matlab-build-simbiology-model

What it does

Build, modify, and diagram SimBiology models using API references, helper functions, and layout patterns. Intended for constructing or editing models programmatically or visually, with diagram features activated when the user requests visual output via the Model Builder.

How it works

The skill instructs users to: add and modify compartments, species, parameters, and reactions using standard SimBiology API (e.g., addcompartment, addspecies, addparameter, addreaction); follow rules for reaction direction and qualified naming; use modern property names (Value, Units, Constant); and manage the Model Builder/Analyzer lifecycle to preserve diagrams when requested. It provides helper functions (in scripts/) such as getModelByUUID, addAndPositionCompartment (to create a compartment with species in one step for diagrams), checkDiagramLayout, repositionAllReactions, positionAncillaryBlocks, and openLiveBuilder. For diagram workflows, it prescribes a sequence: open Builder, plan positions, build compartments with addAndPositionCompartment, then add parameters/reactions/rules/doses/events, run layout checks, reposition reactions, and finally position ancillary blocks. It also includes patterns for safe opening of the Builder and guidelines to avoid closing the Builder mid-modification. It lists API references for common operations (Model, Compartments, Species, Parameters, Reactions, Rules/Events/Doses, Observables/Variants, Simulation Config, and Selection).

When to use it

• Building or modifying SimBiology models (compartments, species, reactions, parameters, rules, events, doses, observables, variants)
• Opening, saving, or loading models in the Model Builder / Analyzer apps
• Designing or adjusting diagram layouts
• Keywords include: build, create, modify, add compartment/species/reaction, diagram, layout

What it can touch

• MATLAB environment requires adding helper scripts to path: addpath(fullfile('<WORKSPACE_ROOT>', '.claude', 'skills', 'matlab-build-simbiology-model', 'scripts'));
• Uses functions from scripts/ such as getModelByUUID, addAndPositionCompartment, checkDiagramLayout, computeSafeReactionPosition, repositionAllReactions, positionAncillaryBlocks, openLiveBuilder, isAppOpen, loadViaBuilder, saveViaBuilder, and diagram utilities like simbio.diagram.*. Commands and file names are referenced exactly as shown in the skill.
• Example code snippets use MATLAB commands: sbiomodel, addcompartment, addspecies, addparameter, addreaction, addkineticlaw, PKModelDesign, loadViaBuilder, loadViaBuilder(filePath), sbioreset, simBiologyModelBuilder, isAppOpen, getModelByUUID, addAndPositionCompartment, checkDiagramLayout, repositionAllReactions, positionAncillaryBlocks, computeSafeReactionPosition, simbio.diagram.setBlock, and related properties like Value, Units, Constant.

Caveats

• Diagram features require the Model Builder app and are activated only when the user requests visual output.
• The rules emphasize using qualified names for species and reaction-scoped parameters and adopting modern property names (Value, Units, Constant).
• Diagram layout steps are conditional on user request; for pure model construction, diagram steps are skipped.
• The approach involves managing Builder state (opening/closing) to avoid orphaned windows or conflicts when sbioreset is called.
• No guarantees of successful diagram rendering beyond the scripted checks (checkDiagramLayout outcomes must indicate zero violations before presenting diagrams).