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

Zhang, Fengkai and Smith, Lucian P. and Blinov, Michael L. and Faeder, James and Hlavacek, William S. and Tapia, Jose Juan and Keating, Sarah M. and Rodriguez, Nicolas and Dräger, Andreas and Harris, Leonard A. and Finney, Andrew and Hu, Bin and Hucka, Michael and Meier-Schellersheim, Martin (2020) Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. Journal of Integrative Bioinformatics, 17 (2-3). Art. No. 20200015. ISSN 1613-4516. https://resolver.caltech.edu/CaltechAUTHORS:20200713-124645293

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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 amedium 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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1515/jib-2020-0015DOIArticle
ORCID:
AuthorORCID
Zhang, Fengkai0000-0001-7112-9328
Smith, Lucian P.0000-0001-7002-6386
Blinov, Michael L.0000-0002-9363-9705
Faeder, James0000-0001-8127-609X
Hlavacek, William S.0000-0003-4383-8711
Keating, Sarah M.0000-0002-3356-3542
Dräger, Andreas0000-0002-1240-5553
Hucka, Michael0000-0001-9105-5960
Meier-Schellersheim, Martin0000-0002-8754-6377
Additional Information:© 2020 Fengkai Zhang et al., published by De Gruyter. Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. Received April 1, 2020; accepted April 20, 2020; Published online: 06 Jul 2020. This work was supported by the Intramural Research Program of the US National Institute of Allergy and Infectious Diseases of the National Institutes of Health. We sincerely thank all the contributors and their funding agencies. L.P.S., S.M.K, N.R., A.D., F.B. and M.H. were supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01 GM070923. In addition, A.D. was supported by 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; and F.B. was supported by the Bundesministeriumfür Bildung und Forschung (BMBF, DE) grant de.NBIModSim1, 031L0104A. M.L.B. was supported by NIH (US) grant P41 GM103313 and R24 GM134211. J.F. and J.J.T. were supported by National Institutes of Health (NIH, US) grant P41 GM103712 to the National Center for Multiscale Modeling of Biological Systems (MMBioS).W.S.H was supported by the National Institute of General Medical Sciences (NIGMS, US) grant R01 GM111510.
Group:Library System Papers and Publications
Funders:
Funding AgencyGrant Number
National Institute of Allergy and Infectious DiseasesUNSPECIFIED
NIHR01 GM070923
Deutsches Zentrum für Infektionsforschung (DZIF)UNSPECIFIED
Deutsche Forschungsgemeinschaft (DFG)EXC 2124
Bundesministerium für Bildung und Forschung (BMBF)de.NBIModSim1
Bundesministerium für Bildung und Forschung (BMBF)031L0104A
NIHP41 GM103313
NIHR24 GM134211
NIHP41 GM103712
NIHR01 GM111510
Subject Keywords:rule-based modeling; specification; standard; systems biology
Issue or Number:2-3
Record Number:CaltechAUTHORS:20200713-124645293
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200713-124645293
Official Citation:Zhang, F., Smith, L. P., Blinov, M. L., Faeder, J., Hlavacek, W. S., Juan Tapia, J., Keating, S. M., Rodriguez, N., Dräger, A., Harris, L. A., Finney, A., Hu, B., Hucka, M., & Meier-Schellersheim, M. (2020). Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2, Journal of Integrative Bioinformatics, 17(2-3), 20200015. doi: https://doi.org/10.1515/jib-2020-0015
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104357
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:13 Jul 2020 20:04
Last Modified:09 Sep 2020 17:18

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