# Exemplar Model Set Up Stages

Although there is no forced order, executing these steps as prescribed is generally the most straightforward method:

- Create molecule templates and register as types.

- Mono-component, no set state molecule pattern,
- Tri-component, no set states molecule pattern,
- Bi-component, no set states molecule pattern,
- Bi-component, with one set state molecule pattern.

- Create species.

- L(r), monovalent ligand,
- R(l,r,a), monovalent receptor,
- A(r,k), bivalent adapter protein,
- K(a,Y~U), kinase.

- Set up reactions rules.

- L(r) + R(l,r) <-> L(r!1).R(l!1,r); forward rate of kpL, backward rate of kmL,
- A(r) + R(a) <-> A(r!1).R(a!1), forward rate of kpA, backward rate of kmA,
- A(k) + K(a) <-> A(k!1).K(a!1), forward rate of kpK, backward rate of KmK,
- R(a!1).A(!1,k!2).K(a!2,Y~P) -> R(a!1).A(r!1,k!2).K(a!2,Y~U), forward rate of dM,
- K(a,Y~P) -> K(a,Y~U), forward rate of dC.

- Specifiy observables.

- Molecules L-tot, L,
- Molecules A-tot, A,
- Molecules K-tot, K,
- Molecules R-tot, R,
- Molecule Rec-A, R(a!1).A(r!1),
- Molecule Rec-K, R(a!1).A(r!1,k!2).K(a!2).

- Set simulation parameters.