sbmlutils.examples.tutorial.model_antimony

Load and modify an existing antimony model.

Module Contents

sbmlutils.examples.tutorial.model_antimony.model_antimony: str = Multiline-String

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"""
    model antimony_repressilator
        # compartment
        compartment cell = 1

        # species
        species PX in cell = 0
        species PY in cell = 0
        species PZ in cell = 0
        species X in cell = 0
        species Y in cell = 20
        species Z in cell = 0

        # parameters
        beta = 0.2
        alpha0 = 0.2164
        alpha = 216.404
        eff = 20
        n = 2
        KM = 40
        tau_mRNA = 2
        tau_prot = 10
        ps_a = 0.5
        ps_0 = 0.0005

        # assignment rules
        t_ave := tau_mRNA/ln(2);
        beta := tau_mRNA/tau_prot;
        k_tl := eff/t_ave;
        a_tr := (ps_a - ps_0)*60;
        a0_tr := ps_0*60;
        kd_prot := ln(2)/tau_prot;
        kd_mRNA := ln(2)/tau_mRNA;
        alpha := a_tr*eff*tau_prot/(ln(2)*KM);
        alpha0 := (a0_tr*eff*tau_prot)/(ln(2)*KM);

        # reactions
        X ->; kd_mRNA*X;
        Y ->; kd_mRNA*Y;
        Z ->; kd_mRNA*Z;
        -> PX; k_tl*X;
        -> PY; k_tl*Y;
        -> PZ; k_tl*Z;
        PX ->; kd_prot*PX;
        PY ->; kd_prot*PY;
        PZ ->; kd_prot*PZ;
        -> X; a0_tr +a_tr *KM^n/(KM^n +PZ ^n);
        -> Y; a0_tr +a_tr *KM^n/(KM^n +PX ^n);
        -> Z; a0_tr +a_tr *KM^n/(KM^n +PY ^n);
    end
"""

sbmlutils.examples.tutorial.model_antimony.model: sbmlutils.factory.Model