Protocols
Protocols define how IBIS data are generated. They specify experimental procedures, assay conditions, and quality controls, and provide the context required to interpret data and analyses. This page gives an overview of the IBIS development pipeline and links to the authoritative protocol descriptions used at each stage.
Protocols in the IBIS pipeline
IBIS structures research and development as a sequence of connected stages:
Discovery → Characterization → Fermentation & Formulation → Field Performance
Each stage is supported by standardized protocols that ensure reproducibility and comparability across experiments and sites.
Pipeline stages and protocol types
Discovery
Identification and initial screening of candidate microorganisms.
Typical protocols include:
- Strain isolation
- Primary trait screening
- Initial biosafety assessment
Characterization
Controlled assays to quantify robustness, performance, and context dependence.
Typical protocols include:
- Eco-robustness assays
- In-planta testing
- Phenotyping workflows
Fermentation & Formulation
Assessment of scalability, stability, and manufacturability.
Typical protocols include:
- Laboratory-scale fermentation
- Formulation testing
- Shelf-life assays
Field Performance
Validation under greenhouse and field conditions.
Typical protocols include:
- Greenhouse trials
- Field trial design
- Performance scoring.
Authoritative sources and versioning
Protocol entries on this page link to their authoritative source, including:
- Peer-reviewed publications
- Versioned GitHub repositories
- Internal operational documents
Relation to other pages
Protocols are linked to:
- The datasets generated using them
- The analyses performed on those datasets