Tentative example file produced in workshop

File contents

<?xml version="1.0" ?>
<ecell-rules>
  <parameters>
    <parameter>
      <name>volume</name>
      <value>1.0</value>
    </parameter>
    <parameter>
      <name>p1</name>
      <value>0.5</value>
    </parameter>
    <parameter>
      <name>ubiquitin-weight</name>
      <value>0.5</value>
    </parameter>
    <parameter>
      <name>p1</name>
      <value>
        <math xmlns="http://www.w3.org/1998/Math/MathML">
          <apply>
            <times/>
            <ci>cytosol</ci>
            <apply>
              <minus/>
              <apply>
                <times/>
                <ci>kon</ci>
                <ci>E</ci>
                <ci>S</ci>
              </apply>
              <apply>
                <times/>
                <ci>koff</ci>
                <ci>ES</ci>
              </apply>
            </apply>
          </apply>
        </math>
      </value>
    </parameter>
  </parameters>

  <modifications>
    <modification>
      <name>none</name>
      <weight>0</weight>
    </modification>
    <modification>
      <name>phosphorylated</name>
      <weight>42</weight>
    </modification>
    <modification>
      <name>ubiquitinated</name>
      <weight><parameter-ref name="ubiquitin-weight" /></weight>
    </modification>
  </modifications>

  <modification-groups>
    <modification-group>
      <name>phosphorylatable</name>
      <default-value>none</default-value>
      <value>phosphorylated</value>
    </modification-group>
    <modification-group>
      <name>ubiquitinatable</name>
      <default-value>none</default-value>
      <value>ubiquitinatable</value>
    </modification-group>
  </modification-groups>

  <mols>
    <simple-mol>
      <name>GTP</name>
      <weight>...</weight>
    </simple-mol>

    <mol>
     <name>Gpa1</name>
     <weight>...</weight>
     <binding-sites>
       <binding-site>
         <name>Ste5</name>
       </binding-site>
       <binding-site>
         <name>Ste4</name>
       </binding-site>
     </binding-sites>
     <modification-sites>
       <modification-site>
         <name>P1</name>
         <modification-group>phosphorylatable</modification-group>
       </modification-site>
     </modification-sites>
   </mol> 

   <mol>
     <name>Ste5</name>
     <weight>...</weight>
     <states>
       <default-state>
         <name>normal</name>
       </default-state>
       <state>
         <name>bbb</name>
       </state>
     </states>
     <binding-sites>
       <binding-site>
         <name>Gpa1</name>
         <default-state>normal</default-state>
         <state>obstructed</state>
       </binding-site>
       <binding-site>
         <name>Ste4</name>
         <default-state>normal</default-state>
       </binding-site>
       <binding-site>
         <name>Ste11</name>
         <default-state>normal</default-state>
       </binding-site>
       <binding-site>
         <name>Fus3</name>
         <default-state>normal</default-state>
       </binding-site>
     </binding-sites>
     <modification-sites>
       <modification-site>
         <name>P1</name>
         <modification-group>phosphorylatable</modification-group>
       </modification-site>
     </modification-sites>
   </mol> 
  </mols>

  <rules>
    <rule>
      <name>Insane Fus3 to Gpa1 binding</name>
      <selectors>
        <selector>
	  <subgraph>
            <mol-instances>
              <mol-instance>
                <name>theFus3</name>
                <mol>Fus3</mol>
                <binding-site-instances>
                  <binding-site-instance id="FreeToGpa1Site">
                    <binding-site>toGpa1</binding-site>
                    <bound>false</bound>
                    <state>active</state>
                  </binding-site-instance>

                </binding-site-instances>
              </mol-instance>
            </mol-instances>
          </subgraph>
        </selector>
        <selector>
          <subgraph>
            <mol-instances>
              <mol-instance id="theGpa1">
                <mol>Gpa1</mol>
                <state>active</state>
                <binding-site-instances>
                  <binding-site-instance id="FreeToFus3Site">
                    <binding-site>toFus3</binding-site>
                    <bound>false</bound>
                  </binding-site-instance>
                </binding-site-instances>
              </mol-instance>
              <mol-instance id="theSte5">
                <mol>Ste5</mol>
                <state>inactive</state>
                <binding-site-instances>
                  <binding-site-instance id="OccludedSte11Site">
                    <binding-site>toSte11</binding-site>
                    <state>occluded</state>
                  </binding-site-instance>
                </binding-site-instances>
                <modification-site-instances>
                  <modification-site-instance id="PhoshorlyatedP03Site">
                    <modification-site>P03</modification-site>
                    <modification>Phosphorylated</modification>
                  </modification-site-instance>
                </modification-site-instances>
              </mol-instance>
              <simple-mol-instance id="Ste5BoundADP">
                <simple-mol>ADP</simple-mol>
              </simple-mol-instance>
            </mol-instances>
            <bindings>
              <binding id="Gpa1ToSte5Bond">
                <mol-instance>
                  <name>theGpa1</name>
                  <binding-site>toSte5</binding-site>
                </mol-instance>
                <mol-instance>
                  <name>theSte5</name>
                  <binding-site>toGpa1</binding-site>
                </mol-instance>
              </binding>
              <simple-mol-binding id="Ste5ADPbond">
                <mol-instance>
                  <name>theSte5</name>
                  <binding-site>toAXPSite</binding-site>
                </mol-instance>
                <simple-mol-instance>
                  <name>theBoundADP</name>
                </mol-instance>
              </simple-mol-binding>
            </bindings>
          </subgraph>
        </selector>
      </selectors>

      <transformation>
        <mol-state-changes>
          <mol-state-change>
            <name>theGpa1</name>
            <state>inactive</state>
          </mol-state-change>
          <mol-state-change>
            <name>theSte5</name>
            <state>active</state>
          </mol-state-change>
        </mol-state-changes>

        <binding-site-state-changes>
          <binding-site-state-change>
            <name>OccludedSte11Site</name>
            <state>active</state>
          </binding-site-state-change>
        </binding-site-state-changes>

        <modification-changes>
          <modification-change>
            <name>PhoshorlyatedP03Site</name>
            <modification>None</modification>
          </modification-change>
        <modification-changes>

        <binding-changes>
          <binding-created>
            <binding-site-name>FreeToGpa1Site</binding-site-name>
            <binding-site-name>FreeToFus3Site</binding-site-name>
          </binding-created>
          <binding-deleted>
            <binding-name>Gpa1ToSte5Bond</binding-name>
          </binding-deleted>
        </binding-changes>

        <simple-mol-exchanges>
          <simple-mol-exchange>
            <name>Ste5ADPbond</name>
            <simple-mol>ATP</simple-mol>
          </simple-mol-exchange>
        </simple-mol-exchanges>
      </transformation>

      <mass-action reversible="false">
        <reversible>true</reversible>
        <default>
          <forward-rate>10.0</forward-rate>
        </default>
        <allosteric-rates>
          <forward-rate>5.0</forward-rate>
          <selector>
            <subgraph>
              <mol-instances>
                <mol-instance>
                  <name>theFus3</name>
                  <mol>Fus3</mol>
                  <binding-site-instances>
                    <binding-site-instance id="FreeToGpa1Site">
                      <binding-site>toGpa1</binding-site>
                      <bound>false</bound>
                      <state>active</state>
                    </binding-site-instance>
                  </binding-site-instances>
                </mol-instance>
              </mol-instances>
            </subgraph>
          </selector>
        </allosteric-rates>

        <allosteric-rates>
          <default>
            <forward-rate>5.0</forward-rate>
          </default>
          <selector>
            <subgraph>
              <mol-instances>
                <mol-instance>
                  <name>theFus3</name>
                  <mol>Fus3</mol>
                  <binding-site-instances>
                    <binding-site-instance id="FreeToGpa1Site">
                      <binding-site>toGpa1</binding-site>
                      <bound>false</bound>
                      <state>active</state>
                    </binding-site-instance>
                  </binding-site-instances>

                  <modification-site-instances>
                    <modification-site-instance>
                      <name>PhoshorlyatedP03Site</name>
                      <modification-site>P03</modification-site>
                      <modification>Phosphorylated</modification>
                    </modification-site-instance>
                  </modification-site-instances>
                </mol-instance>
              </mol-instances>
            </subgraph>
          </selector>
        </allosteric-rates>
      </mass-action>

      <mass-action reversible="true">
        <reversible>true</reversible>
        <forward-rate>10.0</forward-rate>
        <reverse-rate><parameter name="complexReactioOffRate" /></reverse-rate>
      </mass-action>

      <generic-kinetics reversible="false">
        <forward-equation>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>cytosol</ci>
              <apply>
                <minus/>
                <apply>
                  <times/>
                  <ci>kon</ci>
                  <ci>E</ci>
                  <ci>S</ci>
                </apply>
                <apply>
                  <times/>
                  <ci>koff</ci>
                  <ci>ES</ci>
                </apply>
              </apply>
            </apply>
          </math>
        </forward-equation>

        <reverse-equation>
          <math xmlns="http://www.w3.org/1998/Math/MathML">
            <apply>
              <times/>
              <ci>cytosol</ci>
              <apply>
                <minus/>
                <apply>
                  <times/>
                  <ci>kon</ci>
                  <ci>E</ci>
                  <ci>S</ci>
                </apply>
                <apply>
                  <times/>
                  <ci>koff</ci>
                  <ci>ES</ci>
                </apply>
              </apply>
            </apply>
          </math>
        </reverse-equation>
      </generic-kinetics>
    </rule>

    <rule>
      <selectors>
        <selector>
          ...
        </selector>
       </selectors>

       <transformation>
         <explicit-products>
           <mol-instance>
           </mol-instance>
           <simple-mol>
           </simple-mol>
         </explicit-products>
       </transformation>
     </rule>
    </rule>
  </rules>
</ecell-rules>