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2020 | OriginalPaper | Chapter

What is a Cell Cycle Checkpoint? The `TotemBioNet` Answer

Authors : Déborah Boyenval, Gilles Bernot, Hélène Collavizza, Jean-Paul Comet

Published in: Computational Methods in Systems Biology

Publisher: Springer International Publishing

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Abstract

TotemBioNet is a new software platform to assist the design of qualitative regulatory network models by combining “genetically modified Hoare logic”, temporal logic model checking and optimized enumeration techniques. TotemBioNet is particularly efficient to manage parameter identification, the most critical step of formal modelling. It is also remarkably flexible and efficient to check properties in order to explore biological assumptions. To illustrate this efficacy, we address the classical example of the cell cycle, where the passage from one phase to the next one, called checkpoint, is crucial but is usually a rather fuzzy informal concept. The cyclic behaviour of the cell cycle is specified by temporal logic and the order of individual events inside each phase is explored thanks to quantifiers introduced in Hoare logic. This way, TotemBioNet rapidly suggests a sensible formalization of the notion of checkpoint.

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Batt, G., Bergamini, D., de Jong, H., Garavel, H., Mateescu, R.: Model checking genetic regulatory networks using GNA and CADP. In: Graf, S., Mounier, L. (eds.) SPIN 2004. LNCS, vol. 2989, pp. 158–163. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-540-24732-6_12CrossRefMATH

Behaegel, J., Comet, J.P., Bernot, G., Cornillon, E., Delaunay, F.: A hybrid model of cell cycle in mammals. J. Bioinform. Comput. Biol. 14(1), 1640001 (2016)CrossRef

Bernot, G., Comet, J.P., Khalis, Z., Richard, A., Roux, O.F.: A genetically modified Hoare logic. Theor. Comput. Sci. 765, 145–157 (2019)MathSciNetCrossRef

Bernot, G., Comet, J.P., Richard, A., Guespin, J.: Application of formal methods to biological regulatory networks: extending Thomas’ asynchronous logical approach with temporal logic. J. Theor. Biol. 229(3), 339–347 (2004)MathSciNetCrossRef

Chabrier, N., Fages, F.: Symbolic model checking of biochemical networks. In: Priami, C. (ed.) CMSB 2003. LNCS, vol. 2602, pp. 149–162. Springer, Heidelberg (2003). https://doi.org/10.1007/3-540-36481-1_13

Cimatti, A., et al.: NuSMV 2: an OpenSource tool for symbolic model checking. In: Brinksma, E., Larsen, K.G. (eds.) CAV 2002. LNCS, vol. 2404, pp. 359–364. Springer, Heidelberg (2002). https://doi.org/10.1007/3-540-45657-0_29CrossRef

Fages, F., Soliman, S.: On robustness computation and optimization in BIOCHAM-4. In: Češvka, M., Šafránek, D. (eds.) CMSB 2018. LNCS, vol. 11095, pp. 292–299. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-99429-1_18

Folschette, M.: The Hoare-fol tool. Technical report, Univ. Lille & CNRS UMR 9189 (2019). https://hal.archives-ouvertes.fr/hal-02409801

Guziolowski, C., et al.: Exhaustively characterizing feasible logic models of a signaling network using answer set programming. Bioinformatics 30, 1942 (2013)

10.

Kauffman, S.A.: Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22(3), 437–467 (1969)

11.

Naldi, A., et al.: The CoLoMoTo interactive notebook. Front. Physiol. 9, 680 (2018)CrossRef

12.

Remy, E., Ruet, P., Mendoza, L., Thieffry, D., Chaouiya, C.: From logical regulatory graphs to standard Petri nets: dynamical roles and functionality of feedback circuits. In: Transactions on Computational Systems Biology VII, pp. 56–72 (2006)

13.

Richard, A.: Fair Paths in CTL (2008). https://gitlab.com/totembionet/totembionet

14.

Schwab, J., Kühlwein, S., Ikonomi, N., Kühl, M., Kestler, H.: Concepts in Boolean network modeling: what do they all mean? Comput. Struct. Biotechnol. J. 18, 571-582 (2020)

15.

Snoussi, E.: Qualitative dynamics of a piecewise-linear differential equations: a discrete mapping approach. Dyn. Stab. Syst. 4, 189–207 (1989)MathSciNetMATH

16.

Streck, A., Thobe, K., Siebert, H.: Comparative statistical analysis of qualitative parametrization set, September 2015

17.

Thomas, R.: Boolean formalization of genetic control circuits. J. Theor. Biol. 42(3), 563–585 (1973)

18.

Thomas, R.: Logical analysis of systems comprising feedback loops. J. Theor. Biol. 73(4), 631–56 (1978)CrossRef

19.

Thomas, R., Gathoye, A., Lambert, L.: A complex control circuit. Regulation of immunity in temperate bacteriophages. Eur. J. Biochem. 71(1), 211–227 (1976)

Title: What is a Cell Cycle Checkpoint? The TotemBioNet Answer
Authors: Déborah Boyenval
Gilles Bernot
Hélène Collavizza
Jean-Paul Comet
Publisher: Springer International Publishing
Book: Computational Methods in Systems Biology
Print ISBN: 978-3-030-60326-7

Electronic ISBN: 978-3-030-60327-4

Copyright Year: 2020
DOI: https://doi.org/10.1007/978-3-030-60327-4_21

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