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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Zhang, Fengkai; Smith, Lucian P; Blinov, Michael L; Faeder, James; Hlavacek, William S; Juan Tapia, Jose; Keating, Sarah M; Rodriguez, Nicolas; Dräger, Andreas; Harris, Leonard A; Finney, Andrew; Hu, Bin; Hucka, Michael; Meier-Schellersheim, Martin.
Afiliação
  • Zhang F; NIAID/NIH, Bethesda, USA.
  • Smith LP; University of Washington, Seattle, USA.
  • Blinov ML; UConn Health, Farmington, USA.
  • Faeder J; University of Pittsburgh, Pittsburgh, USA.
  • Hlavacek WS; Los Alamos National Laboratory, Los Alamos, USA.
  • Juan Tapia J; University of Pittsburgh, Pittsburgh, USA.
  • Keating SM; European Bioinformatics Institute, Cambridge, UK.
  • Rodriguez N; Babraham Institute, Cambridge, UK.
  • Dräger A; Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany.
  • Harris LA; Vanderbilt University School of Medicine, Nashville, USA.
  • Finney A; Ansys UK Ltd, Abingdon, UK.
  • Hu B; Department of Computer Science, University of Tübingen, Tübingen, Germany.
  • Hucka M; German Center for Infection Research (DZIF), partner site Tübingen, Germany.
  • Meier-Schellersheim M; Los Alamos National Laboratory, Los Alamos, USA.
J Integr Bioinform ; 17(2-3)2020 Jul 06.
Article em En | MEDLINE | ID: mdl-32628633
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Linguagens de Programação / Biologia de Sistemas Idioma: En Ano de publicação: 2020 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Linguagens de Programação / Biologia de Sistemas Idioma: En Ano de publicação: 2020 Tipo de documento: Article