Gamache-Poirier S, Souvane A, Leclerc W, Villeneuve C, Hardy SV. An algorithm for the transformation of the Petri net models of biological signaling networks into influence graphs.
Biosystems 2025;
250:105415. [PMID:
39986345 DOI:
10.1016/j.biosystems.2025.105415]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 02/01/2025] [Accepted: 02/09/2025] [Indexed: 02/24/2025]
Abstract
A common depiction for biological signaling networks is the influence graph in which the activation and inhibition effects between molecular species are shown with vertices and arcs connecting them. Another formalism for reaction-based models is the Petri nets which has a graphical representation and a mathematical notation that enables structural analysis and quantitative simulation. In this paper, we present an algorithm based on Petri nets topological features for the transformation of the computational model of a biological signaling network into an annotated influence graph. We also show the transformation of the Petri nets model of the beta-adrenergic receptor activating the PKA-MAPK signaling network into its representation as an influence graph.
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