A metabolic reaction (left) and its representation as a Petri net (right). Aldolase splits one molecule of Fructose-1,6-bisphosphate into one molecule Dihydroxyacetonephosphate and one molecule Glyceraldehyde-3-phosphate. The Triosephosphateisomerase then transforms one molecule Dihydroxyacetonephosphate into one molecule Glyceraldehyde-3-phosphate (the reversibility of the reaction has been omitted here for the sake of clarity). In the Petri net representation place nodes (circles) are denoted by p, transition nodes (boxes) by t and tokens numbers by m. The place node p1 represents Fructose-1,6-bisphosphate and m1 the number of tokens or number of Fructose-1,6-bisphosphate molecules present. The transition node t1 represents the enzyme Aldolase. The weights on the edges reflect the stoichiometry of the reactions. p2 Dihydroxyacetonephosphate, m2 number of Dihydroxyacetonephosphate molecules, t2 Triosephosphateisomerase, p3 Glyceraldehyde-3-phosphate, m3 number of Glyceraldehyde-3-phosphate molecules.
Schlitt and Brazma BMC Bioinformatics 2007 8(Suppl 6):S9 doi:10.1186/1471-2105-8-S6-S9