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`iSynCJ816` is not valid SBML due to no flux objective and reaction with no reactants or products #389

Open jonrkarr opened 3 years ago

jonrkarr commented 3 years ago

This can be fixed by

  1. Replace 
    <fbc:listOfObjectives fbc:activeObjective="obj">
  <fbc:objective fbc:id="obj" fbc:type="maximize">
    <fbc:listOfFluxObjectives/>
  </fbc:objective>
</fbc:listOfObjectives>

    with

    <fbc:listOfObjectives fbc:activeObjective="obj_auto">
  <fbc:objective fbc:id="obj_auto" fbc:type="maximize">
    <fbc:listOfFluxObjectives>
      <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_SynAuto_1" fbc:coefficient="1"/>
    </fbc:listOfFluxObjectives>
  </fbc:objective>
  <fbc:objective fbc:id="obj_mixo" fbc:type="maximize">
    <fbc:listOfFluxObjectives>
      <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_SynMixo_1" fbc:coefficient="1"/>
    </fbc:listOfFluxObjectives>
  </fbc:objective>
  <fbc:objective fbc:id="obj_hetero" fbc:type="maximize">
    <fbc:listOfFluxObjectives>
      <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_SynHetero_1" fbc:coefficient="1"/>
    </fbc:listOfFluxObjectives>
  </fbc:objective>
</fbc:listOfObjectives>
  2. Remove reaction R_DNADRAIN 
    <reaction id="R_DNADRAIN" fast="false" reversible="false" name="Dna sink transport reaction" metaid="R_DNADRAIN" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
  <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
    <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
      <rdf:Description rdf:about="#R_DNADRAIN">
        <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
          <rdf:Bag>
            <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/DNADRAIN"/>
          </rdf:Bag>
        </bqbiol:is>
      </rdf:Description>
    </rdf:RDF>
  </sbml:annotation>
</reaction>