The Bio-PEPA Eclipse Plug-inUser Manual: Syntax Example: The Enzyme-Substrate model

A.7 Syntax Example: The Enzyme-Substrate model - Reactant and Product

In this example (see Table 3), an enzyme E combines with a substrate S to form a compound E:S. This compound might degrade releasing the enzyme and the substrate or it might convert the substrate into product P, releasing the enzyme (In the Bio-PEPA Eclipse Plug-in editor the two parallel diagonal lines (//) denote comments). The Outline View of the model is shown in Figure 74. According to the species components definition:

$E$ — is a reactant ( $\downarrow$ , <<) in reaction $\mathit{r_1}$ and a product ( $\uparrow$ , >>) in reactions $\mathit{rm_1}$ and $\mathit{r_2}$
$S$ — is a reactant ( $\downarrow$ , <<) in reaction $\mathit{r_1}$ and a product ( $\uparrow$ , >>) in reaction $\mathit{rm_1}$
$E:S$ — is a product ( $\downarrow$ , <<) in reaction $\mathit{r_1}$ and a reactant ( $\uparrow$ , >>) in reactions $\mathit{rm_1}$ and $\mathit{r_2}$
$P$ — is a product in reaction $\mathit{r_2}$

The Bio-PEPA syntax	`//The Bio-PEPA plugin syntax`
Parameter Definitions:	`//Parameter Definitions`
$k_1\; \; \; = 0.01;$	`k1 = 1.0;`
$km_1 = 0.01;$	`km1 = 0.1;`
$k_2\; \; \; = 0.01;$	`k2 = 0.01;`
$\text{[math]}$
Functional Rates	`//Functional Rates`
$r_{1}\; \; \; = k_1 * E * S;$	`r1 = [ k1 * E * S ];`
$rm_{1} = km_1 * E:S;$	`rm1 = [ km1 * E:S ];`
$r_{2}\; \; \; = k_2 * E:S;$	`r2 = [ k2 * E:S ];`
$\text{[math]}$
Species Components	`//Species Components`
$E\; \; \; \; \; \; \rmdef (r_1, 1) \reactant E + (rm_1, 1) \product E + (r_2, 1) \product E$	`E = r1 << + rm1 >> + r2 >> ;`
$S\; \; \; \; \; \; \rmdef (r_1, 1) \reactant S + (rm_1, 1) \product S$	`S = r1 << + rm1 >> ;`
$E:S \rmdef (r_1, 1) \product E:S + (rm_1, 1) \reactant E:S + (r_2, 1) \reactant E:S$	`E:S = r1 >> + rm1 << + r2 << ;`
$P\; \; \; \; \; \rmdef (r_2, 1) \product P$	`P = r2 >> ;`
$\text{[math]}$
Model Component	`//Model Component`
$E[40] \sync{} S[30] \sync{} E:S[0] \sync{*} P[0]$	`E[40] <> S[30] <> E:S[0] <*> P[0]`