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Resources

BY-COVID sustains many open science resources which contribute to the goal of making infectious disease data open and available for everyone. The resources listed below receive funding directly from the BY-COVID project.

Project outcomes are summarised in our Success Stories brochure.

SARS-CoV-2 Data Hubs

Data and tools to accelerate coronavirus research
Guidelines, examples and tools relating to infectious disease data

Pathogen Data Hubs

Data and tools to accelerate pathogen research
Mapping and interlinking databases, standards and policies
Packaging research data with their metadata
Describing, sharing and publishing scientific computational workflows

COVID-19 Disease Map

A repository of SARS-CoV-2 virus-host interaction mechanisms

BY-COVID citizen engagement

An educational toolkit on data sharing for pandemic preparedness

BY-COVID training materials

Course TitleHostCourse Duration 
European Nucleotide Archive - Quick TourEMBL-EBI, Cambridgeshire, UK30 minutesCourse Material
ENA : SARS-CoV-2 Submission WorkshopEMBL-EBI, Cambridgeshire, UK2 hoursCourse Material
WP3 Discoverability hackathon v2 on Feb 8thEMBL-EBI, Tampere University, Finland2 hoursView SlidesView Recording
Unlocking the Power of MetadataSIB Swiss Institute of Bioinformatics Sciensano2 hours 45 minutesSlides & Recording
FAIRsharing in a nutshellFAIRsharing, University of Oxford10 minutesCourse Material
FAIRsharing content: standards overviewFAIRsharing, University of Oxford10 minutesCourse Material
FAIRsharing content: databases overviewFAIRsharing, University of Oxford10 minutesCourse Material
FAIRsharing for you: researchersFAIRsharing, University of Oxford10 minutesCourse Material
FAIRsharing for you: journal publishersFAIRsharing, University of Oxford10 minutesCourse Material
FAIRsharing for you: fundersFAIRsharing, University of Oxford10 minutesCourse Material
GTN Smörgåsbord 2: Tapas - A Very Short Introduction to GalaxyGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Galaxy 101Galaxy Training Network13 minutesCourse Material
GTN Smörgåsbord 2: Tapas - NGS data logistics Galaxy Training Network15 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Quality controlGalaxy Training Network40 minutesCourse Material
GTN Smörgåsbord 2: Tapas - MappingGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Using data collectionsGalaxy Training Network13 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Removal of human reads from SARS-CoV-2 sequencing dataGalaxy Training Network60 minutesCourse Material
GTN Smörgåsbord 2: Tapas - SARS-CoV-2 Monitoring and Analysis with GalaxyGalaxy Training Network13 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing dataGalaxy Training Network1 hour 30 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Automating Galaxy workflows using the command lineGalaxy Training Network30 minutesCourse Material
GTN Smörgåsbord 2: Tapas - The usegalaxy.* SARS-CoV-2 Bot in ActionGalaxy Training Network40 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Accelerating Research through data sharingGalaxy Training Network13 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Upload to ENAGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Uploading data to ENAGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Introduction to viral BeaconGalaxy Training Network24 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Using and Customising ObservableHQGalaxy Training Network15 minutesCourse Material
GTN Smörgåsbord 2: Tapas - SRA Aligned read format in GalaxyGalaxy Training Network15 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome readsGalaxy Training Network25 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Pandemics Research using Mass SpectrometryGalaxy Training Network35 minutesCourse Material
GTN Smörgåsbord 2: Tapas - Scripting Galaxy using the API and BioBlendGalaxy Training NetworkCourse Material
GTN Smörgåsbord 2: Tapas - Case Studies: What you can do with SARS-COV-2 dataGalaxy Training Network32 minutesCourse Material
FAIR Cookbook: hands-on recipes to make and keep data FAIRELIXIR Nodes: UK, Spain, LU, CHCourse Material
FAIRsharing for you: societies and alliancesFAIRsharing | University of Oxfordfactsheet (10 minutes)Course Material
FAIRsharing for you: libraries and trainersFAIRsharing | University of Oxfordfactsheet (10 minutes)Course Material
FAIRsharing for you: developers and curatorsFAIRsharing | University of Oxfordfactsheet (10 minutes)Course Material
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis- Sequencing data analysis for a spectrum of viral genomesGalaxy Training Network12 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysisGalaxy Training Network15 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - Avian influenza viral strain analysis from gene segment sequencing dataGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - Pox virus genome analysis from tiled-amplicon sequencing dataGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Webinar: Implementation of NGS for TB- WHO documents and other considerationsGalaxy Training Network60 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Tuberculosis Variant AnalysisGalaxy Training Network20 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Webinar series: Concepts of drug-resistance prediction and mutation-based clusteringGalaxy Training Network20 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Hands-on: Identifying tuberculosis transmission links: from SNPs to transmission clustersGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Introduction to phylogeneticsGalaxy Training Network60 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - An automated SARS-CoV-2 genome surveillance system built around GalaxyGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing dataGalaxy Training Network55 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Automating Galaxy workflows using the command lineGalaxy Training Network30 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - The usegalaxy.* SARS-CoV-2 Bot in ActionGalaxy Training Network40 minutesCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Removal of human reads from SARS-CoV-2 sequencing dataGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Upload to ENAGalaxy Training Network10 minutesCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - An overview of the RO-Crate concept and its implementationsGalaxy Training Network17 minutesCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - Publishing My First™ RO-CrateGalaxy Training Network17 minutesCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - RO-Crate in PythonGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - Workflow Run RO-Crate IntroductionGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Publishing Workflow RO-Crates with Galaxy - Registering Galaxy workflows in WorkflowHubGalaxy Training Network37 minutesCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Publishing Workflow RO-Crates with Galaxy - Best practices for workflows in GitHub repositoriesGalaxy Training NetworkCourse Material
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Publishing Workflow RO-Crates with Galaxy - Submitting workflows to LifeMonitorGalaxy Training NetworkCourse Material
Data management in social sciences and humanities with DMEGCESSDA, ADP60 minutesCourse Material
Data management in life sciences with RDMkitBSC, ELIXIR-ES60 minutesCourse Material
Challenges and issues in data managementDANS, CESSDA, ADP, EKKE, EMPIRICA, SIB Swiss Institute of Bioinformatics, Euro-BioImaging40 minutesCourse Material
Euro-BioImaging's Guide to FAIR BioImage Data 2023Euro-BioImaging3 hoursCourse Material
Euro-BioImaging's Guide to FAIR BioImage Data 2024Euro-BioImaging3 hoursCourse Material
BY-COVID Spring 24 Baseline Use Case WorkshopSciensano, DANS, IACS1 hourCourse Material
Data sharing and reuse under GDPR - BY-COVID Fest workshop reportDANS, CESSDA, ADP, EKKE, EMPIRICA, SIB Swiss Institute of BioinformaticsCourse Material
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing dataGalaxy Training Network3 hoursCourse Material
Removal of human reads from SARS-CoV-2 sequencing dataGalaxy Training Network1 hourCourse Material
Pox virus genome analysis from tiled-amplicon sequencing dataGalaxy Training Network4 hoursCourse Material
Avian influenza viral strain analysis from gene segment sequencing dataGalaxy Training Network3 hoursCourse Material
Pathway analysis with the MINERVA PlatformGalaxy Training Network1 hourCourse Material
Submitting sequence data to ENAGalaxy Training Network1 hourCourse Material
Maturity Model for Pathogen Data PlatformsSIB Swiss Institute of Bioinformatics1 hourCourse Material