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parkramstandard.hmod
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parkramstandard.hmod
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% --------------------------------------------------------------------------
% hmod model structure
% Species
parkramstandard.nspecies=4;
parkramstandard.species(1).id="PM";
parkramstandard.species(1).val=0;
parkramstandard.species(1).compartment="V";
parkramstandard.species(1).fixed=0;
parkramstandard.species(1).min=0;
parkramstandard.species(1).max=15;
parkramstandard.species(1).isres=1;
parkramstandard.species(2).id="PT";
parkramstandard.species(2).val=0;
parkramstandard.species(2).compartment="V";
parkramstandard.species(2).fixed=0;
parkramstandard.species(2).min=0;
parkramstandard.species(2).max=15;
parkramstandard.species(2).isres=1;
parkramstandard.species(3).id="S";
parkramstandard.species(3).val=5;
parkramstandard.species(3).compartment="V";
parkramstandard.species(3).fixed=0;
parkramstandard.species(3).min=0;
parkramstandard.species(3).max=15;
parkramstandard.species(3).isres=1;
parkramstandard.species(4).id="X";
parkramstandard.species(4).val=1;
parkramstandard.species(4).compartment="V";
parkramstandard.species(4).fixed=0;
parkramstandard.species(4).min=0;
parkramstandard.species(4).max=15;
parkramstandard.species(4).isres=1;
% Compartments
parkramstandard.ncompartments=1;
parkramstandard.compartments(1).id="V";
parkramstandard.compartments(1).val=1;
parkramstandard.compartments(1).fixed=0;
parkramstandard.compartments(1).min=0;
parkramstandard.compartments(1).max=15;
parkramstandard.compartments(1).isres=0;
% Parameters
parkramstandard.nparameters=9;
parkramstandard.parameters(1).id="D";
parkramstandard.parameters(1).val=0.1;
parkramstandard.parameters(1).fixed=0;
parkramstandard.parameters(1).reaction="global";
parkramstandard.parameters(2).id="Feed";
parkramstandard.parameters(2).val=0.525;
parkramstandard.parameters(2).fixed=0;
parkramstandard.parameters(2).reaction="global";
parkramstandard.parameters(3).id="Sin";
parkramstandard.parameters(3).val=20;
parkramstandard.parameters(3).fixed=0;
parkramstandard.parameters(3).reaction="global";
parkramstandard.parameters(4).id="Y";
parkramstandard.parameters(4).val=7.3;
parkramstandard.parameters(4).fixed=1;
parkramstandard.parameters(4).reaction="global";
parkramstandard.parameters(5).id="miu";
parkramstandard.parameters(5).val=0;
parkramstandard.parameters(5).fixed=0;
parkramstandard.parameters(5).reaction="global";
parkramstandard.parameters(6).id="miumax";
parkramstandard.parameters(6).val=21.87;
parkramstandard.parameters(6).fixed=1;
parkramstandard.parameters(6).reaction="global";
parkramstandard.parameters(7).id="u";
parkramstandard.parameters(7).val=0.525;
parkramstandard.parameters(7).fixed=1;
parkramstandard.parameters(7).reaction="global";
parkramstandard.parameters(8).id="vPM";
parkramstandard.parameters(8).val=0;
parkramstandard.parameters(8).fixed=0;
parkramstandard.parameters(8).reaction="global";
parkramstandard.parameters(9).id="vPT";
parkramstandard.parameters(9).val=0;
parkramstandard.parameters(9).fixed=0;
parkramstandard.parameters(9).reaction="global";
% Assignment rules
parkramstandard.nruleAss=3;
parkramstandard.ruleAss(1).id="vPT";
parkramstandard.ruleAss(1).val="S * pow(2.71828182, -5 * S) / (0.1 + S)";
parkramstandard.ruleAss(2).id="vPM";
parkramstandard.ruleAss(2).val="4.75 * (21.87 * S / (S + 0.4) / (S + 62.5)) / (0.12 + 21.87 * S / (S + 0.4) / (S + 62.5))";
parkramstandard.ruleAss(3).id="miu";
parkramstandard.ruleAss(3).val="21.87 * S / (S + 0.4) / (S + 62.5)";
% Events
parkramstandard.nevents=1;
parkramstandard.events(1).id="Controller";
parkramstandard.events(1).trigger="geq(time, 0)";
parkramstandard.events(1).delay="0";
parkramstandard.events(1).var(1)="Feed";
parkramstandard.events(1).var(1)="u";
% Reactions
parkramstandard.nreaction=4;
parkramstandard.reaction(1).id="rPM";
parkramstandard.reaction(1).rate="V * vPM * (PT - PM)";
parkramstandard.reaction(1).rPM="['1', '0', '0', '0']";
parkramstandard.reaction(2).id="rPT";
parkramstandard.reaction(2).rate="V * vPT * X";
parkramstandard.reaction(2).rPT="['0', '1', '0', '0']";
parkramstandard.reaction(3).id="rSin";
parkramstandard.reaction(3).rate="V * D * Sin";
parkramstandard.reaction(3).rSin="['0', '0', '1', '0']";
parkramstandard.reaction(4).id="rX";
parkramstandard.reaction(4).rate="V * miu * X";
parkramstandard.reaction(4).rX="['0', '0', '-7.3', '1']";
% Rate rules
parkramstandard.nraterules=1;
parkramstandard.raterules(1).id="V";
parkramstandard.raterules(1).val="D * V";
parkramstandard.raterules(1).min=0;
parkramstandard.raterules(1).max=1.5;
parkramstandard.raterules(1).isres=0;
end