HOW TO WRITE A BioNetGen2 INPUT FILE

The simplest example

begin parameters
  A0   100
  B0   500
  kp1  0.01
  km1  0.1
end parameters

begin species
  A(b)   A0    
  B(a)   B0
end species

begin reaction rules
   A(b) + B(a) <-> A(b!1,).B(a!1) kp1, km1
end reaction rules

begin observables
  Molecules A  A()
  Molecules B  B(a!?)
  Molecules A_bind A(b!+)
  Molecules B_bind B(a!+)
end observables

generate_network();
writeSBML();
#simulate_ssa({t_end=>50,n_steps=>20});
simulate_ode({t_end=>50,n_steps=>20});

Extension example

begin parameters
  A0   1000
  B0   500
  kp1  0.46e-5
  km1  1.0
  p 100
  d 5
end parameters

begin species
  A(b)   A0    
  B(a,Y~U) B0
end species

begin reaction rules
  A(b) + B(a) <-> A(b!1).B(a!1) kp1, km1
  A(b!1).B(a!1,Y~U) -> A(b!1).B(a!1,Y~P)  p
  B(Y~P) -> B(Y~P)  d
end reaction rules


begin observables
  Molecules A  A()
  Molecules BP  B(a!?,Y~P)
  Molecules BU  B(a!?,Y~U)
  Molecules A_bind A(b!+)
  Molecules B_bind B(a!+) 
  Molecules BP_bind B(a!+,Y~P) 
  Molecules BU_bind B(a!+,Y~U) 
end observables


generate_network();
writeSBML();
#simulate_ssa({t_end=>50,n_steps=>20});
simulate_ode({t_end=>50,n_steps=>20});

Compartmental example

begin parameters
  A0   1000
  B0   500
  kp1  0.46e-5
  km1  1.0
  p 100
  d 5
  t 10
end parameters

begin species
  A(b,loc~Cyt)   A0    
  B(a,Y~U,loc~Cyt) B0
end species

begin reaction rules
  A(b,loc~Cyt) + B(a,loc~Cyt) <-> A(b!1,loc~Cyt).B(a!1,loc~Cyt) kp1, km1
  A(b!1).B(a!1,Y~U) -> A(b!1).B(a!1,Y~P)  p
  B(Y~P,a,loc~Cyt) -> B(Y~P,a,loc~Nuc)  t
  B(Y~P,loc~Nuc) -> B(Y~U,loc~Nuc)  p
end reaction rules

begin observables
  Molecules A  A()
  Molecules BP  B(a!?,Y~P)
  Molecules BPC  B(a!?,Y~P,loc~Cyt)
  Molecules BPN  B(a!?,Y~P,loc~Nuc)
  Molecules BU  B(a!?,Y~U)
  Molecules A_bind A(b!+)
  Molecules B_bind B(a!+) 
end observables

generate_network();
writeSBML();
#simulate_ssa({t_end=>50,n_steps=>20});
simulate_ode({t_end=>50,n_steps=>20});

#%VC% mergeReversibleReactions
#%VC% speciesRenamePattern("\." , "_") 
#%VC% speciesRenamePattern("[\(,][a-zA-Z]\w*", "") 
#%VC% speciesRenamePattern("~|!\d*", "") 
#%VC% speciesRenamePattern("\(\)", "") 
#%VC% speciesRenamePattern("\)", "")  
#%VC% setUnit("all", "default")  
#%VC% compartmentalizeSpecies("loc~Nuc", "Nucleus", "Cytoplasm") 
#%VC% compartmentalizeSpecies("loc~Cyt", "Cytoplasm", "")

Cartoon of a toy model at BioNetGen@VCell screen

Another set of parameters

begin parameters
  1 L0   200
  2 R0   200
  3 A0   50
  4 kp1  0.01
  5 km1  1
  6 kp2  1
  7 km2  1
  8 p1  10
  9 d1   5
 10 kpA  10
 11 kmA  5
end parameters