Innovations of the rule-based modeling approach

Lily A. Chylek, Edward C. Stites, Richard G Posner, William S. Hlavacek

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Citations (Scopus)

Abstract

New modeling approaches are needed to tackle the complexity of cell signaling systems. An emerging approach is rule-based modeling, in which protein-protein interactions are represented at the level of functional components. By using rules to represent interactions, a modeler can avoid enumerating the reachable chemical species in a system, which is a necessity in traditional modeling approaches. A set of rules can be used to generate a reaction network, or to perform simulations with or without network generation. Although the rule-based approach is a relatively recent development in biology, it is based on concepts that have proven useful in other fields. In this chapter, we discuss innovations of the rule-based modeling approach, relative to traditional approaches for modeling chemical kinetics. These innovations include the use of rules to concisely capture the dynamics of molecular interactions, the view of models as programs, and agent-based computational approaches that can be applied to simulate the chemical kinetics of a system characterized by a large traditional model. These innovations should enable the development of models that can relate the molecular state of a cell to its phenotype, even though vast and complex networks bridge perturbations at the molecular level to fates and activities at the cellular level. In the future, we expect that validated rule-based models will be useful for modelguided studies of cell signaling mechanisms, interpretation of temporal phosphoproteomic data, and cell engineering applications.

Original languageEnglish (US)
Title of host publicationSystems Biology: Integrative Biology and Simulation Tools
PublisherSpringer Netherlands
Pages273-300
Number of pages28
ISBN (Print)9789400768031, 9789400768024
DOIs
StatePublished - Jan 1 2013

Fingerprint

Cell Engineering
Molecular Dynamics Simulation
Proteins
Phenotype

Keywords

  • Cell signaling
  • Chemical kinetics
  • Combinatorial complexity
  • Computational modeling
  • Formal languages
  • Proteinprotein interactions
  • Rule-based modeling
  • Simulation algorithms

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Chylek, L. A., Stites, E. C., Posner, R. G., & Hlavacek, W. S. (2013). Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools (pp. 273-300). Springer Netherlands. https://doi.org/10.1007/978-94-007-6803-1_9

Innovations of the rule-based modeling approach. / Chylek, Lily A.; Stites, Edward C.; Posner, Richard G; Hlavacek, William S.

Systems Biology: Integrative Biology and Simulation Tools. Springer Netherlands, 2013. p. 273-300.

Research output: Chapter in Book/Report/Conference proceedingChapter

Chylek, LA, Stites, EC, Posner, RG & Hlavacek, WS 2013, Innovations of the rule-based modeling approach. in Systems Biology: Integrative Biology and Simulation Tools. Springer Netherlands, pp. 273-300. https://doi.org/10.1007/978-94-007-6803-1_9
Chylek LA, Stites EC, Posner RG, Hlavacek WS. Innovations of the rule-based modeling approach. In Systems Biology: Integrative Biology and Simulation Tools. Springer Netherlands. 2013. p. 273-300 https://doi.org/10.1007/978-94-007-6803-1_9
Chylek, Lily A. ; Stites, Edward C. ; Posner, Richard G ; Hlavacek, William S. / Innovations of the rule-based modeling approach. Systems Biology: Integrative Biology and Simulation Tools. Springer Netherlands, 2013. pp. 273-300
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