Protocol for biomodel engineering of unilevel to multilevel biological models using colored Petri nets

Liu, Fei; Heiner, Monika; Gilbert, David

doi:10.1016/j.xpro.2023.102651

Cited by 1 publication

(1 citation statement)

References 52 publications

(104 reference statements)

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“…With Petri nets, a variety of analysis techniques are offered to validate models, including animation by Snoopy, structural and behavioural analysis of Petri nets by Charlie, model checking by both Charlie and Marcie, and deterministic/stochastic/hybrid simulation by Snoopy or Spike. See [ 31 ] and [ 50 ] for a detailed discussion.…”

Section: Resultsmentioning

confidence: 99%

Design patterns for the construction of computational biological models

Herajy,

Liu,

Heiner

2024

Briefings in Bioinformatics

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Computational biological models have proven to be an invaluable tool for understanding and predicting the behaviour of many biological systems. While it may not be too challenging for experienced researchers to construct such models from scratch, it is not a straightforward task for early stage researchers. Design patterns are well-known techniques widely applied in software engineering as they provide a set of typical solutions to common problems in software design. In this paper, we collect and discuss common patterns that are usually used during the construction and execution of computational biological models. We adopt Petri nets as a modelling language to provide a visual illustration of each pattern; however, the ideas presented in this paper can also be implemented using other modelling formalisms. We provide two case studies for illustration purposes and show how these models can be built up from the presented smaller modules. We hope that the ideas discussed in this paper will help many researchers in building their own future models.

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Section: Resultsmentioning

confidence: 99%