(in-package :b-user)

;; include non-dimensional library
(include b-user/ode-biochem) ; or (include b-user/3d-ode-biochem)

;;; define the species-types
(def-species-types compartment 
  (e  :documentation "the enzyme")
  (s  :documentation "the substrate")
  (es :documentation "the enzyme-substrate product")
  (p  :documentation "the product"))


;; define the reactions
{e + s <-> es}.(set-rate-function 'mass-action :fwd .1 :rev 1)

{es -> p}.(set-rate-function 'mass-action .5)

;; define compartments:
(define c1 [[compartment] {.size.value := 1}])

;; put stuff in compartments:
c1.(contains e s)

;; set initial conditions:
{e.(in c1).conc.t0 := .5}
{s.(in c1).conc.t0 := 1}

;; create a matlab model
(create-ode-model "es" :vars (query species.conc))