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.
SARS-CoV-2 Data Hubs
Data and tools to accelerate coronavirus researchPathogen Data Hubs
Data and tools to accelerate pathogen researchCOVID-19 Disease Map
A repository of SARS-CoV-2 virus-host interaction mechanismsBY-COVID citizen engagement
An educational toolkit on data sharing for pandemic preparednessBY-COVID training materials
Course Title | Host | Course Duration | |
---|---|---|---|
European Nucleotide Archive - Quick Tour | EMBL-EBI, Cambridgeshire, UK | 30 minutes | Course Material |
ENA : SARS-CoV-2 Submission Workshop | EMBL-EBI, Cambridgeshire, UK | 2 hours | Course Material |
WP3 Discoverability hackathon v2 on Feb 8th | EMBL-EBI, Tampere University, Finland | 2 hours | View SlidesView Recording |
Unlocking the Power of Metadata | SIB Swiss Institute of Bioinformatics Sciensano | 2 hours 45 minutes | Slides & Recording |
FAIRsharing in a nutshell | FAIRsharing, University of Oxford | 10 minutes | Course Material |
FAIRsharing content: standards overview | FAIRsharing, University of Oxford | 10 minutes | Course Material |
FAIRsharing content: databases overview | FAIRsharing, University of Oxford | 10 minutes | Course Material |
FAIRsharing for you: researchers | FAIRsharing, University of Oxford | 10 minutes | Course Material |
FAIRsharing for you: journal publishers | FAIRsharing, University of Oxford | 10 minutes | Course Material |
FAIRsharing for you: funders | FAIRsharing, University of Oxford | 10 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - A Very Short Introduction to Galaxy | Galaxy Training Network | 10 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Galaxy 101 | Galaxy Training Network | 13 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - NGS data logistics | Galaxy Training Network | 15 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Quality control | Galaxy Training Network | 40 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Mapping | Galaxy Training Network | 10 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Using data collections | Galaxy Training Network | 13 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Removal of human reads from SARS-CoV-2 sequencing data | Galaxy Training Network | 60 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - SARS-CoV-2 Monitoring and Analysis with Galaxy | Galaxy Training Network | 13 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data | Galaxy Training Network | 1 hour 30 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Automating Galaxy workflows using the command line | Galaxy Training Network | 30 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - The usegalaxy.* SARS-CoV-2 Bot in Action | Galaxy Training Network | 40 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Accelerating Research through data sharing | Galaxy Training Network | 13 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Upload to ENA | Galaxy Training Network | 10 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Uploading data to ENA | Galaxy Training Network | 10 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Introduction to viral Beacon | Galaxy Training Network | 24 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Using and Customising ObservableHQ | Galaxy Training Network | 15 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - SRA Aligned read format in Galaxy | Galaxy Training Network | 15 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads | Galaxy Training Network | 25 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Pandemics Research using Mass Spectrometry | Galaxy Training Network | 35 minutes | Course Material |
GTN Smörgåsbord 2: Tapas - Scripting Galaxy using the API and BioBlend | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 2: Tapas - Case Studies: What you can do with SARS-COV-2 data | Galaxy Training Network | 32 minutes | Course Material |
FAIR Cookbook: hands-on recipes to make and keep data FAIR | ELIXIR Nodes: UK, Spain, LU, CH | Course Material | |
FAIRsharing for you: societies and alliances | FAIRsharing | University of Oxford | factsheet (10 minutes) | Course Material |
FAIRsharing for you: libraries and trainers | FAIRsharing | University of Oxford | factsheet (10 minutes) | Course Material |
FAIRsharing for you: developers and curators | FAIRsharing | University of Oxford | factsheet (10 minutes) | Course Material |
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis- Sequencing data analysis for a spectrum of viral genomes | Galaxy Training Network | 12 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis | Galaxy Training Network | 15 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - Avian influenza viral strain analysis from gene segment sequencing data | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: OneHealth - Viral Pathogen Analysis - Pox virus genome analysis from tiled-amplicon sequencing data | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Webinar: Implementation of NGS for TB- WHO documents and other considerations | Galaxy Training Network | 60 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Tuberculosis Variant Analysis | Galaxy Training Network | 20 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Webinar series: Concepts of drug-resistance prediction and mutation-based clustering | Galaxy Training Network | 20 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Hands-on: Identifying tuberculosis transmission links: from SNPs to transmission clusters | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: OneHealth - Tuberculosis Sequence Analysis - Introduction to phylogenetics | Galaxy Training Network | 60 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - An automated SARS-CoV-2 genome surveillance system built around Galaxy | Galaxy Training Network | 10 minutes | Course 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 data | Galaxy Training Network | 55 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Automating Galaxy workflows using the command line | Galaxy Training Network | 30 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - The usegalaxy.* SARS-CoV-2 Bot in Action | Galaxy Training Network | 40 minutes | Course Material |
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Removal of human reads from SARS-CoV-2 sequencing data | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: OneHealth - Building a pathogen surveillance system with Galaxy - Upload to ENA | Galaxy Training Network | 10 minutes | Course 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 implementations | Galaxy Training Network | 17 minutes | Course Material |
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - Publishing My First™ RO-Crate | Galaxy Training Network | 17 minutes | Course Material |
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - RO-Crate in Python | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Building RO-Crates - Workflow Run RO-Crate Introduction | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Publishing Workflow RO-Crates with Galaxy - Registering Galaxy workflows in WorkflowHub | Galaxy Training Network | 37 minutes | Course 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 repositories | Galaxy Training Network | Course Material | |
GTN Smörgåsbord 3: FAIR data and provenance with RO-Crate and Galaxy - Publishing Workflow RO-Crates with Galaxy - Submitting workflows to LifeMonitor | Galaxy Training Network | Course Material | |
Data management in social sciences and humanities with DMEG | CESSDA, ADP | 60 minutes | Course Material |
Data management in life sciences with RDMkit | BSC, ELIXIR-ES | 60 minutes | Course Material |
Challenges and issues in data management | DANS, CESSDA, ADP, EKKE, EMPIRICA, SIB Swiss Institute of Bioinformatics, Euro-BioImaging | 40 minutes | Course Material |
Euro-BioImaging's Guide to FAIR BioImage Data 2023 | Euro-BioImaging | 3 hours | Course Material |
Euro-BioImaging's Guide to FAIR BioImage Data 2024 | Euro-BioImaging | 3 hours | Course Material |
BY-COVID Spring 24 Baseline Use Case Workshop | Sciensano, DANS, IACS | 1 hour | Course Material |
Data sharing and reuse under GDPR - BY-COVID Fest workshop report | DANS, CESSDA, ADP, EKKE, EMPIRICA, SIB Swiss Institute of Bioinformatics | Course Material | |
Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data | Galaxy Training Network | 3 hours | Course Material |
Removal of human reads from SARS-CoV-2 sequencing data | Galaxy Training Network | 1 hour | Course Material |
Pox virus genome analysis from tiled-amplicon sequencing data | Galaxy Training Network | 4 hours | Course Material |
Avian influenza viral strain analysis from gene segment sequencing data | Galaxy Training Network | 3 hours | Course Material |
Pathway analysis with the MINERVA Platform | Galaxy Training Network | 1 hour | Course Material |
Submitting sequence data to ENA | Galaxy Training Network | 1 hour | Course Material |
Maturity Model for Pathogen Data Platforms | SIB Swiss Institute of Bioinformatics | 1 hour | Course Material |