Look for other standards: - BioPAX (composition) - CellML (aggregation) - Other SBML L3 extensions (modules - rule-based modeling)

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Presentation transcript:

Look for other standards: - BioPAX (composition) - CellML (aggregation) - Other SBML L3 extensions (modules - rule-based modeling)

Unique classification and identification of model elements Different types of species: proteins, small molecules, complexes. Different types of reactions: biochemical reaction, complex assembly User-specified grouping: ligand- binding module, Grb2 interactions

Structure consistent with BioPAX ontology BioPax stands for Biological PAthway eXchange Interaction ControlConversion Catalysis Biochemical Reaction Complex Assembly Modulation Transport TransportWith BiochemicalReaction Physical Entity Complex RNA Protein Small Molecule

<species compartment="R_7660" id="REACT_4932_2" metaid="metaid_ " name="REACT_4932_2_Cyclin_A_Cdk2_complex"> <rdf:RDF xmlns:bqbiol=" xmlns:bqmodel=" xmlns:dc=" xmlns:dcterms=" xmlns:rdf=" xmlns:vCard=" Fictional species. Relationships, e.g. has a component, isVersionOf

dEGF/dt = -v1 dR/dt = -v1 dRa/dt = v1

reaction rules = modules begin reaction rules A(b) + B(a) A(b!1).B(a!1) kp1,km1 end reaction rules A B b a + A B a bond between two components molecule types = interfaces begin molecule types A(b, b1, b2, …) B(a, a1, a2, …) end molecule types A B b a b1 a1

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