Model verification framework with application to molecular biology (Work-in-Progress)

Authors:
Valeria Perelman;Judith Somekh;Dov Dori
Affiliations:
Technion, Israel Institute of Technology;Technion, Israel Institute of Technology;Technion, Israel Institute of Technology and Massachusetts Institute of Technology
Venue:
Proceedings of the 2011 Symposium on Theory of Modeling & Simulation: DEVS Integrative M&S Symposium
Year:
2011

Citing 4
Cited 0

Object-Process Methodology: A Holistic Systems Paradigm

Object-Process Methodology: A Holistic Systems Paradigm
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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.