SBOL3 Synthetic Biology Genetic Circuits (.sbol, .ttl, .rdf)

@modelscript/sbol (languages/sbol) provides native WebAssembly parsing, Sequence Ontology (SO) and Systems Biology Ontology (SBO) genetic circuit verification, Hill-function transcriptional activation/repression ODE simulation, DAEBuilder lowering, and SBML / Modelica projections for Synthetic Biology Open Language (SBOL 3.x) genetic designs.

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Supported Extensions & Standards

Extension	Format	Description
.sbol, .rdf, .xml	SBOL RDF/XML	Standard RDF/XML serialization of sbol:Component, sbol:Sequence, sbol:SubComponent, and sbol:Interaction
.ttl	SBOL3 Turtle	Compact RDF Turtle representation of SBOL3 genetic circuits and sequence constraints

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Key Capabilities

1. Genetic Parts, Sequence Constraints & Interactions

• Parses Component definitions typed with Sequence Ontology (SO) roles:
  • Promoter (SO:0000167), RBS (SO:0000139), CDS (SO:0000316), Terminator (SO:0000141), and Engineered Region (SO:0000804).
• Extracts Interaction and Participation graphs typed with Systems Biology Ontology (SBO) terms:
  • Genetic Production (SBO:0000589), Transcriptional Stimulation (SBO:0000170), Transcriptional Inhibition (SBO:0000169), and Degradation (SBO:0000179).

2. Hill-Function Genetic Circuit ODE Solver

• Automatically synthesizes and integrates coupled mRNA and protein concentration ODEs using cooperative Hill kinetics:$$\frac{d[P_i]}{dt}={\alpha }_{0,i}+{\alpha }_i\frac{[A{]}^n}{K_A^n+[A{]}^n}\cdot \frac{K_R^m}{K_R^m+[R{]}^m}-{\gamma }_i[P_i]$$supporting toggle switches, repressilators, and inducible biosensors.

3. DAE Lowering & SBML / Modelica Projection

• Lowers synthetic genetic circuit dynamics into @modelscript/runtime's DAEBuilder arena and exports to SBML Level 3 (sbolToSbml) and Modelica 3.x (sbolToModelica).

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Pre-Flight Diagnostics

10 rules7 error3 warning

Code	Rule	Severity	Message
M9501	invalid-nucleotide-sequence	error	Sequence '<seqId>' contains characters outside the IUPAC nucleic acid alphabet ('<invalidChar>').
M9502	sequence-range-out-of-bounds	error	Feature '<featureId>' location '[<start>..<end>]' exceeds sequence '<seqId>' length '<seqLength>'.
M9503	cds-length-not-multiple-of-three	warning	Coding sequence (CDS) '<cdsId>' nucleotide length ('<length>') is not divisible by 3 or lacks a valid start/stop codon.
M9504	unresolved-subcomponent-reference	error	SubComponent '<subId>' in '<compId>' references undefined Component '<instanceOf>'.
M9505	invalid-transcriptional-unit-order	error	Engineered region '<compId>' places terminator '<termId>' upstream of promoter '<promId>' without an intervening CDS.
M9506	dangling-interaction-participant	error	Interaction '<intId>' participant references undefined component '<participantId>'.
M9507	missing-interaction-role	warning	Participant '<participantId>' in interaction '<intId>' lacks a Systems Biology Ontology (SBO) role (inhibitor, stimulator, template, product).
M9508	circular-component-hierarchy	error	SubComponent hierarchy contains a circular containment reference involving '<compId>'.
M9509	duplicate-display-id	error	displayId '<id>' is declared multiple times within the '<namespace>' namespace.
M9510	missing-cds-ribosome-binding-site	warning	Bacterial transcriptional unit '<compId>' contains CDS '<cdsId>' without an upstream RBS ('SO:0000139').

Generated from languages/sbol/src/errors.ts. All languages →

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CLI Usage

# Validate SO/SBO ontology roles, transcriptional unit ordering, and sequence encoding
msx lint GeneticToggleSwitch.sbol

# Parse and inspect SBOL3 RDF/XML or Turtle circuits
msx parse GeneticToggleSwitch.sbol