Fig 3. Examples of pathways and complexes represented using mEPN.

(A) A model of the human TCA cycle and glycolysis pathways drawn using the mEPN scheme. The insert shows a small section of the pathway demonstrating the different shapes and colours used to depict different classes of molecule and how different types of processes can be distinguished using differently labelled process nodes. This is a purely graphical model, but with parameterisation it could be used to run simulations of this pathway. (B) Depiction of the nuclear pore complex as an example of how the mEPN scheme can be used to represent large structures composed of multiple subunits. In all models constructed by us, standard nomenclature is used to define entities (e.g., Human Genome Nomenclature Committee [HGNC]-approved names for human proteins and genes) to remove ambiguity of what is being represented.