<?xml version="1.0" encoding="UTF-8"?>
<sbml level="1" version="2" xmlns="http://www.sbml.org/sbml/level1">
    <model name="signal_encoding_enzyme_circuits"> 

        <notes>
            <body xmlns="http://www.w3.org/1999/xhtml">
 <p> Constructing network topologies for multiple signal-encoding functions</p>  
                <p> refer to: circuit N5 in Fig.4c, Equqtions 2, Fig. 5</p>
                <p> I1=0.4, I2=I3=0.1, output oscillation </p>
                <p> I2=0.3, I1=I3=0.1, output adaptation </p>
                <p> I3=0.3, I1=I2=0.1, output sustained activation </p>
                <p>The enzymatic reactions look like these:</p>
                <p> ( the sign _ denotes enzyme in its inactive form) </p>
                <p>reaction_1: I1 + R1_ -> R1;       V1*I1*(1-R1)/(K1+1-R1); </p>
                <p>reaction_2: R3 + R1  -> R3 + R1_; V5*R3*R1/(K5+R1);       </p>
                <p>reaction_3: I2 + R2_ -> R2;       V2*I2*(1-R2)/(K2+1-R2); </p>
                <p>reaction_4:  B + R2  -> B + R2_;  V6*B*R2/(K6+R2);        </p>
                <p>reaction_5: I3 + R3_ -> R3;       V3*I3*(1-R3)/(K3+1-R3); </p>
                <p>reaction_6:  O + R3  -> O + R3_;  V7*O*R3/(K7+R3);        </p>
                <p>reaction_7: R2 + O_  -> R2 + O;   V4*R2*(1-O)/(K4+1-O);   </p>
                <p>reaction_8: R1 + O   -> R1 + O_;  V8*R1*O/(K8+O);         </p>  
            </body>
        </notes>  

        <listOfCompartments>
            <compartment name="compartmentOne" volume="1"/>
        </listOfCompartments>

        <listOfSpecies> 
            <species name="I1" initialAmount="0.1" compartment="compartmentOne" boundaryCondition="true"/>
            <species name="I2" initialAmount="0.1" compartment="compartmentOne" boundaryCondition="true"/>
            <species name="I3" initialAmount="0.1" compartment="compartmentOne" boundaryCondition="true"/>

            <species name="R1" initialAmount="0.1179" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="R2" initialAmount="0.3431" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="R3" initialAmount="0.0024" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="O" initialAmount="0.169" compartment="compartmentOne" boundaryCondition="false"/>

            <species name="R1_" initialAmount="0.8821" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="R2_" initialAmount="0.6569" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="R3_" initialAmount="0.9976" compartment="compartmentOne" boundaryCondition="false"/>
            <species name="O_" initialAmount="0.831" compartment="compartmentOne" boundaryCondition="false"/>

            <species name="B" initialAmount="0.5" compartment="compartmentOne" boundaryCondition="true"/>

        </listOfSpecies>


        <listOfReactions>

            <reaction name="reaction_1" reversible="false">
                <listOfReactants>
                    <speciesReference species="I1" stoichiometry="1"/>
                    <speciesReference species="R1_" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R1" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V1*I1*(1-R1)/(K1+1-R1)">
                    <listOfParameters>
                        <parameter name="V1" value="0.3156"/>
                        <parameter name="K1" value="5.116"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_2" reversible="false">
                <listOfReactants>
                    <speciesReference species="R3" stoichiometry="1"/>
                    <speciesReference species="R1" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R3" stoichiometry="1"/>
                    <speciesReference species="R1_" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V5*R3*R1/(K5+R1)">
                    <listOfParameters>
                        <parameter name="V5" value="2.3514"/>
                        <parameter name="K5" value="0.0259"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_3" reversible="false">
                <listOfReactants>
                    <speciesReference species="I2" stoichiometry="1"/>
                    <speciesReference species="R2_" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R2" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V2*I2*(1-R2)/(K2+1-R2))">
                    <listOfParameters>
                        <parameter name="V2" value="1.8362"/>
                        <parameter name="K2" value="0.303"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_4" reversible="false">
                <listOfReactants>
                    <speciesReference species="B" stoichiometry="1"/>
                    <speciesReference species="R2" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="B" stoichiometry="1"/>
                    <speciesReference species="R2_" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V6*B*R2/(K6+R2)">
                    <listOfParameters>
                        <parameter name="V6" value="0.2716"/>
                        <parameter name="K6" value="0.0277"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_5" reversible="false">
                <listOfReactants>
                    <speciesReference species="I3" stoichiometry="1"/>
                    <speciesReference species="R3_" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R3" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V3*I3*(1-R3)/(K3+1-R3)">
                    <listOfParameters>
                        <parameter name="V3" value="0.7503"/>
                        <parameter name="K3" value="0.0111"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_6" reversible="false">
                <listOfReactants>
                    <speciesReference species="O" stoichiometry="1"/>
                    <speciesReference species="R3" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="O" stoichiometry="1"/>
                    <speciesReference species="R3_" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V7*O*R3/(K7+R3)">
                    <listOfParameters>
                        <parameter name="V7" value="0.701"/>         
                        <parameter name="K7" value="0.0014"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_7" reversible="false">
                <listOfReactants>
                    <speciesReference species="R2" stoichiometry="1"/>
                    <speciesReference species="O_" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R2" stoichiometry="1"/>
                    <speciesReference species="O" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V4*R2*(1-O)/(K4+1-O)">
                    <listOfParameters>
                        <parameter name="V4" value="0.5559"/>
                        <parameter name="K4" value="1.2833"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

            <reaction name="reaction_8" reversible="false">
                <listOfReactants>
                    <speciesReference species="R1" stoichiometry="1"/>
                    <speciesReference species="O" stoichiometry="1"/>
                </listOfReactants>
                <listOfProducts>
                    <speciesReference species="R1" stoichiometry="1"/>
                    <speciesReference species="O_" stoichiometry="1"/>
                </listOfProducts>
                <kineticLaw formula="V8*R1*O/(K8+O)">
                    <listOfParameters>
                        <parameter name="V8" value="0.6726"/>
                        <parameter name="K8" value="0.0099"/>
                    </listOfParameters>
                </kineticLaw>
            </reaction>

        </listOfReactions>

    </model>
</sbml>