Biological software developped in Serrano's laboratory

SmartCell Elementary Reaction Examples

Reaction Draw XML Code SmartCell File
Binding of A and B: <reaction id="binding" rate="1e6" reverse-rate="0.1">
   <listOfReactionSites>
      <reaction-site compartment="cytosol" id="cyt">
         <listOfReactants>
            <reactant id="A" multiplicity="1"/>
            <reactant id="B" multiplicity="1"/>
         </listOfReactants>
         <listOfProducts>
            <product id="AB" multiplicity="1"/>
         </listOfProducts>
      </reaction-site>
   </listOfReactionSites>
</reaction>
binding.xml
Activation of AB: <reaction id="activation" rate="1">
   <listOfReactionSites>
      <reaction-site compartment="cytosol" id="cyt">
         <listOfReactants>
            <reactant id="AB" multiplicity="1"/>
         </listOfReactants>
         <listOfProducts>
            <product id="AB_act" multiplicity="1"/>
         </listOfProducts>
      </reaction-site>
   </listOfReactionSites>
</reaction>
activation.xml
Production of C: <reaction id="production" rate="0.0001">
   <listOfReactionSites>
      <reaction-site compartment="cytosol" id="cyt">
         <listOfProducts>
            <product id="C" multiplicity="1"/>
         </listOfProducts>
      </reaction-site>
   </listOfReactionSites>
</reaction>
production.xml
Degradation of D: <reaction id="degradation" rate="0.0001">
   <listOfReactionSites>
      <reaction-site compartment="cytosol" id="cyt">
         <listOfReactants>
            <reactant id="D" multiplicity="1"/>
         </listOfReactants>
      </reaction-site>
   </listOfReactionSites>
</reaction>
degradation.xml
Cofactor of F in the production of G from E: <reaction id="cofactor" rate="0.01">
   <listOfReactionSites>
      <reaction-site compartment="cytosol" id="cyt">
         <listOfReactants>
            <reactant id="E" multiplicity="1"/>
         </listOfReactants>
         <listOfProducts>
            <product id="G" multiplicity="1"/>
         </listOfProducts>
         <listOfModifier>
            <modifier id="F" multiplicity="1"/>
         </listOfModifier>
      </reaction-site>
   </listOfReactionSites>
</reaction>
cofactor.xml