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

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Presentation on theme: "Look for other standards: - BioPAX (composition) - CellML (aggregation) - Other SBML L3 extensions (modules - rule-based modeling)"— Presentation transcript:

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

2 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

3 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

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6 Fictional species. Relationships, e.g. has a component, isVersionOf

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

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9 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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