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Intentional Semantics for Molecular Biology

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Advances in Bioinformatics and Computational Biology (BSB 2023)


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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  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.


  1. Blätke, M.A., Rohr, C., Heiner, M., Marwan, W.: A petri-net-based framework for biomodel engineering. In: Benner, P., Findeisen, R., Flockerzi, D., Reichl, U., Sundmacher, K. (eds.) Large-Scale Networks in Engineering and Life Sciences. MSSET, pp. 317–366. Springer, Cham (2014).

    Chapter  Google Scholar 

  2. Chaudhuri, P.P., Ghosh, S., Dutta, A., Choudhury, S.P.: A New Kind of Computational Biology: Cell Automata Based Models for Genomics and Proteomics (2018)

    Google Scholar 

  3. Crick, F.: Central dogma of molecular biology. Nature 227(5258), 561–563 (1970)

    Article  CAS  PubMed  Google Scholar 

  4. Diercks, C.S., Dik, D.A., Schultz, P.G.: Adding new chemistries to the central dogma of molecular biology. Chem 7(11), 2883–2895 (2021)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Herajy, M., Liu, F., Rohr, C., Heiner, M.: Coloured hybrid petri nets: an adaptable modelling approach for multi-scale biological networks. Comput. Biol. Chem. 76, 87–100 (2018)

    Article  CAS  PubMed  Google Scholar 

  6. Kleene, S.C.: \(\lambda \)-definability and recursiveness. Duke Math. J. 2(2), 340–353 (1936)

    Article  Google Scholar 

  7. Koch, I., Reisig, W., Schreiber, F.: Modeling in Systems Biology: The Petri Net Approach, vol. 16. Springer, London (2010).

  8. Köhler, M., Rölke, H.: Properties of object petri nets. In: Cortadella, J., Reisig, W. (eds.) ICATPN 2004. LNCS, vol. 3099, pp. 278–297. Springer, Heidelberg (2004).

    Chapter  Google Scholar 

  9. Lakos, C.A.: The object orientation of object Petri nets. Department of Computer Science, University of Tasmania (1995)

    Google Scholar 

  10. Petri, C.A.: Kommunikation mit automaten. Ph.D. thesis, Math. Uni. Bonn (1962)

    Google Scholar 

  11. Piques, M., et al.: Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol. Syst. Biol. 5(1), 314 (2009)

    Article  PubMed  PubMed Central  Google Scholar 

  12. Singh, N., Singh, A., Singh, S., Kumar, V.: Modeling and analysis of biological systems using petri nets: a review. J. Theor. Biol. 335, 94–105 (2013)

    Google Scholar 

  13. Tan, C.L., Anderson, E.: The new central dogma of molecular biology. Resonance 14(3), 1–32 (2020)

    Google Scholar 

  14. Turing, A.M.: On computable numbers, with an application to the Entscheidungsproblem. Proc. London Math. Soc. s2–42(1), 230–265 (1937)

    Google Scholar 

  15. Valk, R.: Object petri nets. In: Desel, J., Reisig, W., Rozenberg, G. (eds.) ACPN 2003. LNCS, vol. 3098, pp. 819–848. Springer, Heidelberg (2004).

    Chapter  Google Scholar 

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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.

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  • Print ISBN: 978-3-031-42714-5

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