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Clocked Transition System as an OPM Formalism with Application to Systems Biology

Valeria Perelman, Dov Dori and Judith Somekh

Symposium On Theory of Modeling and Simulation - DEVS Integrative M&S Symposium (TMS/DEVS 2011)
Boston, MA, USA, April 4-9, 2011


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. A framework for supporting the biological researcher for hypotheses verification is proposed. The framework includes molecular biological systems modeling and verification against pertinent literature. Object-Process Methodology (OPM) is a holistic modeling language which is proposed to represent complex biological systems intuitively yet formally. A Clocked Transition System (CTS) is also part of the framework, as is a set of translation rules from OPM to CTS. We apply the translation rules for verification of OPM models. An example from the mRNA transcription subsystem of gene expression demonstrates the value of our system to filling knowledge gap and assessing the feasibility of given conjectures.

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