sbmlutils.examples.tutorial.model_antimony

Load and modify an existing antimony model.

Module Contents

sbmlutils.examples.tutorial.model_antimony.model_antimony :str = Multiline-String[source]
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 1    model antimony_repressilator
 2        # compartment
 3        compartment cell = 1
 4
 5        # species
 6        species PX in cell = 0
 7        species PY in cell = 0
 8        species PZ in cell = 0
 9        species X in cell = 0
10        species Y in cell = 20
11        species Z in cell = 0
12
13        # parameters
14        beta = 0.2
15        alpha0 = 0.2164
16        alpha = 216.404
17        eff = 20
18        n = 2
19        KM = 40
20        tau_mRNA = 2
21        tau_prot = 10
22        ps_a = 0.5
23        ps_0 = 0.0005
24
25        # assignment rules
26        t_ave := tau_mRNA/ln(2);
27        beta := tau_mRNA/tau_prot;
28        k_tl := eff/t_ave;
29        a_tr := (ps_a - ps_0)*60;
30        a0_tr := ps_0*60;
31        kd_prot := ln(2)/tau_prot;
32        kd_mRNA := ln(2)/tau_mRNA;
33        alpha := a_tr*eff*tau_prot/(ln(2)*KM);
34        alpha0 := (a0_tr*eff*tau_prot)/(ln(2)*KM);
35
36        # reactions
37        X ->; kd_mRNA*X;
38        Y ->; kd_mRNA*Y;
39        Z ->; kd_mRNA*Z;
40        -> PX; k_tl*X;
41        -> PY; k_tl*Y;
42        -> PZ; k_tl*Z;
43        PX ->; kd_prot*PX;
44        PY ->; kd_prot*PY;
45        PZ ->; kd_prot*PZ;
46        -> X; a0_tr +a_tr *KM^n/(KM^n +PZ ^n);
47        -> Y; a0_tr +a_tr *KM^n/(KM^n +PX ^n);
48        -> Z; a0_tr +a_tr *KM^n/(KM^n +PY ^n);
49    end
sbmlutils.examples.tutorial.model_antimony.model :sbmlutils.factory.Model[source]