Dependent shrink of transitions for calculating firing frequencies in signaling pathway Petri net model

DOI10.3390/A10010004MaRDI QIDQ1662584zbMATH OpenOpenAlexFDO

Authors Atsushi Mizuta, Qi-Wei Ge, Hiroshi Matsuno

Publication date 20 August 2018

Published in Algorithms (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://doi.org/10.3390/a10010004

zbMATH Keywords

dependency relationdependent shrinkPetri netretention-free Petri netsignaling pathway

Mathematics Subject Classification ID

Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Biochemistry, molecular biology (92C40)

Review text

Summary: Despite the recent rapid progress in high throughput measurements of biological data, it is still difficult to gather all of the reaction speed data in biological pathways. This paper presents a Petri net-based algorithm that can derive estimated values for non-valid reaction speeds in a signaling pathway from biologically-valid data. In fact, these reaction speeds are reflected based on the delay times in the timed Petri net model of the signaling pathway. We introduce the concept of a ``dependency relation over a transition set of a Petri net and derive the properties of the dependency relation through a structural analysis. Based on the theoretical results, the proposed algorithm can efficiently shrink the transitions with two elementary structures into a single transition repeatedly to reduce the Petri net size in order to eventually discover all transition sets with a dependency relation. Finally, to show the usefulness of our algorithm, we apply our algorithm to the IL-3 Petri net model.

Recommendations

• Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks
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• Applications and Theory of Petri Nets 2004
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Cites work

• Applications and Theory of Petri Nets 2004
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Uses Software

• TRANSPATH
• PNML

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