Writing brief. This monograph has been assigned but the manuscript is not yet written or approved. What follows is the commissioning brief: its question, outline, evidence instructions, and review requirements.
Central question
What must travel with a parameter when it moves from a curated record into a computational model?
Reader promise
The reader will be able to inspect any exported parameter and ask whether it carries units, conditions, evidence, uncertainty, version, and intended use, and will understand what each of SBML, CellML, and OMEX contributes to a model exchange and what none of them contributes alone. The monograph presents the NucLex handoff as a design with a stated demonstration gate, not as a working interface.
Required development
- Describe units, conditions, evidence, uncertainty, versions, and intended use as six separate requirements, each with an example of what goes wrong when it is missing.
- Research the roles of SBML (Systems Biology Markup Language), CellML, and OMEX (Open Modeling EXchange format, used by the COMBINE archive): what each represents, what it leaves to annotation, and how a parameter with uncertainty would be expressed in each, citing the current specification version.
- Design a provenance-preserving handoff: what a NucLex export would contain, how the record version is carried into the model, and how a modeler's later change to a value is distinguished from the curated value.
- State the demonstration gate: a small model built from exported records, run in two independent tools, with the provenance of every parameter recoverable from the model file.
- Connect to the interaction layer. Show how an Interaction record would supply parameters and how a Compartment model would consume them.
Evidence and review
Evidence to obtain: the current SBML specification and its "What is SBML" page (sbml.org), the CellML specification, the COMBINE archive and OMEX publication, and the MIRIAM annotation guidelines, each with version and access date; peer-reviewed reports of model exchange between tools documenting what was lost or re-entered; and published guidance on expressing parameter uncertainty in exchange formats. A standards list is not evidence of compatibility; only a documented test is.
Review concern: the manuscript names standards without showing a worked exchange. The demonstration gate must be stated concretely enough that a reader could tell whether it has been met.
Planned internal links
Parameter, Uncertainty, Context, Provenance, Interaction, Compartment model, Interactional ontology for the record a parameter comes from, and Theranostic digital twins for the model that consumes it.
Review requirements
Domain review by a computational modeler who has exchanged models between tools using SBML or CellML. Source check of every statement about a format against the cited specification version. Editorial check that no exchange or API is described as existing.
Review gate for this monograph
Compatibility and validation require tests, not a standards list.
The assignment exists. The manuscript has not been written or approved.