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


Links: Screening and discovery protocols will be made available here.

Characterization

Controlled assays to quantify robustness, performance, and context dependence.
Typical protocols include:

  • Eco-robustness assays
  • In-planta testing
  • Phenotyping workflows

Links: Characterization protocols will be made available here.

Fermentation & Formulation

Assessment of scalability, stability, and manufacturability.
Typical protocols include:

  • Laboratory-scale fermentation
  • Formulation testing
  • Shelf-life assays

Links: Fermentation and formulation protocols will be made available here.

Field Performance

Validation under greenhouse and field conditions.
Typical protocols include:

  • Greenhouse trials
  • Field trial design
  • Performance scoring.

Links: Greenhouse and field trial protocols will be made available here.

Authoritative sources and versioning

Protocol entries on this page link to their authoritative source, including:

  • Peer-reviewed publications
  • Versioned GitHub repositories
  • Internal operational documents

Protocols are versioned, ensuring that datasets and analyses can be interpreted within the correct experimental context.

Relation to other pages

Protocols are linked to:

  • The datasets generated using them
  • The analyses performed on those datasets

This ensures traceability across the IBIS Knowledge Base, connecting experimental procedures with resulting data and analyses.