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The stresses predicted by our formalism, using the material parameters obtained for the two systems, agreed well with the measured stresses.
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Our formalism uses non-linear Hill functions to describe transcriptional interactions and a phenomenological law to describe the protein-protein interaction triggered by the input.
The conceptual level must be reflected by the formalism used.
Logarithmic transformation can convert a non-linear model represented by the S-system formalism used widely in biochemical systems theory (BST) to a linear model if we consider systems at steady state only [ 7, 12].
In order to meet this requirement, an analysis of the UMLS SN semantics in the light of description logics and its transformation into the formalism used by BioTop had to be performed.
The intrinsic structural meaning is obtained by interpreting the given model specification with respect to the formalism used.
Boolean (or logical) formalism is another formalism used to model signaling pathways where genes/proteins are parameterized by 0s and 1s only.
The formalism used to derive the logic based ODEs was developed by [ 36] and is also implemented in the MATLAB toolbox Odefy [ 31].
The deformable model formalism used has previously been described [ 10].
This graph-theoretical formalism uses exchange relations between neighboring values.
The study is motivated by the potential benefits of using formalisms using Coloured Petri Nets with sufficient abstraction.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com