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]¶
Show Value
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