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 and the states and binding status of the involved components. Conceptually, fine-grained spatial information such as locations 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 systems biology markup language (SBML) Level 3 Multi Package Version 1 extends the SBML Level 3 Version 1 core with the “type” concept in the Species and Compartment classes. Therefore, reaction rules may contain species that can be patterns and exist in multiple locations. Multiple software tools such as Simmune and BioNetGen support this standard that thus also becomes a medium for exchanging rule-based models. This document provides the specification for Release 2 of Version 1 of the SBML Level 3 Multi package. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the correction of errata and the addition of clarifications.
Highlights
This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of systems biology markup language (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
This 8 specification includes the feature for multicompartment species as described in the releases of the Multi proposal 9
For other matters involving the use of UML, XML and typographical conventions, this document follows the 31 conventions used in the SBML Level 3 Core specification document [Hucka et al (2016)]
Summary
This Multistate, Multicomponent and Multicompartment Species (Multi) package provides an extension of SBML 2. One of its goals is to provide a platform for 4 sharing models based on the specifications of molecular transformations/interactions and the rules governing such 5 reactions [Angermann et al (2012); Feret et al (2009); Hlavacek et al (2006); Zhang et al (2013)]. This specification 6 covers the goals and features described in the previous Multi proposal [Le Novère and Oellrich (2010)] for extending 7. [Zhang and Meier-Schellersheim (2013a), Zhang et al (2012)]
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