from pathlib import Path
import libsbml
from combine_notebooks.validation.validation_sbml import validate_sbml
def create_repressilator(sbml_path: Path) -> libsbml.SBMLDocument:
"""Create repressilator."""
print("Create SBML model")
# create a new document
doc: libsbml.SBMLDocument = libsbml.SBMLDocument(3, 2)
model: libsbml.Model = doc.createModel()
# --- compartments ---
# add compartment
c1: libsbml.Compartment = model.createCompartment()
c1.setId("cell")
c1.setSize(1.0)
c1.setMetaId("meta_cell")
c1.setSBOTerm("SBO:0000290")
# set annotation
c1_cv: libsbml.CVTerm = libsbml.CVTerm()
c1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
c1_cv.setBiologicalQualifierType(libsbml.BQB_IS)
c1_cv.addResource("http://identifiers.org/GO:0005623")
c1.addCVTerm(c1_cv)
# --- species ---
# add species for the 3 mRNAs and 3 Proteins
s1: libsbml.Species = model.createSpecies()
s1.setId("PX")
s1.setMetaId("PX")
s1.setCompartment("cell")
s1.setName("LacI protein")
s1.setSBOTerm("SBO:0000252")
s1.setInitialAmount(0)
s1.setHasOnlySubstanceUnits(True)
# set annotation
s1_cv: libsbml.CVTerm = libsbml.CVTerm()
s1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s1_cv.setBiologicalQualifierType(libsbml.BQB_IS)
s1_cv.addResource("http://identifiers.org/uniprot/P03023")
s1.addCVTerm(s1_cv)
s2: libsbml.Species = model.createSpecies()
s2.setId("PY")
s2.setMetaId("PY")
s2.setCompartment("cell")
s2.setName("TetR protein")
s2.setSBOTerm("SBO:0000252")
s2.setInitialAmount(0)
s2.setHasOnlySubstanceUnits(True)
# set annotation
s2_cv: libsbml.CVTerm = libsbml.CVTerm()
s2_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s2_cv.setBiologicalQualifierType(libsbml.BQB_IS)
s2_cv.addResource("http://identifiers.org/uniprot/P04483")
s2.addCVTerm(s2_cv)
s3: libsbml.Species = model.createSpecies()
s3.setId("PZ")
s3.setMetaId("PZ")
s3.setCompartment("cell")
s3.setName("cI protein")
s3.setSBOTerm("SBO:0000252")
s3.setInitialAmount(0)
s3.setHasOnlySubstanceUnits(True)
# set annotation
s3_cv: libsbml.CVTerm = libsbml.CVTerm()
s3_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s3_cv.setBiologicalQualifierType(libsbml.BQB_IS)
# example setting a model qualifier
# s3_cv.setQualifierType(libsbml.MODEL_QUALIFIER)
# s3_cv.setBiologicalQualifierType(libsbml.BQM_IS)
s3_cv.addResource("http://identifiers.org/uniprot/P03034")
s3.addCVTerm(s3_cv)
s4: libsbml.Species = model.createSpecies()
s4.setId("X")
s4.setMetaId("meta_X")
s4.setCompartment("cell")
s4.setName("LacI mRNA")
s4.setSBOTerm("SBO:0000250")
s4.setInitialAmount(0)
s4.setHasOnlySubstanceUnits(True)
# set annotation
s4_cv: libsbml.CVTerm = libsbml.CVTerm()
s4_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s4_cv.addResource("http://identifiers.org/CHEBI:33699")
s4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s4_cv.addResource("http://identifiers.org/kegg.compound/C00046")
s4.addCVTerm(s4_cv)
s4_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)
s4_cv.addResource("http://identifiers.org/uniprot/P03023")
s4.addCVTerm(s4_cv)
s5: libsbml.Species = model.createSpecies()
s5.setId("Y")
s5.setMetaId("meta_Y")
s5.setCompartment("cell")
s5.setName("TetR mRNA")
s5.setSBOTerm("SBO:0000250")
s5.setInitialAmount(20)
s5.setHasOnlySubstanceUnits(True)
# set annotation
s5_cv: libsbml.CVTerm = libsbml.CVTerm()
s5_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s5_cv.addResource("http://identifiers.org/CHEBI:33699")
s5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s5_cv.addResource("http://identifiers.org/kegg.compound/C00046")
s5.addCVTerm(s5_cv)
s5_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)
s5_cv.addResource("http://identifiers.org/uniprot/P04483")
s5.addCVTerm(s5_cv)
s6: libsbml.Species = model.createSpecies()
s6.setId("Z")
s6.setMetaId("meta_Z")
s6.setCompartment("cell")
s6.setName("cl mRNA")
s6.setSBOTerm("SBO:0000250")
s6.setInitialAmount(0)
s6.setHasOnlySubstanceUnits(True)
# set annotation
s6_cv: libsbml.CVTerm = libsbml.CVTerm()
s6_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
s6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s6_cv.addResource("http://identifiers.org/CHEBI:33699")
s6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
s6_cv.addResource("http://identifiers.org/kegg.compound/C00046")
s6.addCVTerm(s6_cv)
s6_cv.setBiologicalQualifierType(libsbml.BQB_ENCODES)
s6_cv.addResource("http://identifiers.org/uniprot/P03034")
s6.addCVTerm(s6_cv)
# --- parameters ---
# <parameter id="kd_mRNA" constant="false" name="kd_mRNA" sboTerm="SBO:0000356">
p1: libsbml.Parameter = model.createParameter()
p1.setId("tau_mRNA")
p1.setName("mRNA half life")
p1.setConstant(True)
p1.setValue(2.0)
# <parameter id="kd_mRNA" constant="false" name="kd_mRNA" sboTerm="SBO:0000356">
p2: libsbml.Parameter = model.createParameter()
p2.setId("kd_mRNA")
p2.setName("kd_mRNA")
p2.setSBOTerm("SBO:0000356")
p2.setConstant(False)
# <parameter metaid="metaid_0000233" sboTerm="SBO:0000016" id="k_tl" name="k_tl" constant="false">
p3: libsbml.Parameter = model.createParameter()
p3.setId("k_tl")
p3.setName("k_tl")
p3.setSBOTerm("SBO:0000016")
p3.setConstant(False)
# <parameter metaid="metaid_0000025" id="eff" name="translation efficiency" value="20">
p4: libsbml.Parameter = model.createParameter()
p4.setId("eff")
p4.setName("translation efficiency")
p4.setConstant(True)
p4.setValue(20)
# <parameter metaid="metaid_0000032" sboTerm="SBO:0000348" id="t_ave" name="average mRNA life time" constant="false"/>
p5: libsbml.Parameter = model.createParameter()
p5.setId("t_ave")
p5.setName("average mRNA life time")
p5.setSBOTerm("SBO:0000348")
p5.setConstant(False)
# <parameter metaid="metaid_0000133" sboTerm="SBO:0000356" id="kd_prot" name="kd_prot" constant="false">
p6: libsbml.Parameter = model.createParameter()
p6.setId("kd_prot")
p6.setName("kd_prot")
p6.setSBOTerm("SBO:0000356")
p6.setConstant(False)
# <parameter metaid="metaid_0000128" sboTerm="SBO:0000332" id="tau_prot" name="protein half life" value="10"/>
p7: libsbml.Parameter = model.createParameter()
p7.setId("tau_prot")
p7.setName("protien half life")
p7.setConstant(True)
p7.setValue(10)
# <parameter metaid="metaid_0000234" sboTerm="SBO:0000485" id="a0_tr" name="a0_tr" constant="false">
p8: libsbml.Parameter = model.createParameter()
p8.setId("a0_tr")
p8.setName("a0_tr")
p8.setSBOTerm("SBO:0000485")
p8.setConstant(False)
# <parameter metaid="metaid_0500235" sboTerm="SBO:0000485" id="ps_0" name="tps_repr" value="0.0005">
p9: libsbml.Parameter = model.createParameter()
p9.setId("ps_0")
p9.setName("tps_repr")
p9.setConstant(True)
p9.setValue(0.0005)
# <parameter metaid="metaid_0900235" sboTerm="SBO:0000186" id="a_tr" name="a_tr" constant="false">
p10: libsbml.Parameter = model.createParameter()
p10.setId("a_tr")
p10.setName("a_tr")
p10.setSBOTerm("SBO:0000186")
p10.setConstant(False)
# <parameter metaid="metaid_0800235" sboTerm="SBO:0000186" id="ps_a" name="tps_active" value="0.5">
p11: libsbml.Parameter = model.createParameter()
p11.setId("ps_a")
p11.setName("tps_active")
p11.setConstant(True)
p11.setValue(0.5)
# <parameter metaid="metaid_0000027" sboTerm="SBO:0000288" id="KM" name="KM" value="40">
p12: libsbml.Parameter = model.createParameter()
p12.setId("KM")
p12.setName("KM")
p12.setConstant(True)
p12.setValue(40)
# <parameter metaid="metaid_0000026" sboTerm="SBO:0000190" id="n" name="n" value="2">
p13: libsbml.Parameter = model.createParameter()
p13.setId("n")
p13.setName("n")
p13.setConstant(True)
p13.setValue(2.0)
# TODO: a0_tr, a_tr, n, KM
# --- rules ---
a1: libsbml.AssignmentRule = model.createAssignmentRule()
a1.setVariable("kd_mRNA")
math_ast1: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"ln(2) / tau_mRNA", model
)
a1.setMath(math_ast1)
a2: libsbml.AssignmentRule = model.createAssignmentRule()
a2.setVariable("t_ave")
math_ast2: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"tau_mRNA / ln(2)", model
)
a2.setMath(math_ast2)
a3: libsbml.AssignmentRule = model.createAssignmentRule()
a3.setVariable("k_tl")
math_ast3: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("eff / t_ave", model)
a3.setMath(math_ast3)
a4: libsbml.AssignmentRule = model.createAssignmentRule()
a4.setVariable("kd_prot")
math_ast4: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"ln(2) / tau_prot", model
)
a4.setMath(math_ast4)
a5: libsbml.AssignmentRule = model.createAssignmentRule()
a5.setVariable("a0_tr")
math_ast5: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("ps_0 * 60", model)
a5.setMath(math_ast5)
a6: libsbml.AssignmentRule = model.createAssignmentRule()
a6.setVariable("a_tr")
math_ast6: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"(ps_a - ps_0) * 60", model
)
a6.setMath(math_ast6)
# --- reaction ---
# X -> None
r1: libsbml.Reaction = model.createReaction()
r1.setId("Reaction1"), # set reaction id
r1.setMetaId("meta_Reaction1")
r1.setSBOTerm("SBO:0000179")
r1.setName("degradation of LacI transcripts")
r1.setReversible(False)
# set annotation
r1_cv: libsbml.CVTerm = libsbml.CVTerm()
r1_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r1_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r1_cv.addResource("http://identifiers.org/GO:0006402")
r1.addCVTerm(r1_cv)
species_ref1: libsbml.SpeciesReference = r1.createReactant()
species_ref1.setSpecies("X") # assign reactant species
math_ast7: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_mRNA * X", model)
kinetic_law = r1.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast7)
r2 = model.createReaction()
r2.setId("Reaction2"), # set reaction id
r2.setMetaId("meta_Reaction2")
r2.setSBOTerm("SBO:0000179")
r2.setName("degradation of TetR transcripts")
r2.setReversible(False)
r2_cv: libsbml.CVTerm = libsbml.CVTerm()
r2_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r2_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r2_cv.addResource("http://identifiers.org/GO:0006402")
r2.addCVTerm(r1_cv)
species_ref2 = r2.createReactant()
species_ref2.setSpecies("Y") # assign reactant species
math_ast8: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_mRNA * Y", model)
kinetic_law = r2.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast8)
r3 = model.createReaction()
r3.setId("Reaction3"), # set reaction id
r3.setMetaId("meta_Reaction3")
r3.setSBOTerm("SBO:0000179")
r3.setName("degradation of CI transcripts")
r3.setReversible(False)
# set annotation
r3_cv: libsbml.CVTerm = libsbml.CVTerm()
r3_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r3_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r3_cv.addResource("http://identifiers.org/GO:0006402")
r3.addCVTerm(r3_cv)
species_ref3 = r3.createReactant()
species_ref3.setSpecies("Z") # assign reactant species
math_ast9: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_mRNA * Z", model)
kinetic_law = r3.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast9)
r4 = model.createReaction()
r4.setId("Reaction4"), # set reaction id
r4.setMetaId("meta_Reaction4")
r4.setSBOTerm("SBO:0000184")
r4.setName("translation of LacI")
r4.setReversible(False)
# set annotation
r4_cv: libsbml.CVTerm = libsbml.CVTerm()
r4_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r4_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r4_cv.addResource("http://identifiers.org/GO:0006412")
r4.addCVTerm(r4_cv)
species_ref4 = r4.createProduct()
species_ref4.setSpecies("PX") # assign product species
species_ref_4 = r4.createModifier()
species_ref_4.setSpecies("X")
species_ref_4.setSBOTerm("SBO:0000461")
math_ast10: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("k_tl * X", model)
kinetic_law = r4.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast10)
r5 = model.createReaction()
r5.setId("Reaction5"), # set reaction id
r5.setMetaId("meta_Reaction5")
r5.setSBOTerm("SBO:0000184")
r5.setName("translation of TetR")
r5.setReversible(False)
s3_cv = libsbml.CVTerm()
# set annotation
r5_cv: libsbml.CVTerm = libsbml.CVTerm()
r5_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r5_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r5_cv.addResource("http://identifiers.org/GO:0006412")
r5.addCVTerm(r5_cv)
species_ref5 = r5.createProduct()
species_ref5.setSpecies("PY") # assign product species
species_ref_5 = r5.createModifier()
species_ref_5.setSpecies("Y")
species_ref_5.setSBOTerm("SBO:0000461")
math_ast11: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("k_tl * Y", model)
kinetic_law = r5.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast11)
r6 = model.createReaction()
r6.setId("Reaction6"), # set reaction id
r6.setMetaId("meta_Reaction6")
r6.setSBOTerm("SBO:0000184")
r6.setName("translation of CI")
r6.setReversible(False)
# set annotation
r6_cv: libsbml.CVTerm = libsbml.CVTerm()
r6_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r6_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r6_cv.addResource("http://identifiers.org/GO:0006412")
r6.addCVTerm(r6_cv)
species_ref6 = r6.createProduct()
species_ref6.setSpecies("PZ") # assign product species
species_ref_6 = r6.createModifier()
species_ref_6.setSpecies("Z")
species_ref_6.setSBOTerm("SBO:0000461")
math_ast12: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("k_tl * Z", model)
kinetic_law = r6.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast12)
r7 = model.createReaction()
r7.setId("Reaction7"), # set reaction id
r7.setMetaId("meta_Reaction7")
r7.setSBOTerm("SBO:0000179")
r7.setName("degradation of LacI")
r7.setReversible(False)
# set annotation
r7_cv: libsbml.CVTerm = libsbml.CVTerm()
r7_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r7_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r7_cv.addResource("http://identifiers.org/GO:0030163")
r7.addCVTerm(r7_cv)
species_ref7 = r7.createReactant()
species_ref7.setSpecies("PX") # assign reactant species
math_ast13: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_prot * PX", model)
kinetic_law = r7.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast13)
r8 = model.createReaction()
r8.setId("Reaction8"), # set reaction id
r8.setMetaId("meta_Reaction8")
r8.setSBOTerm("SBO:0000179")
r8.setName("degradation of TetR")
r8.setReversible(False)
# set annotation
r8_cv: libsbml.CVTerm = libsbml.CVTerm()
r8_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r8_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r8_cv.addResource("http://identifiers.org/GO:0030163")
r8.addCVTerm(r8_cv)
species_ref8 = r8.createReactant()
species_ref8.setSpecies("PY") # assign reactant species
math_ast14: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_prot * PY", model)
kinetic_law = r8.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast14)
r9 = model.createReaction()
r9.setId("Reaction9"), # set reaction id
r9.setMetaId("meta_Reaction9")
r9.setSBOTerm("SBO:0000179")
r9.setName("degradation of CI")
r9.setReversible(False)
# set annotation
r9_cv: libsbml.CVTerm = libsbml.CVTerm()
r9_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r9_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r9_cv.addResource("http://identifiers.org/GO:0030163")
r9.addCVTerm(r9_cv)
species_ref9 = r9.createReactant()
species_ref9.setSpecies("PZ") # assign reactant species
math_ast15: libsbml.ASTNode = libsbml.parseL3FormulaWithModel("kd_prot * PZ", model)
kinetic_law = r9.createKineticLaw()
kinetic_law.setSBOTerm("SBO:0000049")
kinetic_law.setMath(math_ast15)
r10 = model.createReaction()
r10.setId("Reaction10"), # set reaction id
r10.setMetaId("meta_Reaction10")
r10.setSBOTerm("SBO:0000183")
r10.setName("transcription of LacI")
r10.setReversible(False)
# set annotation
r10_cv: libsbml.CVTerm = libsbml.CVTerm()
r10_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r10_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r10_cv.addResource("http://identifiers.org/GO:0006351")
r10.addCVTerm(r10_cv)
species_ref10 = r10.createProduct()
species_ref10.setSpecies("X") # assign product species
species_ref_10 = r10.createModifier()
species_ref_10.setSpecies("PZ")
species_ref_10.setSBOTerm("SBO:0000536")
math_ast16: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PZ, n))", model
)
kinetic_law = r10.createKineticLaw()
kinetic_law.setMath(math_ast16)
r11 = model.createReaction()
r11.setId("Reaction11"), # set reaction id
r11.setMetaId("meta_Reaction11")
r11.setSBOTerm("SBO:0000183")
r11.setName("transcription of TetR")
r11.setReversible(False)
# set annotation
r11_cv: libsbml.CVTerm = libsbml.CVTerm()
r11_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r11_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r11_cv.addResource("http://identifiers.org/GO:0006351")
r11.addCVTerm(r11_cv)
species_ref11 = r11.createProduct()
species_ref11.setSpecies("Y") # assign product species
species_ref_11 = r11.createModifier()
species_ref_11.setSpecies("PX")
species_ref_11.setSBOTerm("SBO:0000536")
math_ast17: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PX, n))", model
)
kinetic_law = r11.createKineticLaw()
kinetic_law.setMath(math_ast17)
r12 = model.createReaction()
r12.setId("Reaction12"), # set reaction id
r12.setMetaId("meta_Reaction12")
r12.setSBOTerm("SBO:0000183")
r12.setName("transcription of CI")
r12.setReversible(False)
# set annotation
r12_cv: libsbml.CVTerm = libsbml.CVTerm()
r12_cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)
r12_cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF)
r12_cv.addResource("http://identifiers.org/GO:0006351")
r12.addCVTerm(r12_cv)
species_ref12 = r12.createProduct()
species_ref12.setSpecies("Z") # assign product species
species_ref_12 = r12.createModifier()
species_ref_12.setSpecies("PY")
species_ref_12.setSBOTerm("SBO:0000536")
math_ast18: libsbml.ASTNode = libsbml.parseL3FormulaWithModel(
"a0_tr + (a_tr * power(KM, n)) / (power(KM, n) + power(PY, n))", model
)
kinetic_law = r12.createKineticLaw()
kinetic_law.setMath(math_ast18)
print("-" * 80)
print(libsbml.writeSBMLToString(doc))
print("-" * 80)
# write to file
libsbml.writeSBMLToFile(doc, str(sbml_path))
# validate file
validate_sbml(doc, units_consistency=False)
return doc
if __name__ == "__main__":
from combine_notebooks import RESULTS_DIR
# RESOURCES_DIR: Path = Path(__file__).parent / "resources"
# RESULTS_DIR: Path = RESOURCES_DIR / "results"
doc: libsbml.SBMLDocument = create_repressilator(
sbml_path=RESULTS_DIR / "repressilator_libsbml.xml"
)
# <markdowncell>
Create SBML model
--------------------------------------------------------------------------------
<?xml version="1.0" encoding="UTF-8"?>
<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
<model>
<listOfCompartments>
<compartment metaid="meta_cell" sboTerm="SBO:0000290" id="cell" size="1">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_cell">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0005623"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="PX" sboTerm="SBO:0000252" id="PX" name="LacI protein" compartment="cell" initialAmount="0" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#PX">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03023"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="PY" sboTerm="SBO:0000252" id="PY" name="TetR protein" compartment="cell" initialAmount="0" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#PY">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04483"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="PZ" sboTerm="SBO:0000252" id="PZ" name="cI protein" compartment="cell" initialAmount="0" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#PZ">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03034"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="meta_X" sboTerm="SBO:0000250" id="X" name="LacI mRNA" compartment="cell" initialAmount="0" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_X">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/CHEBI:33699"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
</rdf:Bag>
</bqbiol:isVersionOf>
<bqbiol:encodes>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03023"/>
</rdf:Bag>
</bqbiol:encodes>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="meta_Y" sboTerm="SBO:0000250" id="Y" name="TetR mRNA" compartment="cell" initialAmount="20" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Y">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/CHEBI:33699"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
</rdf:Bag>
</bqbiol:isVersionOf>
<bqbiol:encodes>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04483"/>
</rdf:Bag>
</bqbiol:encodes>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="meta_Z" sboTerm="SBO:0000250" id="Z" name="cl mRNA" compartment="cell" initialAmount="0" hasOnlySubstanceUnits="true">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Z">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/CHEBI:33699"/>
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
</rdf:Bag>
</bqbiol:isVersionOf>
<bqbiol:encodes>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03034"/>
</rdf:Bag>
</bqbiol:encodes>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfParameters>
<parameter id="tau_mRNA" name="mRNA half life" value="2" constant="true"/>
<parameter sboTerm="SBO:0000356" id="kd_mRNA" name="kd_mRNA" constant="false"/>
<parameter sboTerm="SBO:0000016" id="k_tl" name="k_tl" constant="false"/>
<parameter id="eff" name="translation efficiency" value="20" constant="true"/>
<parameter sboTerm="SBO:0000348" id="t_ave" name="average mRNA life time" constant="false"/>
<parameter sboTerm="SBO:0000356" id="kd_prot" name="kd_prot" constant="false"/>
<parameter id="tau_prot" name="protien half life" value="10" constant="true"/>
<parameter sboTerm="SBO:0000485" id="a0_tr" name="a0_tr" constant="false"/>
<parameter id="ps_0" name="tps_repr" value="0.0005" constant="true"/>
<parameter sboTerm="SBO:0000186" id="a_tr" name="a_tr" constant="false"/>
<parameter id="ps_a" name="tps_active" value="0.5" constant="true"/>
<parameter id="KM" name="KM" value="40" constant="true"/>
<parameter id="n" name="n" value="2" constant="true"/>
</listOfParameters>
<listOfRules>
<assignmentRule variable="kd_mRNA">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<ln/>
<cn type="integer"> 2 </cn>
</apply>
<ci> tau_mRNA </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="t_ave">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> tau_mRNA </ci>
<apply>
<ln/>
<cn type="integer"> 2 </cn>
</apply>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="k_tl">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<ci> eff </ci>
<ci> t_ave </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="kd_prot">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<divide/>
<apply>
<ln/>
<cn type="integer"> 2 </cn>
</apply>
<ci> tau_prot </ci>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="a0_tr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> ps_0 </ci>
<cn type="integer"> 60 </cn>
</apply>
</math>
</assignmentRule>
<assignmentRule variable="a_tr">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<apply>
<minus/>
<ci> ps_a </ci>
<ci> ps_0 </ci>
</apply>
<cn type="integer"> 60 </cn>
</apply>
</math>
</assignmentRule>
</listOfRules>
<listOfReactions>
<reaction metaid="meta_Reaction1" sboTerm="SBO:0000179" id="Reaction1" name="degradation of LacI transcripts" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction1">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006402"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="X"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_mRNA </ci>
<ci> X </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction2" sboTerm="SBO:0000179" id="Reaction2" name="degradation of TetR transcripts" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction2">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006402"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="Y"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_mRNA </ci>
<ci> Y </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction3" sboTerm="SBO:0000179" id="Reaction3" name="degradation of CI transcripts" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction3">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006402"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="Z"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_mRNA </ci>
<ci> Z </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction4" sboTerm="SBO:0000184" id="Reaction4" name="translation of LacI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction4">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006412"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="PX"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000461" species="X"/>
</listOfModifiers>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k_tl </ci>
<ci> X </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction5" sboTerm="SBO:0000184" id="Reaction5" name="translation of TetR" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction5">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006412"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="PY"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000461" species="Y"/>
</listOfModifiers>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k_tl </ci>
<ci> Y </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction6" sboTerm="SBO:0000184" id="Reaction6" name="translation of CI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction6">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006412"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="PZ"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000461" species="Z"/>
</listOfModifiers>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> k_tl </ci>
<ci> Z </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction7" sboTerm="SBO:0000179" id="Reaction7" name="degradation of LacI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction7">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0030163"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="PX"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_prot </ci>
<ci> PX </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction8" sboTerm="SBO:0000179" id="Reaction8" name="degradation of TetR" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction8">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0030163"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="PY"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_prot </ci>
<ci> PY </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction9" sboTerm="SBO:0000179" id="Reaction9" name="degradation of CI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction9">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0030163"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference species="PZ"/>
</listOfReactants>
<kineticLaw sboTerm="SBO:0000049">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> kd_prot </ci>
<ci> PZ </ci>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction10" sboTerm="SBO:0000183" id="Reaction10" name="transcription of LacI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction10">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006351"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="X"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000536" species="PZ"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> a0_tr </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> a_tr </ci>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
<apply>
<power/>
<ci> PZ </ci>
<ci> n </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction11" sboTerm="SBO:0000183" id="Reaction11" name="transcription of TetR" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction11">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006351"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="Y"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000536" species="PX"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> a0_tr </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> a_tr </ci>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
<apply>
<power/>
<ci> PX </ci>
<ci> n </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction metaid="meta_Reaction12" sboTerm="SBO:0000183" id="Reaction12" name="transcription of CI" reversible="false">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#meta_Reaction12">
<bqbiol:isVersionOf>
<rdf:Bag>
<rdf:li rdf:resource="http://identifiers.org/GO:0006351"/>
</rdf:Bag>
</bqbiol:isVersionOf>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfProducts>
<speciesReference species="Z"/>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference sboTerm="SBO:0000536" species="PY"/>
</listOfModifiers>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<plus/>
<ci> a0_tr </ci>
<apply>
<divide/>
<apply>
<times/>
<ci> a_tr </ci>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<power/>
<ci> KM </ci>
<ci> n </ci>
</apply>
<apply>
<power/>
<ci> PY </ci>
<ci> n </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
validation error(s) : 0
validation warning(s) : 0
--------------------------------------------------------------------------------