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. 2022 Mar 30;23(3):bbac081. doi: 10.1093/bib/bbac081

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© The Author(s) 2022. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Popular modelling formalisms for biological systems. The inner circle comprises the four basic modelling formalisms: topology-based modelling, ordinary differential equations (ODEs), continuous time Markov chain (CTMC) and Boolean logic modelling. Further, topology-based modelling is extended to constraint-based modelling (CBM), and Boolean logic to fuzzy logic. The outer ring is labelled with higher modelling formalisms including Petri nets and rule-based modelling, which can adopt the basic formalisms as underlying semantics.