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A Reappraisal of How to Build Modular, Reusable Models of Biological Systems

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A modular model composition task using traditional, information-hiding approaches versus semantics-based, adaptable interface modularity (SAIM).

A: Predefined interfaces applied to publicly-available glycolysis, pentose phosphate pathway (PPP) and tricarboxylic acid cycle (TCA) modules may allow appropriate computational linkage (double-headed arrows) between the first two models but prevent linkage with the third. The interfaces on the glycolysis and PPP models expose codewords representing the concentrations of glucose 6-phosphate (“Gluc6P,” “g6p”), fructose 6-phosphate (“Fruc6P,” “f6p”), and glyceraldehyde 3-phosphate (“Glyc3P,” “g3p”) but conceal the glycolysis model codeword representing pyruvate concentration (“Pyr”), a critical coupling point between the glycolysis and TCA cycle models. B: Using SAIM, all modeling elements are exposed and semantically defined, allowing biologically consistent coupling of the three modeling components at the time of composition.

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1003849.g001