Intentional Semantics for Molecular Biology

Resumo


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.

Referências

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). https://doi.org/10.1007/978-3-319-08437-4_6

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)

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

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)

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)

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

Koch, I., Reisig, W., Schreiber, F.: Modeling in Systems Biology: The Petri Net Approach, vol. 16. Springer, London (2010). https://doi.org/10.1007/978-1-84996-474-6

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). https://doi.org/10.1007/978-3-540-27793-4_16

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

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

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

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)

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

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

Valk, R.: Object petri nets. In: Desel, J., Reisig, W., Rozenberg, G. (eds.) ACPN 2003. LNCS, vol. 3098, pp. 819–848. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-540-27755-2_23
Publicado
13/06/2023
HAEUSLER, Edward H. et al. Intentional Semantics for Molecular Biology. In: SIMPÓSIO BRASILEIRO DE BIOINFORMÁTICA (BSB), 16. , 2023, Curitiba/PR. Anais [...]. Porto Alegre: Sociedade Brasileira de Computação, 2023 . p. 94-105. ISSN 2316-1248.