# HG changeset patch
# User tduigou
# Date 1663753294 0
# Node ID e8d56cb2be03edc076550e7ae2a5c30e807220d4
# Parent  fcc8f3e2d4da801540f953d56011f6720752c986
planemo upload commit f40274f6b9f6a15eb4022aab21286d4c96cd8475-dirty

diff -r fcc8f3e2d4da -r e8d56cb2be03 rpcompletion.xml
--- a/rpcompletion.xml	Wed May 04 10:05:47 2022 +0000
+++ b/rpcompletion.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -1,7 +1,7 @@
-<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="19.09">
+<tool id="rpcompletion" name="Complete Reactions" version="@TOOL_VERSION@" profile="21.09">
     <description>From the output of RP2Paths and RetroPath2.0, generate SBML unique and complete (with cofactors) pathways with mono-component reactions</description>
     <macros>
-        <token name="@TOOL_VERSION@">5.12.3</token>
+        <token name="@TOOL_VERSION@">5.13.1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rptools</requirement>
@@ -27,9 +27,9 @@
         <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 metabolic network" />
         <param name="sink" type="data" format="csv" label="Sink from SBML" />
         <section name="adv" title="Advanced Options" expanded="false">
-            <param name="max_subpaths_filter" type="integer" value="10" label="Max subpaths generated per pathway" />
-            <param name="upper_flux_bound" type="integer" value="999999" label="Upper flux bound" />
-            <param name="lower_flux_bound" type="integer" value="0" label="Lower flux bound" />
+            <param argument="max_subpaths_filter" type="integer" value="10" min="1" max="1000" label="Max subpaths generated per pathway" help="Maximal number of subpaths to be created per master pathway." />
+            <param argument="upper_flux_bound" type="integer" value="10000" min="-10000" max="10000" label="Upper flux bound" help="Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
+            <param argument="lower_flux_bound" type="integer" value="0" min="-10000" max="10000" label="Lower flux bound" help="Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created." />
         </section>
     </inputs>
     <outputs>
@@ -61,24 +61,28 @@
 rpCompletion
 ============
 
-Completes mono-component reactions output by RetroPath2.0 with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
+Completes mono-component reactions output by `RetroPath2.0 <https://www.sciencedirect.com/science/article/pii/S1096717617301337>`_ with the appropriate cofactors. Creates sub-paths when multiple reaction rules are associated with a single reaction. Input is a single pathways file produced by RP2Paths. It stands on rpCache which store pre-computed data.
 
 Input
 -----
 
 Required:
 
-* **rp2_pathways**: (string) Path to the RetroPath2.0 pathways file
-* **rp2_sink**: (string) Path to the rpextractsink file containing infos on molecules in the sink
-* **rp2paths_compounds**: (string) Path to the rp2paths compounds file
-* **rp2paths_pathways**: (string) Path to the rp2paths pathways file
-* **outdir**: (string) Path to the output directory containing sbml completed pathways
+* **RetroPath2.0 metabolic network**: RetroPath2.0 pathways file
+* **Sink from SBML**: rpextractsink file containing infos on molecules in the sink
+* **RP2paths compounds**: rp2paths compounds file
+* **RP2paths pathways**: rp2paths pathways file
 
 Advanced options:
 
-* **-upper_flux_bound**: (integer, default=9999) Upper flux bound value
-* **-lower_flux_bound**: (integer, default=0) Lower flux bound value
-* **-max_subpaths_filter**: (integer, default=10, 0=nofilter) Number of subpaths per path
+* **Upper flux bound**: (integer, default=9999) Upper flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
+* **Lower flux bound**: (integer, default=0) Lower flux bound value to be used in outputted SBML models (fbc SBML package) for new reactions created.
+* **Max subpaths generated per pathway**: (integer, default=10, 0=nofilter) Maximal number of subpaths to be created per master pathway.
+
+Output
+------
+
+* **pathways**: SBML completed pathways
 
 Project Links
 ---------------------
@@ -87,7 +91,7 @@
 Version
 ----------
 
-5.12.1
+5.13.1
 
 Authors
 -------
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0001.xml
--- a/test-data/rp_001_0001.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_001_0001.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,78 +23,6 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="dimethylallyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -113,24 +41,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
-                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -167,13 +77,103 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc" id="MNXM132" name="dimethylallyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_212c5940beac5625a2636d3d14fbc63cc5a8107d9dd39020ac544f296debabcc">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="CBIDRCWHNCKSTO-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -323,11 +323,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM132"/>
-          <groups:member groups:idRef="TARGET_0000000001"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -339,9 +339,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM11"/>
           <groups:member groups:idRef="MNXM8975"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -353,9 +353,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM132"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0006.xml
--- a/test-data/rp_001_0006.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_001_0006.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,19 +23,55 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -59,6 +95,42 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -77,24 +149,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -113,67 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -323,11 +323,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM132"/>
-          <groups:member groups:idRef="TARGET_0000000001"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -339,8 +339,8 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM8975"/>
         </groups:listOfMembers>
       </groups:group>
@@ -353,9 +353,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM132"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_001_0011.xml
--- a/test-data/rp_001_0011.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_001_0011.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,19 +23,55 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -59,19 +95,19 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -131,49 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -323,11 +323,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM132"/>
-          <groups:member groups:idRef="TARGET_0000000001"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -339,9 +339,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM35"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -353,9 +353,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM132"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0001.xml
--- a/test-data/rp_002_0001.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_002_0001.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,60 +23,6 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -95,42 +41,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
-                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
-                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -167,13 +77,103 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
+                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -326,11 +326,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM100"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -342,9 +342,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM11"/>
           <groups:member groups:idRef="MNXM8975"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -357,8 +357,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM100"/>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0011.xml
--- a/test-data/rp_002_0011.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_002_0011.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,6 +23,78 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -41,6 +113,24 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
+                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -59,24 +149,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -95,85 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
-                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -326,11 +326,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM100"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -342,8 +342,8 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM8975"/>
         </groups:listOfMembers>
       </groups:group>
@@ -357,8 +357,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM100"/>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_002_0021.xml
--- a/test-data/rp_002_0021.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_002_0021.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,6 +23,60 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -41,19 +95,19 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
+                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -113,67 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36" id="MNXM100" name="(2E)-geranyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_3f5eb2f4341086942fd1241ec422493fc345830f18b33b0deb223866e06ace36">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)"/>
-                <brsynth:inchikey value="GVVPGTZRZFNKDS-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -326,11 +326,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM100"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -342,9 +342,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM35"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -357,8 +357,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM100"/>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0001.xml
--- a/test-data/rp_003_0001.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_003_0001.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,60 +23,6 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
-                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
-                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -95,24 +41,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
-                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -149,6 +77,60 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="O=P(O)(O)OP(=O)(O)O"/>
+                <brsynth:inchi value="InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)"/>
+                <brsynth:inchikey value="XPPKVPWEQAFLFU-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4" id="MNXM8975" name="MNXM8975" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2f4b2d21d00b43a266620e821de533b08c3e42ff09ca008f915ca4400eb7d8c4">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -167,13 +149,31 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -364,11 +364,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
-          <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -380,9 +380,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM11"/>
           <groups:member groups:idRef="MNXM8975"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -394,9 +394,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM11"/>
+          <groups:member groups:idRef="MNXM34"/>
           <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="MNXM11"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0131.xml
--- a/test-data/rp_003_0131.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_003_0131.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,6 +23,78 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -59,19 +131,19 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+            <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
+                <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -95,85 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a" id="MNXM36" name="MNXM36" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_04b973bebf0de87c9fe23384ce8fd1fef71a33cbb0b827ade48cd364bf14a23a">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
-                <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -364,11 +364,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
-          <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -380,8 +380,8 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM36"/>
           <groups:member groups:idRef="MNXM8975"/>
         </groups:listOfMembers>
       </groups:group>
@@ -394,9 +394,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM11"/>
+          <groups:member groups:idRef="MNXM34"/>
           <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="MNXM11"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>
diff -r fcc8f3e2d4da -r e8d56cb2be03 test-data/rp_003_0261.xml
--- a/test-data/rp_003_0261.xml	Wed May 04 10:05:47 2022 +0000
+++ b/test-data/rp_003_0261.xml	Wed Sep 21 09:41:34 2022 +0000
@@ -23,6 +23,60 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
+      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
+                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
+                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="a6e267be12defb7184259624f5adc519108c6c6adfe6be13f64b649567cb6df1" id="MNXM11" name="diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -41,24 +95,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002" id="TARGET_0000000001" name="TARGET_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_6817bb5f7133f50744b232330f1f3009343f785b8f77602ce5f44cdd9458f002">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])=C([H])C([H])=C(C([H])=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H56/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,15-22,25-32H,13-14,23-24H2,1-10H3"/>
-                <brsynth:inchikey value="OAIJSZIZWZSQBC-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
       <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -77,6 +113,24 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
+                <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -113,67 +167,13 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="isopentenyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)"/>
-                <brsynth:inchikey value="OINNEUNVOZHBOX-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f" id="MNXM34" name="(2E,6E)-farnesyl diphosphate" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_10a025d408ecc91b5894e1d66d8a31d96e4ac530a63de61f99720be74086a29f">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C15H28O7P2/c1-13(2)7-5-8-14(3)9-6-10-15(4)11-12-21-24(19,20)22-23(16,17)18/h7,9,11H,5-6,8,10,12H2,1-4H3,(H,19,20)(H2,16,17,18)"/>
-                <brsynth:inchikey value="VWFJDQUYCIWHTN-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
-      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_999999" value="999999" units="mmol_per_gDW_per_hr" constant="true"/>
+      <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000" value="10000" units="mmol_per_gDW_per_hr" constant="true"/>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_0" value="0" units="mmol_per_gDW_per_hr" constant="true"/>
     </listOfParameters>
     <listOfReactions>
-      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d" sboTerm="SBO:0000176" id="rxn_3" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_376841fa42ba139764a5509b9d817e2e540d0e228582c970025c73ae1ee77c0d">
@@ -208,7 +208,7 @@
           <speciesReference species="TARGET_0000000001" stoichiometry="1" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff" sboTerm="SBO:0000176" id="rxn_2" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -248,7 +248,7 @@
           <speciesReference species="MNXM11" stoichiometry="2" constant="true"/>
         </listOfProducts>
       </reaction>
-      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_999999">
+      <reaction metaid="_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4" sboTerm="SBO:0000176" id="rxn_1" reversible="false" fast="false" fbc:lowerFluxBound="BRS_FBC_0" fbc:upperFluxBound="BRS_FBC_10000">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
             <rdf:Description rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -364,11 +364,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
-          <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -380,9 +380,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM35"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -394,9 +394,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM11"/>
+          <groups:member groups:idRef="MNXM34"/>
           <groups:member groups:idRef="MNXM83"/>
-          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="MNXM11"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>