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BY-NC-ND 4.0 license Open Access Published by De Gruyter April 20, 2018

SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1

Fengkai Zhang ORCID logo EMAIL logo and Martin Meier-Schellersheim

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.

Received: 2017-12-8
Accepted: 2018-2-1
Published Online: 2018-4-20

©2018 Fengkai Zhang et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Downloaded on 29.1.2023 from https://www.degruyter.com/document/doi/10.1515/jib-2017-0077/html
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