Paper Info
Title
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
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.
Year
DOI
Venue
2020
10.1515/jib-2020-0015
JOURNAL OF INTEGRATIVE BIOINFORMATICS
Keywords
DocType
Volume
rule-based modeling,specification,standard,systems biology
Journal
17
Issue
ISSN
Citations 
2-3
1613-4516
1
PageRank 
References 
Authors
0.35
0
14
Name
Order
Citations
PageRank
Fengkai Zhang1121.94
Lucian Smith2588.79
Michael L. Blinov319318.13
James R Faeder440931.02
William S. Hlavacek527724.15
Jose Juan Tapia610.35
Sarah M. Keating725317.80
Nicolas Rodriguez838820.80
Andreas Dräger929222.16
Leonard A Harris1010.35
Andrew Finney1110.35
Bin Hu1210.69
Hucka M131733170.84
Martin Meier-Schellersheim14354.06