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

  • 1 NIAID/NIH, Bethesda, USA
  • 2 University of Washington, Seattle, USA
  • 3 UConn Health, Farmington, USA
  • 4 University of Pittsburgh, Pittsburgh, USA
  • 5 Los Alamos National Laboratory, Los Alamos, USA
  • 6 European Bioinformatics Institute, Cambridge, UK
  • 7 Babraham Institute, Cambridge, UK
  • 8 Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
  • 9 Vanderbilt University School of Medicine, Nashville, USA
  • 10 Ansys UK Ltd, Abingdon, UK
  • 11 California Institute of Technology, Pasadena, USA
  • 12 Department of Computer Science, University of Tübingen, Tübingen, Germany
  • 13 German Center for Infection Research (DZIF), partner site Tübingen, Germany

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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Journal + Issues

The Journal of Integrative Bioinformatics is an international journal dedicated to methods and tools of computer science and electronic infrastructure applied to biotechnology. The journal covers mainly but not exclusively data/method integration, modeling, simulation and visualization in combination with applications of theoretical/computational tools and any other approach supporting an integrative view of complex biological systems.

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