Introduction to FAIR principles - Open science through FAIR health data networks: dream or reality?

Data Gravity in the Life Sciences: Lessons learned from the HCA and other federated data projects

CINECA discovery service catalog

MGnify quick tour

Structural volume data

Discovering scientific evidence using Europe PMC SciLite annotation

Finding the data behind research publications with Europe PMC

Discovering scientific evidence using Europe PMC SciLite annotation

Managing a Bioinformatics Core Facility: CABANA Virtual Workshop Handbook

Annotate your proteins with the UniProt Functional Annotation system UniFire

Preprint discovery 101: Tips & tricks for authors and readers

The International Mouse Phenotyping Consortium: Finding phenotypes for your gene of interest

Workflows: Combining tools for data analysis

Integrating publications into bioinformatics analysis

Methods in bioinformatics: Biological data analysis and interpretation

FEBS: In Silico Systems Biology: Network Reconstruction, Analysis and Network-based Modelling

EBI - Joint EBI-Wellcome Trust Proteomics Bioinformatics workshop

Using the Ensembl Genome Browser

Managing a bioinformatics core facility

Genome bioinformatics: from short- to long-read sequencing

Structural bioinformatics

Introduction to multi-omics data integration and visualisation

Introduction to RNA-seq and functional interpretation

Single-cell RNA-seq analysis with Python

Introduction to metabolomics analysis

Data-driven approaches to understanding dementia

Microscopy data analysis: machine learning and the BioImage Archive

Genome bioinformatics: from short- to long-read sequencing

Structural bioinformatics

Metagenomics bioinformatics at MGnify

Bioinformatics for immunologists

Proteomics bioinformatics

Data science for life scientists

Systems biology: from large datasets to biological insight

Causality in biomedicine: going beyond associations

Chemicals in a biological context: metabolites, drugs, and beyond

From sequences to structures: Protein characterisation using EMBL-EBI APIs

Computational Biology Training in Hematology 2025, Module 2

Pangenome annotations and resources in Ensembl

Pangenome graphs as a new paradigm in comparative genomics

Making sense of massive genomic data by indexing at scale

Concepts, methods, and resources in pangenomics

UniProt

Redefining UniProt reference proteomes and upcoming changes in UniProtKB

CINECA PROJECT

European Bioinformatics Institute (EBI)