LV_comp.bngl

## title: LV_comp.bgl
## description: Compartment version fo the Lotka-Volterra predator-prey model. These 
#               parameters correspond to the
#               reaction-limited regime, and give rise to regular oscillations when simulated
#               both with ODE's and SSA.
## author: Jim Faeder
## date: 22April2015
begin model

begin parameters
 NA_um3 6.02e8
  V 0.5*0.5*0.01 # volume in cubic microns 
 k1 1.29e5 # 1/s
 k2 (1e8)/NA_um3  # 1/M -> um^3/s 
 k3 1.3e5  # 1/s
end parameters
begin compartments
  cell 3 V
end compartments

begin species
  S()@cell 1000
  W()@cell  500
end species

begin observables
  Molecules Stot S()
  Molecules Wtot W()
end observables

begin reaction rules
  S() -> S() + S() k1
  S() + W() -> W() + W() k2
  W() -> 0 k3
end reaction rules

end model

#generate_network()
#writeSBML()
#simulate({method=>"ode",t_end=>0.001,n_steps=>1000})
#simulate({method=>"ssa",t_end=>0.001,n_steps=>1000})