Abstract
Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains (components) and the states such as phosphorylation and binding status of the involved components. Fine-grained spatial information such as the locations of the molecular components relative to a membrane (e.g. whether a modeled molecular domain is embedded into the inner leaflet of the cellular plasma membrane) can also be provided. Through wildcards representing component states entire families of molecule complexes sharing certain properties can be specified as patterns. This can significantly simplify the definition of models involving species with multiple components, multiple states and multiple compartments. The SBML Level 3 Multi Package (Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3) extends the SBML Level 3 core with the “type” concept in the Species and Compartment classes and therefore reaction rules may contain species that can be patterns and be in multiple locations in reaction rules. Multiple software tools such as Simmune and BioNetGen support the SBML Level 3 Multi package that thus also becomes a medium for exchanging rule-based models.
Highlights
This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of SBML 2Level 3 [Hucka et al (2016)] that supports encoding models with molecular complexes that have multiple compo- 3 nents and can exist in multiple states and in multiple compartments
[Angermann et al (2012); Feret et al (2009); Hlavacek et al (2006); Zhang et al (2013)]. This specification covers the 6 goals and features described in the previous Multi proposal [Le Novère and Oellrich (2010)] for extending SBML 7 to carry the information for multistate multicomponent species with revised data structure
This 8 specification includes the feature for multicompartment species as described in the releases of the Multi proposal 9
Summary
This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of SBML 2. [Angermann et al (2012); Feret et al (2009); Hlavacek et al (2006); Zhang et al (2013)] This specification covers the 6 goals and features described in the previous Multi proposal [Le Novère and Oellrich (2010)] for extending SBML 7 to carry the information for multistate multicomponent species with revised data structure. This 8 specification includes the feature for multicompartment species as described in the releases of the Multi proposal 9. [Zhang and Meier-Schellersheim (2013a), Zhang et al (2012)]
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