Omics and Bioinformatics
The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.
See also: Omics and Bioinformatics in EDAM.
Related use cases
JAX BioConnect is an index of research data that supports data sharing, high-quality curation, and consistent data description.
DataPLANT's mission is to provide a sustainable and well annotated data management platform for plant sciences.
Galaxy is a platform for FAIR data analysis which supports the building and execution of workflows. It can import and export RO-Crates for both regular datasets and workflow executions.
LabID is an all-in-one research data management platform for life sciences institutes. It uses RO-Crate as a format to import/export workflows and workflow runs.
LifeMonitor is a testing and monitoring service for computational workflows being developed as part of the EOSC-Life project. It aims to facilitate the execution, monitoring and sharing of workflow tests over time, allowing to detect deviations from expected workflow operation and provide useful feedback to the workflow authors
WorkflowHub imports and exports Workflow RO-Crates, using it as an exchange format. They are a specialization of RO-Crate for packaging an executable workflow with all necessary documentation. It is aligned with, and intends to strictly extend, the more general Bioschemas ComputationalWorkflow profile.
Related tools
| Tool | Description | Status |
|---|---|---|
| arc-to-roc | Generate RO-Crate from an Annotated Research Context (ARC), see DataPlant. Outdated, use ARCtrl instead | deprecated |
| ARCtrl |
Software library (Python/.NET/JS) to work with Annotated Research Contexts (ARCs) and export as RO-Crate
|
stable |
| Galaxy |
Workflow system and web platform that exports Workflow RO-Crates and Workflow Run Crates of histories and invocations (from Galaxy 23.1.1)
|
production |
| galaxy2cwl | Wraps Galaxy workflow as Workflow RO-Crate | alpha |
| nf-core RO-Crate tool | Nextflow tool to generate a Workflow RO-Crate for a Nextflow pipeline | production |
| nf-prov | Nextflow plugin to render Workflow Run RO-Crates for pipeline runs | production |
| repo2crate | Generate a Workflow Testing RO-Crate from a "best-practices" workflow repository | |
| Sapporo | GA4GH WES workflow execution service that returns Workflow Run Crates for its runs | production |
| sfprov - Workflow Provenance Parser | Extract, store, and query provenance from Nextflow pipelines into Neo4j. | production |
| snakemake-report-plugin-rocrate |
Snakemake report plugin that creates a Provenance Run Crate after a workflow run
|
alpha |
| tonkaz | Tool to verify workflow reproducibility, compares RO-Crates of workflow execution results. | |
| WfExS-backend |
Workflow Execution Service backend that runs Nextflow, CWL and Galaxy workflows reproducibly, including in Trusted Research Environments, and describes executions as Workflow Run Crates
|
beta |
See the tools and resources list for all RO-Crate tools.