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Table 1 Typical questions to answer in order to account for the meaning facets of a bio-model.

From: How to formalise the meaning of a bio-model: a case study

Intrinsic Extrinsic
Intentional
Which mathematical formalism is used? How is the formalism interpreted and executed? How is the formalism used to simulate the behaviour? Which biological system is addressed? What does the model stand for in the biological reality? What is the aim of the model?
Structural
What is the structure of the mathematical expression? What are the mathematical entities of the model (equations, terms, variables, rules)? Which biological components are addressed by model? What are the modelled biological objects and relations? How do model entities map these biological components?
Behavioural
Which simulation results does the model show? What are characteristic types of dynamical behaviour (e.g. attractors)? Which parameter settings are used therefore? Which biological phenomenon correlates with which type of dynamical behaviour of the model? Which experimental data are reproduced by simulation results?