🟣Bioinformatics Open Source Tools
Bioinformatics Open Source Tools: FAIR and Open Science
🧬 Bioinformatics FAIR and Open Science Tools
Galaxy
Workflow management & analysis platform
✔️ Findable via ToolShed✔️ Accessible via public instances✔️ Interoperable (CWL/Bioconda)✔️ Reusable workflows
Public instances, DOI export, reproducibility tracking
Bioconductor
R-based genomic analysis packages
✔️ Indexed metadata✔️ Accessible source code✔️ Ontology integration (GO)✔️ Reusable across studies
Peer-reviewed packages, versioned releases
Nextflow
Scalable workflow orchestration
✔️ Workflow versioning✔️ Accessible scripts✔️ Container support✔️ Metadata-rich
GitHub integration, containerized pipelines
nf-core
Community-curated Nextflow pipelines
✔️ FAIR metadata templates✔️ Version control✔️ Standardized formats
Open peer review, citation export, GitHub workflows
RO-Crate
FAIR metadata packaging standard
✔️ Interoperable (JSON-LD)✔️ Enhances Findability✔️ Reusability & provenance
Compatible with repositories and workflow engines
OpenRefine
Data cleaning and wrangling
✔️ Interoperable formats✔️ Reusable scripts✔️ Exportable metadata
RDF extension, version control of changes
MetaboLights
Metabolomics data repository
✔️ Ontology-rich metadata✔️ Persistent IDs✔️ Reusable datasets
Supports ISA-Tab, ELIXIR integration
ENA
Nucleotide sequence archive
✔️ Persistent accession numbers✔️ Open APIs✔️ Standardized formats
Mandatory MIxS, XML metadata, open access
Public Domain / Open Terms
Zenodo
General-purpose research repository
✔️ DOI generation✔️ FAIR metadata✔️ Format-agnostic
GitHub & ORCID integration, open access
Dockstore
Workflow and tool registry
✔️ GA4GH-compliant✔️ Interoperable (WDL, CWL, Nextflow)✔️ Reusable containers
Git sync, FAIR metrics, BioContainers support
✅ FAIR Principle Key
Findable – Indexed, persistent identifiers
Accessible – Open/public APIs or repositories
Interoperable – Standard formats, ontologies
Reusable – Licensing, provenance, rich metadata
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