Tellurium Introduction - part II:

In [5]:

    

import tellurium as te; te.setDefaultPlottingEngine('matplotlib')
import matplotlib.pyplot as plt
%matplotlib inline

model = '''

function rhill(k,Km,I,n)
    k * Km^n / (Km^n + I^n)
end

function ahill(k,Km,S,n)
    k * S^n / (Km^n + S^n)
end

model usingfunctions

    X=0;
    Y=10;
    X'=ahill(0.3,1.2,Y,3)
    Y'=-ahill(0.3,1.2,Y,3)

end

'''

r = te.loada(model)
r.simulate(0,100)
r.plot()


    

In [4]:

    

import tellurium as te;# te.setDefaultPlottingEngine('matplotlib')
import matplotlib.pyplot as plt
r = te.loada('example.antimony')
def draw(model):
    diagram = te.visualization.SBMLDiagram(model.getSBML())
    diagram.draw()
    
    
#r.draw()
draw(r)

model_circle = '''
import "example.antimony"

model circle
    A: example()
    B: example()
    C: example()
    
    X0: A.TOM1 -> B.TOM1;
    X1: B.TOM1 -> C.TOM1;
    X2: C.TOM1 ->  A.TOM1;
end

'''

circle = te.loada(model_circle)
#draw(circle)


    

In [29]:

    

circle = te.loada(model_circle)
print circle.getAntimony()


    

    




// Created by libAntimony v2.9.4
model *circle()

  // Compartments and Species:
  compartment A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  species A_TOM1 in A_cell, A_A_c in A_cell, A_A_m in A_mitochondria, B_TOM1 in B_cell;
  species B_A_c in B_cell, B_A_m in B_mitochondria, C_TOM1 in C_cell, C_A_c in C_cell;
  species C_A_m in C_mitochondria;

  // Assignment Rules:
  A_kineticLaw := A_k1*A_TOM1*(A_A_c - A_A_m)/A_I;
  B_kineticLaw := B_k1*B_TOM1*(B_A_c - B_A_m)/B_I;
  C_kineticLaw := C_k1*C_TOM1*(C_A_c - C_A_m)/C_I;

  // Reactions:
  A_T0: A_A_c + A_TOM1 -> 2 A_A_m + A_TOM1; A_kineticLaw;
  B_T0: B_A_c + B_TOM1 -> 2 B_A_m + B_TOM1; B_kineticLaw;
  C_T0: C_A_c + C_TOM1 -> 2 C_A_m + C_TOM1; C_kineticLaw;
  X0: A_TOM1 -> B_TOM1; ;
  X1: B_TOM1 -> C_TOM1; ;
  X2: C_TOM1 -> A_TOM1; ;

  // Species initializations:
  A_TOM1 = 10;
  A_A_c = 100;
  A_A_m = 1;
  B_TOM1 = 10;
  B_A_c = 100;
  B_A_m = 1;
  C_TOM1 = 10;
  C_A_c = 100;
  C_A_m = 1;

  // Compartment initializations:
  A_cell = 100;
  A_mitochondria = 10;
  B_cell = 100;
  B_mitochondria = 10;
  C_cell = 100;
  C_mitochondria = 10;

  // Variable initializations:
  A_I = 1;
  A_k1 = 0.01;
  B_I = 1;
  B_k1 = 0.01;
  C_I = 1;
  C_k1 = 0.01;

  // Other declarations:
  var A_kineticLaw, B_kineticLaw, C_kineticLaw;
  const A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  const A_I, A_k1, B_I, B_k1, C_I, C_k1;
end

In [30]:

    

model_circle = '''
import "example.antimony"

model circle
    A: example()
    B: example()
    C: example()
    
    X0: A.TOM1 -> B.TOM1;
    X1: B.TOM1 -> C.TOM1;
    X2: C.TOM1 ->  A.TOM1;
    
    delete C.A_m
    C.kineticLaw := 0.1;
    
end

'''

circle = te.loada(model_circle)
print circle.getAntimony()


    

    




// Created by libAntimony v2.9.4
model *circle()

  // Compartments and Species:
  compartment A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  species A_TOM1 in A_cell, A_A_c in A_cell, A_A_m in A_mitochondria, B_TOM1 in B_cell;
  species B_A_c in B_cell, B_A_m in B_mitochondria, C_TOM1 in C_cell, C_A_c in C_cell;

  // Assignment Rules:
  A_kineticLaw := A_k1*A_TOM1*(A_A_c - A_A_m)/A_I;
  B_kineticLaw := B_k1*B_TOM1*(B_A_c - B_A_m)/B_I;
  C_kineticLaw := 0.1;

  // Reactions:
  A_T0: A_A_c + A_TOM1 -> 2 A_A_m + A_TOM1; A_kineticLaw;
  B_T0: B_A_c + B_TOM1 -> 2 B_A_m + B_TOM1; B_kineticLaw;
  C_T0: C_A_c + C_TOM1 -> C_TOM1; ;
  X0: A_TOM1 -> B_TOM1; ;
  X1: B_TOM1 -> C_TOM1; ;
  X2: C_TOM1 -> A_TOM1; ;

  // Species initializations:
  A_TOM1 = 10;
  A_A_c = 100;
  A_A_m = 1;
  B_TOM1 = 10;
  B_A_c = 100;
  B_A_m = 1;
  C_TOM1 = 10;
  C_A_c = 100;

  // Compartment initializations:
  A_cell = 100;
  A_mitochondria = 10;
  B_cell = 100;
  B_mitochondria = 10;
  C_cell = 100;
  C_mitochondria = 10;

  // Variable initializations:
  A_I = 1;
  A_k1 = 0.01;
  B_I = 1;
  B_k1 = 0.01;
  C_I = 1;
  C_k1 = 0.01;

  // Other declarations:
  var A_kineticLaw, B_kineticLaw, C_kineticLaw;
  const A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  const A_I, A_k1, B_I, B_k1, C_I, C_k1;
end

In [3]:

    

model_circle = '''
import "example.antimony"

model circle
    A: example()
    B: example()
    C: example()
    
    X0: A.TOM1 -> B.TOM1;
    X1: B.TOM1 -> C.TOM1;
    X2: C.TOM1 ->  A.TOM1;
        
    # Assignment rule-> ODE:
    C.kineticLaw := ;
    C.kineticLaw '= 0.1;
    C.kineticLaw = 0.1;
    
    # Delete reaction:
    #delete A.T0
    
    # Overwrite reaction
    A_TO: A.A_c -> A.A_m; 0.1; # Note, the Underline, Submodels are flattened in sbml!
end

'''

circle = te.loada(model_circle)
print circle.getAntimony()


    

    




// Created by libAntimony v2.9.4
model *circle()

  // Compartments and Species:
  compartment A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  species A_TOM1 in A_cell, A_A_c in A_cell, A_A_m in A_mitochondria, B_TOM1 in B_cell;
  species B_A_c in B_cell, B_A_m in B_mitochondria, C_TOM1 in C_cell, C_A_c in C_cell;
  species C_A_m in C_mitochondria;

  // Assignment Rules:
  A_kineticLaw := A_k1*A_TOM1*(A_A_c - A_A_m)/A_I;
  B_kineticLaw := B_k1*B_TOM1*(B_A_c - B_A_m)/B_I;

  // Rate Rules:
  C_kineticLaw' = 0.1;

  // Reactions:
  A_T0: A_A_c + A_TOM1 -> 2 A_A_m + A_TOM1; A_kineticLaw;
  B_T0: B_A_c + B_TOM1 -> 2 B_A_m + B_TOM1; B_kineticLaw;
  C_T0: C_A_c + C_TOM1 -> 2 C_A_m + C_TOM1; C_kineticLaw;
  X0: A_TOM1 -> B_TOM1; ;
  X1: B_TOM1 -> C_TOM1; ;
  X2: C_TOM1 -> A_TOM1; ;
  A_TO: A_A_c -> A_A_m; 0.1;

  // Species initializations:
  A_TOM1 = 10;
  A_A_c = 100;
  A_A_m = 1;
  B_TOM1 = 10;
  B_A_c = 100;
  B_A_m = 1;
  C_TOM1 = 10;
  C_A_c = 100;
  C_A_m = 1;

  // Compartment initializations:
  A_cell = 100;
  A_mitochondria = 10;
  B_cell = 100;
  B_mitochondria = 10;
  C_cell = 100;
  C_mitochondria = 10;

  // Variable initializations:
  A_I = 1;
  A_k1 = 0.01;
  B_I = 1;
  B_k1 = 0.01;
  C_I = 1;
  C_kineticLaw = 0.1;
  C_k1 = 0.01;

  // Other declarations:
  var A_kineticLaw, B_kineticLaw, C_kineticLaw;
  const A_cell, A_mitochondria, B_cell, B_mitochondria, C_cell, C_mitochondria;
  const A_I, A_k1, B_I, B_k1, C_I, C_k1;
end