Model verification framework with application to molecular biology

Valeria Perelman, Judith Somekh, Dov Dori

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

A myriad of detailed pieces of knowledge regarding the structure and function of the living cell have been accumulating at an alarmingly increasing rate. Emphasis is shifting from the study of a single molecular process to cellular pathways, cycles, and the entire cell as a system. Object-Process Methodology (OPM) is a holistic graphical modeling methodology that combines the behavioral and structural aspects of a system in a single model. The OPM methodology includes OPM-based development process, OPM Case Tool (OPCAT), and a modeling language. A framework for supporting the biological researcher for hypotheses modeling and verification is proposed. The framework consists of (1) OPM modeling of complex molecular biological systems intuitively yet formally and (2) a set of translation rules from OPM to a finite-state transition system (FTS) to enable model verification. An example from the mRNA transcription subsystem of gene expression demonstrates OPM-based modeling and its translation into FTS.

Original languageEnglish
Title of host publicationTheory of Modeling and Simulation
Subtitle of host publicationDEVS Integrative M and S Symposium 2011, TMS-DEVS 2011 - 2011 Spring Simulation Multiconference, SpringSim 2011
Pages140-145
Number of pages6
Edition1 BOOK 4
StatePublished - 2011
Externally publishedYes
EventTheory of Modeling and Simulation: DEVS Integrative M and S Symposium 2011, TMS-DEVS 2011, Part of the 2011 Spring Simulation Multiconference, SpringSim 2011 - Boston, MA, United States
Duration: 3 Apr 20117 Apr 2011

Publication series

NameSimulation Series
Number1 BOOK 4
Volume43
ISSN (Print)0735-9276

Conference

ConferenceTheory of Modeling and Simulation: DEVS Integrative M and S Symposium 2011, TMS-DEVS 2011, Part of the 2011 Spring Simulation Multiconference, SpringSim 2011
Country/TerritoryUnited States
CityBoston, MA
Period3/04/117/04/11

Keywords

  • Finite-state transition systems
  • Formal verification
  • Systems biology

ASJC Scopus subject areas

  • Computer Networks and Communications

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