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Intentional Semantics for Molecular Biology

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Advances in Bioinformatics and Computational Biology (BSB 2023)

Abstract

This article presents an intentional semantics, using Object Petri Nets (OPNs), to assign activity to each biological molecule and complex, such as mRNA, tRNA, ribosomes, and protein synthesis. The work differs from traditional uses of Petri Nets in Biology and Chemistry for being a bottom-up and general semantics and not only a formalization of some molecular biological phenomenon. Assigning activities to every molecule and the difference between biological function and activity is also a conceptual contribution of this work. To illustrate our semantics, we set to tRNA, mRNA, ribosome, and the protein transcription molecular complex the respective activities expressed by OPNs.

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Notes

  1. 1.

    The time is not explicitly used in this paper. It appears here due to the completeness of the intended model.

  2. 2.

    We must not confuse model of computation with computational model; the latter is a mathematical model of something that can be simulated or performed in a computer.

  3. 3.

    The alphabet in question is \(\{s,z,P,\circ ,Rec_{p},\langle , \rangle , \mu ,\ldots \}\) with 20 letters.

  4. 4.

    A true concurrency model can be taken as a framework to describe systems that allow many independent processes or threads to run simultaneously without interfering with each other model.

  5. 5.

    If \(\pi \) is an OPN, then \(pl(\pi )\) is the number of output and input places in \(\pi \), \([\pi ]\) is the equivalence class of \(\pi \) under isomorphism on OPNs and P is the natural projection.

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Correspondence to Edward H. Haeusler .

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Haeusler, E.H. et al. (2023). Intentional Semantics for Molecular Biology. In: Reis, M.S., de Melo-Minardi, R.C. (eds) Advances in Bioinformatics and Computational Biology. BSB 2023. Lecture Notes in Computer Science(), vol 13954. Springer, Cham. https://doi.org/10.1007/978-3-031-42715-2_9

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  • DOI: https://doi.org/10.1007/978-3-031-42715-2_9

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