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BY 4.0 license Open Access Published by De Gruyter July 6, 2020

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Fengkai Zhang ORCID logo EMAIL logo , Lucian P. Smith ORCID logo , Michael L. Blinov ORCID logo , James Faeder ORCID logo , William S. Hlavacek ORCID logo , Jose Juan Tapia ORCID logo , Sarah M. Keating ORCID logo , Nicolas Rodriguez ORCID logo , Andreas Dräger ORCID logo , Leonard A. Harris ORCID logo , Andrew Finney , Bin Hu ORCID logo , Michael Hucka ORCID logo and Martin Meier-Schellersheim ORCID logo

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.


Corresponding author: Fengkai Zhang, NIAID/NIH, Bethesda, USA, E-mail:

Funding source: the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health

Funding source: National Institute of GeneralMedical Sciences (NIGMS, US)

Award Identifier / Grant number: R01 GM070923

Funding source: the DZIF (German Center for Infection Research) and by infrastructural funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections

Funding source: the Bundesministeriumfür Bildung und Forschung (BMBF, DE)

Award Identifier / Grant number: de.NBIModSim1, 031L0104A

Funding source: NIH (US)

Award Identifier / Grant number: P41 GM103712

Funding source: National Institute of General Medical Sciences (NIGMS, US)

Award Identifier / Grant number: R01 GM111510

Received: 2020-04-01
Accepted: 2020-04-20
Published Online: 2020-07-06

© 2020 Fengkai Zhang et al., published by De Gruyter. Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

Downloaded on 9.12.2022 from https://www.degruyter.com/document/doi/10.1515/jib-2020-0015/html
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