This paper proposes a simplification of the stochastic Petri nets graphical notation with the purpose of defining a more compact and clearer graphical way of building formal models of biological phenomena. Three biological examples are first presented, then modeled with the classical SPN modeling formalism, and their key modeling patterns distilled to identify the main features that need to be represented in a stochastic model. The key features are then the object of the original part of the paper, in which a simplified and more concise, although formal, graphical notation, is proposed, and applied to the selected examples. The paper demonstrates the effectiveness of the simplified notation in producing more compact and understandable models of biological phenomena, still retaining the nice properties of Stochastic Petri Nets, i.e., their flexible abstraction level and formal semantics.

Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena / Mura, Ivan. - ELETTRONICO. - (2007), pp. 1-29.

Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena

2007-01-01

Abstract

This paper proposes a simplification of the stochastic Petri nets graphical notation with the purpose of defining a more compact and clearer graphical way of building formal models of biological phenomena. Three biological examples are first presented, then modeled with the classical SPN modeling formalism, and their key modeling patterns distilled to identify the main features that need to be represented in a stochastic model. The key features are then the object of the original part of the paper, in which a simplified and more concise, although formal, graphical notation, is proposed, and applied to the selected examples. The paper demonstrates the effectiveness of the simplified notation in producing more compact and understandable models of biological phenomena, still retaining the nice properties of Stochastic Petri Nets, i.e., their flexible abstraction level and formal semantics.
2007
Trento
The Microsoft Research - University of Trento Centre for Computational and Systems Biology
Simplifying the Stochastic Petri Nets Formalism for Representing Biological Phenomena / Mura, Ivan. - ELETTRONICO. - (2007), pp. 1-29.
Mura, Ivan
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/358549
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