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Failed
tests / testsuite-gcc / flattening_libraries_biochem.BiochemModels.mos (from (result.xml))
Stacktrace
Output mismatch (see stdout for details)
Standard Output
+ BioChem.Examples ... equation mismatch [time: 3] ==== Log /tmp/omc-rtest-unknown/flattening/libraries/biochem/BiochemModels.mos_temp7898/log-BiochemModels.mos true "" "class BioChem_Examples_CircadianOscillator_Container Real V(quantity = \"Volume\", unit = \"l\", start = 1.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real nucleus.V(quantity = \"Volume\", unit = \"l\", start = 1.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real nucleus.Nucleus_V = nucleus.V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real nucleus.y3.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 1.1, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real nucleus.y3.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real nucleus.y3.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real nucleus.y3.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y3.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y3.n1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.y6.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 1.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real nucleus.y6.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real nucleus.y6.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real nucleus.y6.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y6.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y6.n1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.y7.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 1.05, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real nucleus.y7.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real nucleus.y7.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real nucleus.y7.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y7.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y7.n1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.y3_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y3_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y3_node.V(quantity = \"Volume\", unit = \"l\"); parameter Real nucleus.k3t = k3t; Real nucleus.y2_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y2_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y2_node.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.per2_cry_nuclear_export.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.per2_cry_nuclear_export.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.per2_cry_nuclear_export.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.per2_cry_nuclear_export.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.per2_cry_nuclear_export.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.per2_cry_nuclear_export.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.per2_cry_nuclear_export.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.per2_cry_nuclear_export.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.per2_cry_nuclear_export.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.per2_cry_nuclear_export.k3t = nucleus.k3t; Real nucleus.ambientSubstance.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real nucleus.ambientSubstance.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real nucleus.ambientSubstance.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real nucleus.ambientSubstance.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.ambientSubstance.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.ambientSubstance.n1.V(quantity = \"Volume\", unit = \"l\"); parameter Real nucleus.k3d = k3d; Real nucleus.nuclear_per2_cry_complex_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.nuclear_per2_cry_complex_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.nuclear_per2_cry_complex_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.nuclear_per2_cry_complex_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.nuclear_per2_cry_complex_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.nuclear_per2_cry_complex_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.nuclear_per2_cry_complex_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.nuclear_per2_cry_complex_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.nuclear_per2_cry_complex_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.nuclear_per2_cry_complex_degradation.k3d = nucleus.k3d; Real nucleus.y6_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y6_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y6_node.V(quantity = \"Volume\", unit = \"l\"); parameter Real nucleus.k6t = k6t; Real nucleus.y5_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.y5_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.y5_node.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_nuclear_export.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.BMAL1_nuclear_export.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_nuclear_export.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_nuclear_export.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_nuclear_export.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_nuclear_export.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_nuclear_export.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_nuclear_export.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.BMAL1_nuclear_export.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.BMAL1_nuclear_export.k6t = nucleus.k6t; parameter Real nucleus.k6d = k6d; Real nucleus.nuclear_BMAL1_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.nuclear_BMAL1_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.nuclear_BMAL1_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.nuclear_BMAL1_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.nuclear_BMAL1_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.nuclear_BMAL1_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.nuclear_BMAL1_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.nuclear_BMAL1_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.nuclear_BMAL1_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.nuclear_BMAL1_degradation.k6d = nucleus.k6d; parameter Real nucleus.k6a = k6a; Real nucleus.BMAL1_activation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.BMAL1_activation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_activation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_activation.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_activation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_activation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_activation.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_activation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.BMAL1_activation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.BMAL1_activation.k6a = nucleus.k6a; parameter Real nucleus.k7a = k7a; Real nucleus.BMAL1_deactivation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.BMAL1_deactivation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_deactivation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_deactivation.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_deactivation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.BMAL1_deactivation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.BMAL1_deactivation.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.BMAL1_deactivation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.BMAL1_deactivation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.BMAL1_deactivation.k7a = nucleus.k7a; parameter Real nucleus.k7d = k7d; Real nucleus.Active_BMAL1_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real nucleus.Active_BMAL1_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.Active_BMAL1_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.Active_BMAL1_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.Active_BMAL1_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real nucleus.Active_BMAL1_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real nucleus.Active_BMAL1_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real nucleus.Active_BMAL1_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real nucleus.Active_BMAL1_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real nucleus.Active_BMAL1_degradation.k7d = nucleus.k7d; Real cytoplasm.V(quantity = \"Volume\", unit = \"l\", start = 1.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real cytoplasm.Cytoplasm_V = cytoplasm.V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real cytoplasm.y1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.2, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytoplasm.y1.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytoplasm.y1.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytoplasm.y1.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y1.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y1.n1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.y2.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytoplasm.y2.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytoplasm.y2.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytoplasm.y2.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y2.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y2.n1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.y4.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.8, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytoplasm.y4.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytoplasm.y4.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytoplasm.y4.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y4.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y4.n1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.y5.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 1.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytoplasm.y5.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytoplasm.y5.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytoplasm.y5.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y5.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y5.n1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.ambientSubstance.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytoplasm.ambientSubstance.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytoplasm.ambientSubstance.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytoplasm.ambientSubstance.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.ambientSubstance.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.ambientSubstance.n1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.trans_per2_cry = trans_per2_cry; Real cytoplasm.per2_cry_transcription.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.per2_cry_transcription.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_transcription.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_transcription.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_transcription.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_transcription.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_transcription.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_transcription.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.per2_cry_transcription.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; Real cytoplasm.per2_cry_transcription.trans_per2_cry = cytoplasm.trans_per2_cry; parameter Real cytoplasm.k1d = k1d; Real cytoplasm.per2_cry_mRNA_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.per2_cry_mRNA_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_mRNA_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_mRNA_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_mRNA_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_mRNA_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_mRNA_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_mRNA_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.per2_cry_mRNA_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.per2_cry_mRNA_degradation.k1d = cytoplasm.k1d; parameter Real cytoplasm.k2b = k2b; parameter Real cytoplasm.q = q; Real cytoplasm.per2_cry_complex_formation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.per2_cry_complex_formation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_complex_formation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_complex_formation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_complex_formation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_complex_formation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_complex_formation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_complex_formation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.per2_cry_complex_formation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; Real cytoplasm.per2_cry_complex_formation.m1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_complex_formation.m1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_complex_formation.m1.V(quantity = \"Volume\", unit = \"l\"); parameter Real cytoplasm.per2_cry_complex_formation.k2b = cytoplasm.k2b; parameter Real cytoplasm.per2_cry_complex_formation.q = cytoplasm.q; parameter Real cytoplasm.k2d = k2d; Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.cytoplasmic_per2_cry_complex_degradation.k2d = cytoplasm.k2d; parameter Real cytoplasm.k2t = k2t; Real cytoplasm.y3_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y3_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y3_node.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_nuclear_import.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.per2_cry_nuclear_import.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_nuclear_import.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_nuclear_import.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_nuclear_import.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.per2_cry_nuclear_import.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.per2_cry_nuclear_import.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.per2_cry_nuclear_import.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.per2_cry_nuclear_import.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.per2_cry_nuclear_import.k2t = cytoplasm.k2t; Real cytoplasm.y2_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y2_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y2_node.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.trans_Bmal1 = trans_Bmal1; Real cytoplasm.Bmal1_transcription.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.Bmal1_transcription.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.Bmal1_transcription.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.Bmal1_transcription.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.Bmal1_transcription.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.Bmal1_transcription.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.Bmal1_transcription.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.Bmal1_transcription.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.Bmal1_transcription.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; Real cytoplasm.Bmal1_transcription.trans_Bmal1 = cytoplasm.trans_Bmal1; parameter Real cytoplasm.k4d = k4d; Real cytoplasm.Bmal1_mRNA_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.Bmal1_mRNA_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.Bmal1_mRNA_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.Bmal1_mRNA_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.Bmal1_mRNA_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.Bmal1_mRNA_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.Bmal1_mRNA_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.Bmal1_mRNA_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.Bmal1_mRNA_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.Bmal1_mRNA_degradation.k4d = cytoplasm.k4d; parameter Real cytoplasm.k5b = k5b; Real cytoplasm.BMAL1_translation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.BMAL1_translation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.BMAL1_translation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.BMAL1_translation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.BMAL1_translation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.BMAL1_translation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.BMAL1_translation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.BMAL1_translation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.BMAL1_translation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; Real cytoplasm.BMAL1_translation.m1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.BMAL1_translation.m1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.BMAL1_translation.m1.V(quantity = \"Volume\", unit = \"l\"); parameter Real cytoplasm.BMAL1_translation.k5b = cytoplasm.k5b; parameter Real cytoplasm.k5d = k5d; Real cytoplasm.cytoplasmic_BMAL1_degradation.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.cytoplasmic_BMAL1_degradation.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.cytoplasmic_BMAL1_degradation.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.cytoplasmic_BMAL1_degradation.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.cytoplasmic_BMAL1_degradation.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.cytoplasmic_BMAL1_degradation.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.cytoplasmic_BMAL1_degradation.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.cytoplasmic_BMAL1_degradation.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.cytoplasmic_BMAL1_degradation.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.cytoplasmic_BMAL1_degradation.k5d = cytoplasm.k5d; parameter Real cytoplasm.k5t = k5t; Real cytoplasm.y6_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y6_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y6_node.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.BMAL1_nuclear_import.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real cytoplasm.BMAL1_nuclear_import.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.BMAL1_nuclear_import.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.BMAL1_nuclear_import.s1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.BMAL1_nuclear_import.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.BMAL1_nuclear_import.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.BMAL1_nuclear_import.p1.V(quantity = \"Volume\", unit = \"l\"); Real cytoplasm.BMAL1_nuclear_import.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real cytoplasm.BMAL1_nuclear_import.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real cytoplasm.BMAL1_nuclear_import.k5t = cytoplasm.k5t; Real cytoplasm.y5_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytoplasm.y5_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real cytoplasm.y5_node.V(quantity = \"Volume\", unit = \"l\"); Real Nucleus_V = nucleus.V \"Variable used to make the compartment volume of inner compartments accessible. Do not edit.\"; Real Cytoplasm_V = cytoplasm.V \"Variable used to make the compartment volume of inner compartments accessible. Do not edit.\"; Real Container_V = V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real trans_per2_cry(start = 0.0); parameter Real v1b = 9.0; parameter Real c_sbml = 0.01; parameter Real k1b = 1.0; parameter Real k1i = 0.5600000000000001; parameter Real hill_coeff = 8.0; Real trans_Bmal1(start = 0.0); parameter Real v4b = 3.6; parameter Real r_sbml = 3.0; parameter Real k4b = 2.16; Real y5_y6_y7(start = 3.05); parameter Real k1d = 0.12; parameter Real k2b = 0.3; parameter Real q = 2.0; parameter Real k2d = 0.05; parameter Real k2t = 0.24; parameter Real k3t = 0.02; parameter Real k3d = 0.12; parameter Real k4d = 0.75; parameter Real k5b = 0.24; parameter Real k5d = 0.06; parameter Real k5t = 0.45; parameter Real k6t = 0.06; parameter Real k6d = 0.12; parameter Real k6a = 0.09; parameter Real k7a = 0.003; parameter Real k7d = 0.09; equation der(nucleus.y3.n) = nucleus.y3.rNet; nucleus.y3.rNet = nucleus.y3.n1.r; nucleus.y3.c = nucleus.y3.n1.c; nucleus.V = nucleus.y3.n1.V; nucleus.y3.c = nucleus.y3.n / nucleus.V; der(nucleus.y6.n) = nucleus.y6.rNet; nucleus.y6.rNet = nucleus.y6.n1.r; nucleus.y6.c = nucleus.y6.n1.c; nucleus.V = nucleus.y6.n1.V; nucleus.y6.c = nucleus.y6.n / nucleus.V; der(nucleus.y7.n) = nucleus.y7.rNet; nucleus.y7.rNet = nucleus.y7.n1.r; nucleus.y7.c = nucleus.y7.n1.c; nucleus.V = nucleus.y7.n1.V; nucleus.y7.c = nucleus.y7.n / nucleus.V; nucleus.per2_cry_nuclear_export.rr = nucleus.Nucleus_V * nucleus.per2_cry_nuclear_export.k3t * nucleus.per2_cry_nuclear_export.s1.c; nucleus.per2_cry_nuclear_export.s1.r = nucleus.per2_cry_nuclear_export.nS1 * nucleus.per2_cry_nuclear_export.rr; nucleus.per2_cry_nuclear_export.p1.r = (-nucleus.per2_cry_nuclear_export.nP1) * nucleus.per2_cry_nuclear_export.rr; der(nucleus.ambientSubstance.n) = 0.0; nucleus.ambientSubstance.rNet = nucleus.ambientSubstance.n1.r; nucleus.ambientSubstance.c = nucleus.ambientSubstance.n1.c; nucleus.V = nucleus.ambientSubstance.n1.V; nucleus.ambientSubstance.c = nucleus.ambientSubstance.n / nucleus.V; nucleus.nuclear_per2_cry_complex_degradation.rr = nucleus.Nucleus_V * nucleus.nuclear_per2_cry_complex_degradation.k3d * nucleus.nuclear_per2_cry_complex_degradation.s1.c; nucleus.nuclear_per2_cry_complex_degradation.s1.r = nucleus.nuclear_per2_cry_complex_degradation.nS1 * nucleus.nuclear_per2_cry_complex_degradation.rr; nucleus.nuclear_per2_cry_complex_degradation.p1.r = (-nucleus.nuclear_per2_cry_complex_degradation.nP1) * nucleus.nuclear_per2_cry_complex_degradation.rr; nucleus.BMAL1_nuclear_export.rr = nucleus.Nucleus_V * nucleus.BMAL1_nuclear_export.k6t * nucleus.BMAL1_nuclear_export.s1.c; nucleus.BMAL1_nuclear_export.s1.r = nucleus.BMAL1_nuclear_export.nS1 * nucleus.BMAL1_nuclear_export.rr; nucleus.BMAL1_nuclear_export.p1.r = (-nucleus.BMAL1_nuclear_export.nP1) * nucleus.BMAL1_nuclear_export.rr; nucleus.nuclear_BMAL1_degradation.rr = nucleus.Nucleus_V * nucleus.nuclear_BMAL1_degradation.k6d * nucleus.nuclear_BMAL1_degradation.s1.c; nucleus.nuclear_BMAL1_degradation.s1.r = nucleus.nuclear_BMAL1_degradation.nS1 * nucleus.nuclear_BMAL1_degradation.rr; nucleus.nuclear_BMAL1_degradation.p1.r = (-nucleus.nuclear_BMAL1_degradation.nP1) * nucleus.nuclear_BMAL1_degradation.rr; nucleus.BMAL1_activation.rr = nucleus.Nucleus_V * nucleus.BMAL1_activation.k6a * nucleus.BMAL1_activation.s1.c; nucleus.BMAL1_activation.s1.r = nucleus.BMAL1_activation.nS1 * nucleus.BMAL1_activation.rr; nucleus.BMAL1_activation.p1.r = (-nucleus.BMAL1_activation.nP1) * nucleus.BMAL1_activation.rr; nucleus.BMAL1_deactivation.rr = nucleus.Nucleus_V * nucleus.BMAL1_deactivation.k7a * nucleus.BMAL1_deactivation.s1.c; nucleus.BMAL1_deactivation.s1.r = nucleus.BMAL1_deactivation.nS1 * nucleus.BMAL1_deactivation.rr; nucleus.BMAL1_deactivation.p1.r = (-nucleus.BMAL1_deactivation.nP1) * nucleus.BMAL1_deactivation.rr; nucleus.Active_BMAL1_degradation.rr = nucleus.Nucleus_V * nucleus.Active_BMAL1_degradation.k7d * nucleus.Active_BMAL1_degradation.s1.c; nucleus.Active_BMAL1_degradation.s1.r = nucleus.Active_BMAL1_degradation.nS1 * nucleus.Active_BMAL1_degradation.rr; nucleus.Active_BMAL1_degradation.p1.r = (-nucleus.Active_BMAL1_degradation.nP1) * nucleus.Active_BMAL1_degradation.rr; der(nucleus.V) = 0.0 \"Compartment volume is constant\"; der(cytoplasm.y1.n) = cytoplasm.y1.rNet; cytoplasm.y1.rNet = cytoplasm.y1.n1.r; cytoplasm.y1.c = cytoplasm.y1.n1.c; cytoplasm.V = cytoplasm.y1.n1.V; cytoplasm.y1.c = cytoplasm.y1.n / cytoplasm.V; der(cytoplasm.y2.n) = cytoplasm.y2.rNet; cytoplasm.y2.rNet = cytoplasm.y2.n1.r; cytoplasm.y2.c = cytoplasm.y2.n1.c; cytoplasm.V = cytoplasm.y2.n1.V; cytoplasm.y2.c = cytoplasm.y2.n / cytoplasm.V; der(cytoplasm.y4.n) = cytoplasm.y4.rNet; cytoplasm.y4.rNet = cytoplasm.y4.n1.r; cytoplasm.y4.c = cytoplasm.y4.n1.c; cytoplasm.V = cytoplasm.y4.n1.V; cytoplasm.y4.c = cytoplasm.y4.n / cytoplasm.V; der(cytoplasm.y5.n) = cytoplasm.y5.rNet; cytoplasm.y5.rNet = cytoplasm.y5.n1.r; cytoplasm.y5.c = cytoplasm.y5.n1.c; cytoplasm.V = cytoplasm.y5.n1.V; cytoplasm.y5.c = cytoplasm.y5.n / cytoplasm.V; der(cytoplasm.ambientSubstance.n) = 0.0; cytoplasm.ambientSubstance.rNet = cytoplasm.ambientSubstance.n1.r; cytoplasm.ambientSubstance.c = cytoplasm.ambientSubstance.n1.c; cytoplasm.V = cytoplasm.ambientSubstance.n1.V; cytoplasm.ambientSubstance.c = cytoplasm.ambientSubstance.n / cytoplasm.V; cytoplasm.per2_cry_transcription.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_transcription.trans_per2_cry; cytoplasm.per2_cry_transcription.s1.r = cytoplasm.per2_cry_transcription.nS1 * cytoplasm.per2_cry_transcription.rr; cytoplasm.per2_cry_transcription.p1.r = (-cytoplasm.per2_cry_transcription.nP1) * cytoplasm.per2_cry_transcription.rr; cytoplasm.per2_cry_mRNA_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_mRNA_degradation.k1d * cytoplasm.per2_cry_mRNA_degradation.s1.c; cytoplasm.per2_cry_mRNA_degradation.s1.r = cytoplasm.per2_cry_mRNA_degradation.nS1 * cytoplasm.per2_cry_mRNA_degradation.rr; cytoplasm.per2_cry_mRNA_degradation.p1.r = (-cytoplasm.per2_cry_mRNA_degradation.nP1) * cytoplasm.per2_cry_mRNA_degradation.rr; cytoplasm.per2_cry_complex_formation.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_complex_formation.k2b * cytoplasm.per2_cry_complex_formation.m1.c ^ cytoplasm.per2_cry_complex_formation.q; cytoplasm.per2_cry_complex_formation.s1.r = cytoplasm.per2_cry_complex_formation.nS1 * cytoplasm.per2_cry_complex_formation.rr; cytoplasm.per2_cry_complex_formation.p1.r = (-cytoplasm.per2_cry_complex_formation.nP1) * cytoplasm.per2_cry_complex_formation.rr; cytoplasm.per2_cry_complex_formation.m1.r = 0.0; cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.cytoplasmic_per2_cry_complex_degradation.k2d * cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.r = cytoplasm.cytoplasmic_per2_cry_complex_degradation.nS1 * cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr; cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.r = (-cytoplasm.cytoplasmic_per2_cry_complex_degradation.nP1) * cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr; cytoplasm.per2_cry_nuclear_import.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_nuclear_import.k2t * cytoplasm.per2_cry_nuclear_import.s1.c; cytoplasm.per2_cry_nuclear_import.s1.r = cytoplasm.per2_cry_nuclear_import.nS1 * cytoplasm.per2_cry_nuclear_import.rr; cytoplasm.per2_cry_nuclear_import.p1.r = (-cytoplasm.per2_cry_nuclear_import.nP1) * cytoplasm.per2_cry_nuclear_import.rr; cytoplasm.Bmal1_transcription.rr = cytoplasm.Cytoplasm_V * cytoplasm.Bmal1_transcription.trans_Bmal1; cytoplasm.Bmal1_transcription.s1.r = cytoplasm.Bmal1_transcription.nS1 * cytoplasm.Bmal1_transcription.rr; cytoplasm.Bmal1_transcription.p1.r = (-cytoplasm.Bmal1_transcription.nP1) * cytoplasm.Bmal1_transcription.rr; cytoplasm.Bmal1_mRNA_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.Bmal1_mRNA_degradation.k4d * cytoplasm.Bmal1_mRNA_degradation.s1.c; cytoplasm.Bmal1_mRNA_degradation.s1.r = cytoplasm.Bmal1_mRNA_degradation.nS1 * cytoplasm.Bmal1_mRNA_degradation.rr; cytoplasm.Bmal1_mRNA_degradation.p1.r = (-cytoplasm.Bmal1_mRNA_degradation.nP1) * cytoplasm.Bmal1_mRNA_degradation.rr; cytoplasm.BMAL1_translation.rr = cytoplasm.Cytoplasm_V * cytoplasm.BMAL1_translation.k5b * cytoplasm.BMAL1_translation.m1.c; cytoplasm.BMAL1_translation.s1.r = cytoplasm.BMAL1_translation.nS1 * cytoplasm.BMAL1_translation.rr; cytoplasm.BMAL1_translation.p1.r = (-cytoplasm.BMAL1_translation.nP1) * cytoplasm.BMAL1_translation.rr; cytoplasm.BMAL1_translation.m1.r = 0.0; cytoplasm.cytoplasmic_BMAL1_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.cytoplasmic_BMAL1_degradation.k5d * cytoplasm.cytoplasmic_BMAL1_degradation.s1.c; cytoplasm.cytoplasmic_BMAL1_degradation.s1.r = cytoplasm.cytoplasmic_BMAL1_degradation.nS1 * cytoplasm.cytoplasmic_BMAL1_degradation.rr; cytoplasm.cytoplasmic_BMAL1_degradation.p1.r = (-cytoplasm.cytoplasmic_BMAL1_degradation.nP1) * cytoplasm.cytoplasmic_BMAL1_degradation.rr; cytoplasm.BMAL1_nuclear_import.rr = cytoplasm.Cytoplasm_V * cytoplasm.BMAL1_nuclear_import.k5t * cytoplasm.BMAL1_nuclear_import.s1.c; cytoplasm.BMAL1_nuclear_import.s1.r = cytoplasm.BMAL1_nuclear_import.nS1 * cytoplasm.BMAL1_nuclear_import.rr; cytoplasm.BMAL1_nuclear_import.p1.r = (-cytoplasm.BMAL1_nuclear_import.nP1) * cytoplasm.BMAL1_nuclear_import.rr; der(cytoplasm.V) = 0.0 \"Compartment volume is constant\"; trans_per2_cry = v1b * (nucleus.y7.c + c_sbml) / (k1b * (1.0 + (nucleus.y3.c / k1i) ^ hill_coeff) + nucleus.y7.c + c_sbml); trans_Bmal1 = v4b * nucleus.y3.c ^ r_sbml / (k4b ^ r_sbml + nucleus.y3.c ^ r_sbml); y5_y6_y7 = cytoplasm.y5.c + nucleus.y6.c + nucleus.y7.c; der(V) = 0.0 \"Compartment volume is constant\"; cytoplasm.y1.n1.r + cytoplasm.per2_cry_transcription.p1.r + cytoplasm.per2_cry_mRNA_degradation.s1.r + cytoplasm.per2_cry_complex_formation.m1.r = 0.0; cytoplasm.y2.n1.r + (-cytoplasm.y2_node.r) + cytoplasm.per2_cry_complex_formation.p1.r + cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.r + cytoplasm.per2_cry_nuclear_import.s1.r = 0.0; cytoplasm.y4.n1.r + cytoplasm.Bmal1_transcription.p1.r + cytoplasm.Bmal1_mRNA_degradation.s1.r + cytoplasm.BMAL1_translation.m1.r = 0.0; cytoplasm.y5.n1.r + (-cytoplasm.y5_node.r) + cytoplasm.BMAL1_translation.p1.r + cytoplasm.cytoplasmic_BMAL1_degradation.s1.r + cytoplasm.BMAL1_nuclear_import.s1.r = 0.0; cytoplasm.ambientSubstance.n1.r + cytoplasm.per2_cry_transcription.s1.r + cytoplasm.per2_cry_mRNA_degradation.p1.r + cytoplasm.per2_cry_complex_formation.s1.r + cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.r + cytoplasm.Bmal1_transcription.s1.r + cytoplasm.Bmal1_mRNA_degradation.p1.r + cytoplasm.BMAL1_translation.s1.r + cytoplasm.cytoplasmic_BMAL1_degradation.p1.r = 0.0; cytoplasm.y3_node.r + nucleus.y3_node.r = 0.0; cytoplasm.y2_node.r + nucleus.y2_node.r = 0.0; cytoplasm.y6_node.r + nucleus.y6_node.r = 0.0; cytoplasm.y5_node.r + nucleus.y5_node.r = 0.0; (-cytoplasm.y3_node.r) + cytoplasm.per2_cry_nuclear_import.p1.r = 0.0; (-cytoplasm.y6_node.r) + cytoplasm.BMAL1_nuclear_import.p1.r = 0.0; cytoplasm.BMAL1_nuclear_import.p1.V = cytoplasm.y6_node.V; cytoplasm.BMAL1_nuclear_import.p1.c = cytoplasm.y6_node.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.per2_cry_complex_formation.p1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.per2_cry_nuclear_import.s1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.y2.n1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.y2_node.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.per2_cry_complex_formation.p1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.per2_cry_nuclear_import.s1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.y2.n1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.y2_node.c; cytoplasm.per2_cry_nuclear_import.p1.V = cytoplasm.y3_node.V; cytoplasm.per2_cry_nuclear_import.p1.c = cytoplasm.y3_node.c; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.BMAL1_translation.p1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.cytoplasmic_BMAL1_degradation.s1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.y5.n1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.y5_node.V; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.BMAL1_translation.p1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.cytoplasmic_BMAL1_degradation.s1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.y5.n1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.y5_node.c; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.per2_cry_mRNA_degradation.s1.V; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.per2_cry_transcription.p1.V; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.y1.n1.V; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.per2_cry_mRNA_degradation.s1.c; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.per2_cry_transcription.p1.c; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.y1.n1.c; cytoplasm.BMAL1_translation.s1.V = cytoplasm.Bmal1_mRNA_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.Bmal1_transcription.s1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.ambientSubstance.n1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.cytoplasmic_BMAL1_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_complex_formation.s1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_mRNA_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_transcription.s1.V; cytoplasm.BMAL1_translation.s1.c = cytoplasm.Bmal1_mRNA_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.Bmal1_transcription.s1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.ambientSubstance.n1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.cytoplasmic_BMAL1_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_complex_formation.s1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_mRNA_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_transcription.s1.c; cytoplasm.BMAL1_translation.m1.V = cytoplasm.Bmal1_mRNA_degradation.s1.V; cytoplasm.BMAL1_translation.m1.V = cytoplasm.Bmal1_transcription.p1.V; cytoplasm.BMAL1_translation.m1.V = cytoplasm.y4.n1.V; cytoplasm.BMAL1_translation.m1.c = cytoplasm.Bmal1_mRNA_degradation.s1.c; cytoplasm.BMAL1_translation.m1.c = cytoplasm.Bmal1_transcription.p1.c; cytoplasm.BMAL1_translation.m1.c = cytoplasm.y4.n1.c; nucleus.y3.n1.r + (-nucleus.y3_node.r) + nucleus.per2_cry_nuclear_export.s1.r + nucleus.nuclear_per2_cry_complex_degradation.s1.r = 0.0; nucleus.y6.n1.r + (-nucleus.y6_node.r) + nucleus.BMAL1_nuclear_export.s1.r + nucleus.nuclear_BMAL1_degradation.s1.r + nucleus.BMAL1_activation.s1.r + nucleus.BMAL1_deactivation.p1.r = 0.0; nucleus.y7.n1.r + nucleus.BMAL1_activation.p1.r + nucleus.BMAL1_deactivation.s1.r + nucleus.Active_BMAL1_degradation.s1.r = 0.0; nucleus.ambientSubstance.n1.r + nucleus.nuclear_per2_cry_complex_degradation.p1.r + nucleus.nuclear_BMAL1_degradation.p1.r + nucleus.Active_BMAL1_degradation.p1.r = 0.0; (-nucleus.y2_node.r) + nucleus.per2_cry_nuclear_export.p1.r = 0.0; (-nucleus.y5_node.r) + nucleus.BMAL1_nuclear_export.p1.r = 0.0; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.per2_cry_nuclear_export.s1.V; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.y3.n1.V; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.y3_node.V; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.per2_cry_nuclear_export.s1.c; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.y3.n1.c; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.y3_node.c; nucleus.Active_BMAL1_degradation.s1.V = nucleus.BMAL1_activation.p1.V; nucleus.Active_BMAL1_degradation.s1.V = nucleus.BMAL1_deactivation.s1.V; nucleus.Active_BMAL1_degradation.s1.V = nucleus.y7.n1.V; nucleus.Active_BMAL1_degradation.s1.c = nucleus.BMAL1_activation.p1.c; nucleus.Active_BMAL1_degradation.s1.c = nucleus.BMAL1_deactivation.s1.c; nucleus.Active_BMAL1_degradation.s1.c = nucleus.y7.n1.c; nucleus.BMAL1_activation.s1.V = nucleus.BMAL1_deactivation.p1.V; nucleus.BMAL1_activation.s1.V = nucleus.BMAL1_nuclear_export.s1.V; nucleus.BMAL1_activation.s1.V = nucleus.nuclear_BMAL1_degradation.s1.V; nucleus.BMAL1_activation.s1.V = nucleus.y6.n1.V; nucleus.BMAL1_activation.s1.V = nucleus.y6_node.V; nucleus.BMAL1_activation.s1.c = nucleus.BMAL1_deactivation.p1.c; nucleus.BMAL1_activation.s1.c = nucleus.BMAL1_nuclear_export.s1.c; nucleus.BMAL1_activation.s1.c = nucleus.nuclear_BMAL1_degradation.s1.c; nucleus.BMAL1_activation.s1.c = nucleus.y6.n1.c; nucleus.BMAL1_activation.s1.c = nucleus.y6_node.c; nucleus.Active_BMAL1_degradation.p1.V = nucleus.ambientSubstance.n1.V; nucleus.Active_BMAL1_degradation.p1.V = nucleus.nuclear_BMAL1_degradation.p1.V; nucleus.Active_BMAL1_degradation.p1.V = nucleus.nuclear_per2_cry_complex_degradation.p1.V; nucleus.Active_BMAL1_degradation.p1.c = nucleus.ambientSubstance.n1.c; nucleus.Active_BMAL1_degradation.p1.c = nucleus.nuclear_BMAL1_degradation.p1.c; nucleus.Active_BMAL1_degradation.p1.c = nucleus.nuclear_per2_cry_complex_degradation.p1.c; nucleus.BMAL1_nuclear_export.p1.V = nucleus.y5_node.V; nucleus.BMAL1_nuclear_export.p1.c = nucleus.y5_node.c; nucleus.per2_cry_nuclear_export.p1.V = nucleus.y2_node.V; nucleus.per2_cry_nuclear_export.p1.c = nucleus.y2_node.c; cytoplasm.y5_node.V = nucleus.y5_node.V; cytoplasm.y5_node.c = nucleus.y5_node.c; cytoplasm.y6_node.V = nucleus.y6_node.V; cytoplasm.y6_node.c = nucleus.y6_node.c; cytoplasm.y2_node.V = nucleus.y2_node.V; cytoplasm.y2_node.c = nucleus.y2_node.c; cytoplasm.y3_node.V = nucleus.y3_node.V; cytoplasm.y3_node.c = nucleus.y3_node.c; end BioChem_Examples_CircadianOscillator_Container; " "[flattening/libraries/biochem/ContainerSimple.mo:177:9-177:51:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. [flattening/libraries/biochem/ContainerSimple.mo:178:9-178:51:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. [flattening/libraries/biochem/ContainerSimple.mo:179:9-179:51:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. [flattening/libraries/biochem/ContainerSimple.mo:180:9-180:51:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. " "Check of BioChem_Examples_CircadianOscillator_Container completed successfully. Class BioChem_Examples_CircadianOscillator_Container has 252 equation(s) and 252 variable(s). 180 of these are trivial equation(s)." "[flattening/libraries/biochem/ContainerSimple.mo:177:9-177:51:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. [flattening/libraries/biochem/ContainerSimple.mo:178:9-178:51:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. [flattening/libraries/biochem/ContainerSimple.mo:179:9-179:51:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. [flattening/libraries/biochem/ContainerSimple.mo:180:9-180:51:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. " true true "" "class BioChem_Examples_centralMetabolism_extra_cellular Real V(quantity = \"Volume\", unit = \"l\", start = 2.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real cytosol.V(quantity = \"Volume\", unit = \"l\", start = 2.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real cytosol.cytosol_V = cytosol.V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real cytosol.NADH.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.00406177, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real cytosol.NADH.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real cytosol.NADH.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real cytosol.NADH.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real cytosol.NADH.n1.r ...[truncated 86032 chars]... .rr; nucleus.BMAL1_deactivation.rr = nucleus.Nucleus_V * nucleus.BMAL1_deactivation.k7a * nucleus.BMAL1_deactivation.s1.c; nucleus.BMAL1_deactivation.s1.r = nucleus.BMAL1_deactivation.nS1 * nucleus.BMAL1_deactivation.rr; nucleus.BMAL1_deactivation.p1.r = (-nucleus.BMAL1_deactivation.nP1) * nucleus.BMAL1_deactivation.rr; nucleus.Active_BMAL1_degradation.rr = nucleus.Nucleus_V * nucleus.Active_BMAL1_degradation.k7d * nucleus.Active_BMAL1_degradation.s1.c; nucleus.Active_BMAL1_degradation.s1.r = nucleus.Active_BMAL1_degradation.nS1 * nucleus.Active_BMAL1_degradation.rr; nucleus.Active_BMAL1_degradation.p1.r = (-nucleus.Active_BMAL1_degradation.nP1) * nucleus.Active_BMAL1_degradation.rr; der(nucleus.V) = 0.0 \"Compartment volume is constant\"; der(cytoplasm.y1.n) = cytoplasm.y1.rNet; cytoplasm.y1.rNet = cytoplasm.y1.n1.r; cytoplasm.y1.c = cytoplasm.y1.n1.c; cytoplasm.V = cytoplasm.y1.n1.V; cytoplasm.y1.c = cytoplasm.y1.n / cytoplasm.V; der(cytoplasm.y2.n) = cytoplasm.y2.rNet; cytoplasm.y2.rNet = cytoplasm.y2.n1.r; cytoplasm.y2.c = cytoplasm.y2.n1.c; cytoplasm.V = cytoplasm.y2.n1.V; cytoplasm.y2.c = cytoplasm.y2.n / cytoplasm.V; der(cytoplasm.y4.n) = cytoplasm.y4.rNet; cytoplasm.y4.rNet = cytoplasm.y4.n1.r; cytoplasm.y4.c = cytoplasm.y4.n1.c; cytoplasm.V = cytoplasm.y4.n1.V; cytoplasm.y4.c = cytoplasm.y4.n / cytoplasm.V; der(cytoplasm.y5.n) = cytoplasm.y5.rNet; cytoplasm.y5.rNet = cytoplasm.y5.n1.r; cytoplasm.y5.c = cytoplasm.y5.n1.c; cytoplasm.V = cytoplasm.y5.n1.V; cytoplasm.y5.c = cytoplasm.y5.n / cytoplasm.V; der(cytoplasm.ambientSubstance.n) = 0.0; cytoplasm.ambientSubstance.rNet = cytoplasm.ambientSubstance.n1.r; cytoplasm.ambientSubstance.c = cytoplasm.ambientSubstance.n1.c; cytoplasm.V = cytoplasm.ambientSubstance.n1.V; cytoplasm.ambientSubstance.c = cytoplasm.ambientSubstance.n / cytoplasm.V; cytoplasm.per2_cry_transcription.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_transcription.trans_per2_cry; cytoplasm.per2_cry_transcription.s1.r = cytoplasm.per2_cry_transcription.nS1 * cytoplasm.per2_cry_transcription.rr; cytoplasm.per2_cry_transcription.p1.r = (-cytoplasm.per2_cry_transcription.nP1) * cytoplasm.per2_cry_transcription.rr; cytoplasm.per2_cry_mRNA_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_mRNA_degradation.k1d * cytoplasm.per2_cry_mRNA_degradation.s1.c; cytoplasm.per2_cry_mRNA_degradation.s1.r = cytoplasm.per2_cry_mRNA_degradation.nS1 * cytoplasm.per2_cry_mRNA_degradation.rr; cytoplasm.per2_cry_mRNA_degradation.p1.r = (-cytoplasm.per2_cry_mRNA_degradation.nP1) * cytoplasm.per2_cry_mRNA_degradation.rr; cytoplasm.per2_cry_complex_formation.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_complex_formation.k2b * cytoplasm.per2_cry_complex_formation.m1.c ^ cytoplasm.per2_cry_complex_formation.q; cytoplasm.per2_cry_complex_formation.s1.r = cytoplasm.per2_cry_complex_formation.nS1 * cytoplasm.per2_cry_complex_formation.rr; cytoplasm.per2_cry_complex_formation.p1.r = (-cytoplasm.per2_cry_complex_formation.nP1) * cytoplasm.per2_cry_complex_formation.rr; cytoplasm.per2_cry_complex_formation.m1.r = 0.0; cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.cytoplasmic_per2_cry_complex_degradation.k2d * cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.r = cytoplasm.cytoplasmic_per2_cry_complex_degradation.nS1 * cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr; cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.r = (-cytoplasm.cytoplasmic_per2_cry_complex_degradation.nP1) * cytoplasm.cytoplasmic_per2_cry_complex_degradation.rr; cytoplasm.per2_cry_nuclear_import.rr = cytoplasm.Cytoplasm_V * cytoplasm.per2_cry_nuclear_import.k2t * cytoplasm.per2_cry_nuclear_import.s1.c; cytoplasm.per2_cry_nuclear_import.s1.r = cytoplasm.per2_cry_nuclear_import.nS1 * cytoplasm.per2_cry_nuclear_import.rr; cytoplasm.per2_cry_nuclear_import.p1.r = (-cytoplasm.per2_cry_nuclear_import.nP1) * cytoplasm.per2_cry_nuclear_import.rr; cytoplasm.Bmal1_transcription.rr = cytoplasm.Cytoplasm_V * cytoplasm.Bmal1_transcription.trans_Bmal1; cytoplasm.Bmal1_transcription.s1.r = cytoplasm.Bmal1_transcription.nS1 * cytoplasm.Bmal1_transcription.rr; cytoplasm.Bmal1_transcription.p1.r = (-cytoplasm.Bmal1_transcription.nP1) * cytoplasm.Bmal1_transcription.rr; cytoplasm.Bmal1_mRNA_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.Bmal1_mRNA_degradation.k4d * cytoplasm.Bmal1_mRNA_degradation.s1.c; cytoplasm.Bmal1_mRNA_degradation.s1.r = cytoplasm.Bmal1_mRNA_degradation.nS1 * cytoplasm.Bmal1_mRNA_degradation.rr; cytoplasm.Bmal1_mRNA_degradation.p1.r = (-cytoplasm.Bmal1_mRNA_degradation.nP1) * cytoplasm.Bmal1_mRNA_degradation.rr; cytoplasm.BMAL1_translation.rr = cytoplasm.Cytoplasm_V * cytoplasm.BMAL1_translation.k5b * cytoplasm.BMAL1_translation.m1.c; cytoplasm.BMAL1_translation.s1.r = cytoplasm.BMAL1_translation.nS1 * cytoplasm.BMAL1_translation.rr; cytoplasm.BMAL1_translation.p1.r = (-cytoplasm.BMAL1_translation.nP1) * cytoplasm.BMAL1_translation.rr; cytoplasm.BMAL1_translation.m1.r = 0.0; cytoplasm.cytoplasmic_BMAL1_degradation.rr = cytoplasm.Cytoplasm_V * cytoplasm.cytoplasmic_BMAL1_degradation.k5d * cytoplasm.cytoplasmic_BMAL1_degradation.s1.c; cytoplasm.cytoplasmic_BMAL1_degradation.s1.r = cytoplasm.cytoplasmic_BMAL1_degradation.nS1 * cytoplasm.cytoplasmic_BMAL1_degradation.rr; cytoplasm.cytoplasmic_BMAL1_degradation.p1.r = (-cytoplasm.cytoplasmic_BMAL1_degradation.nP1) * cytoplasm.cytoplasmic_BMAL1_degradation.rr; cytoplasm.BMAL1_nuclear_import.rr = cytoplasm.Cytoplasm_V * cytoplasm.BMAL1_nuclear_import.k5t * cytoplasm.BMAL1_nuclear_import.s1.c; cytoplasm.BMAL1_nuclear_import.s1.r = cytoplasm.BMAL1_nuclear_import.nS1 * cytoplasm.BMAL1_nuclear_import.rr; cytoplasm.BMAL1_nuclear_import.p1.r = (-cytoplasm.BMAL1_nuclear_import.nP1) * cytoplasm.BMAL1_nuclear_import.rr; der(cytoplasm.V) = 0.0 \"Compartment volume is constant\"; trans_per2_cry = v1b * (nucleus.y7.c + c_sbml) / (k1b * (1.0 + (nucleus.y3.c / k1i) ^ hill_coeff) + nucleus.y7.c + c_sbml); trans_Bmal1 = v4b * nucleus.y3.c ^ r_sbml / (k4b ^ r_sbml + nucleus.y3.c ^ r_sbml); y5_y6_y7 = cytoplasm.y5.c + nucleus.y6.c + nucleus.y7.c; der(V) = 0.0 \"Compartment volume is constant\"; cytoplasm.y1.n1.r + cytoplasm.per2_cry_transcription.p1.r + cytoplasm.per2_cry_mRNA_degradation.s1.r + cytoplasm.per2_cry_complex_formation.m1.r = 0.0; cytoplasm.y2.n1.r + (-cytoplasm.y2_node.r) + cytoplasm.per2_cry_complex_formation.p1.r + cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.r + cytoplasm.per2_cry_nuclear_import.s1.r = 0.0; cytoplasm.y4.n1.r + cytoplasm.Bmal1_transcription.p1.r + cytoplasm.Bmal1_mRNA_degradation.s1.r + cytoplasm.BMAL1_translation.m1.r = 0.0; cytoplasm.y5.n1.r + (-cytoplasm.y5_node.r) + cytoplasm.BMAL1_translation.p1.r + cytoplasm.cytoplasmic_BMAL1_degradation.s1.r + cytoplasm.BMAL1_nuclear_import.s1.r = 0.0; cytoplasm.ambientSubstance.n1.r + cytoplasm.per2_cry_transcription.s1.r + cytoplasm.per2_cry_mRNA_degradation.p1.r + cytoplasm.per2_cry_complex_formation.s1.r + cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.r + cytoplasm.Bmal1_transcription.s1.r + cytoplasm.Bmal1_mRNA_degradation.p1.r + cytoplasm.BMAL1_translation.s1.r + cytoplasm.cytoplasmic_BMAL1_degradation.p1.r = 0.0; cytoplasm.y3_node.r + nucleus.y3_node.r = 0.0; cytoplasm.y2_node.r + nucleus.y2_node.r = 0.0; cytoplasm.y6_node.r + nucleus.y6_node.r = 0.0; cytoplasm.y5_node.r + nucleus.y5_node.r = 0.0; (-cytoplasm.y3_node.r) + cytoplasm.per2_cry_nuclear_import.p1.r = 0.0; (-cytoplasm.y6_node.r) + cytoplasm.BMAL1_nuclear_import.p1.r = 0.0; cytoplasm.BMAL1_nuclear_import.p1.V = cytoplasm.y6_node.V; cytoplasm.BMAL1_nuclear_import.p1.c = cytoplasm.y6_node.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.per2_cry_complex_formation.p1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.per2_cry_nuclear_import.s1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.y2.n1.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.V = cytoplasm.y2_node.V; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.per2_cry_complex_formation.p1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.per2_cry_nuclear_import.s1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.y2.n1.c; cytoplasm.cytoplasmic_per2_cry_complex_degradation.s1.c = cytoplasm.y2_node.c; cytoplasm.per2_cry_nuclear_import.p1.V = cytoplasm.y3_node.V; cytoplasm.per2_cry_nuclear_import.p1.c = cytoplasm.y3_node.c; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.BMAL1_translation.p1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.cytoplasmic_BMAL1_degradation.s1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.y5.n1.V; cytoplasm.BMAL1_nuclear_import.s1.V = cytoplasm.y5_node.V; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.BMAL1_translation.p1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.cytoplasmic_BMAL1_degradation.s1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.y5.n1.c; cytoplasm.BMAL1_nuclear_import.s1.c = cytoplasm.y5_node.c; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.per2_cry_mRNA_degradation.s1.V; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.per2_cry_transcription.p1.V; cytoplasm.per2_cry_complex_formation.m1.V = cytoplasm.y1.n1.V; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.per2_cry_mRNA_degradation.s1.c; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.per2_cry_transcription.p1.c; cytoplasm.per2_cry_complex_formation.m1.c = cytoplasm.y1.n1.c; cytoplasm.BMAL1_translation.s1.V = cytoplasm.Bmal1_mRNA_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.Bmal1_transcription.s1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.ambientSubstance.n1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.cytoplasmic_BMAL1_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_complex_formation.s1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_mRNA_degradation.p1.V; cytoplasm.BMAL1_translation.s1.V = cytoplasm.per2_cry_transcription.s1.V; cytoplasm.BMAL1_translation.s1.c = cytoplasm.Bmal1_mRNA_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.Bmal1_transcription.s1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.ambientSubstance.n1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.cytoplasmic_BMAL1_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.cytoplasmic_per2_cry_complex_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_complex_formation.s1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_mRNA_degradation.p1.c; cytoplasm.BMAL1_translation.s1.c = cytoplasm.per2_cry_transcription.s1.c; cytoplasm.BMAL1_translation.m1.V = cytoplasm.Bmal1_mRNA_degradation.s1.V; cytoplasm.BMAL1_translation.m1.V = cytoplasm.Bmal1_transcription.p1.V; cytoplasm.BMAL1_translation.m1.V = cytoplasm.y4.n1.V; cytoplasm.BMAL1_translation.m1.c = cytoplasm.Bmal1_mRNA_degradation.s1.c; cytoplasm.BMAL1_translation.m1.c = cytoplasm.Bmal1_transcription.p1.c; cytoplasm.BMAL1_translation.m1.c = cytoplasm.y4.n1.c; nucleus.y3.n1.r + (-nucleus.y3_node.r) + nucleus.per2_cry_nuclear_export.s1.r + nucleus.nuclear_per2_cry_complex_degradation.s1.r = 0.0; nucleus.y6.n1.r + (-nucleus.y6_node.r) + nucleus.BMAL1_nuclear_export.s1.r + nucleus.nuclear_BMAL1_degradation.s1.r + nucleus.BMAL1_activation.s1.r + nucleus.BMAL1_deactivation.p1.r = 0.0; nucleus.y7.n1.r + nucleus.BMAL1_activation.p1.r + nucleus.BMAL1_deactivation.s1.r + nucleus.Active_BMAL1_degradation.s1.r = 0.0; nucleus.ambientSubstance.n1.r + nucleus.nuclear_per2_cry_complex_degradation.p1.r + nucleus.nuclear_BMAL1_degradation.p1.r + nucleus.Active_BMAL1_degradation.p1.r = 0.0; (-nucleus.y2_node.r) + nucleus.per2_cry_nuclear_export.p1.r = 0.0; (-nucleus.y5_node.r) + nucleus.BMAL1_nuclear_export.p1.r = 0.0; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.per2_cry_nuclear_export.s1.V; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.y3.n1.V; nucleus.nuclear_per2_cry_complex_degradation.s1.V = nucleus.y3_node.V; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.per2_cry_nuclear_export.s1.c; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.y3.n1.c; nucleus.nuclear_per2_cry_complex_degradation.s1.c = nucleus.y3_node.c; nucleus.Active_BMAL1_degradation.s1.V = nucleus.BMAL1_activation.p1.V; nucleus.Active_BMAL1_degradation.s1.V = nucleus.BMAL1_deactivation.s1.V; nucleus.Active_BMAL1_degradation.s1.V = nucleus.y7.n1.V; nucleus.Active_BMAL1_degradation.s1.c = nucleus.BMAL1_activation.p1.c; nucleus.Active_BMAL1_degradation.s1.c = nucleus.BMAL1_deactivation.s1.c; nucleus.Active_BMAL1_degradation.s1.c = nucleus.y7.n1.c; nucleus.BMAL1_activation.s1.V = nucleus.BMAL1_deactivation.p1.V; nucleus.BMAL1_activation.s1.V = nucleus.BMAL1_nuclear_export.s1.V; nucleus.BMAL1_activation.s1.V = nucleus.nuclear_BMAL1_degradation.s1.V; nucleus.BMAL1_activation.s1.V = nucleus.y6.n1.V; nucleus.BMAL1_activation.s1.V = nucleus.y6_node.V; nucleus.BMAL1_activation.s1.c = nucleus.BMAL1_deactivation.p1.c; nucleus.BMAL1_activation.s1.c = nucleus.BMAL1_nuclear_export.s1.c; nucleus.BMAL1_activation.s1.c = nucleus.nuclear_BMAL1_degradation.s1.c; nucleus.BMAL1_activation.s1.c = nucleus.y6.n1.c; nucleus.BMAL1_activation.s1.c = nucleus.y6_node.c; nucleus.Active_BMAL1_degradation.p1.V = nucleus.ambientSubstance.n1.V; nucleus.Active_BMAL1_degradation.p1.V = nucleus.nuclear_BMAL1_degradation.p1.V; nucleus.Active_BMAL1_degradation.p1.V = nucleus.nuclear_per2_cry_complex_degradation.p1.V; nucleus.Active_BMAL1_degradation.p1.c = nucleus.ambientSubstance.n1.c; nucleus.Active_BMAL1_degradation.p1.c = nucleus.nuclear_BMAL1_degradation.p1.c; nucleus.Active_BMAL1_degradation.p1.c = nucleus.nuclear_per2_cry_complex_degradation.p1.c; nucleus.BMAL1_nuclear_export.p1.V = nucleus.y5_node.V; nucleus.BMAL1_nuclear_export.p1.c = nucleus.y5_node.c; nucleus.per2_cry_nuclear_export.p1.V = nucleus.y2_node.V; nucleus.per2_cry_nuclear_export.p1.c = nucleus.y2_node.c; cytoplasm.y5_node.V = nucleus.y5_node.V; cytoplasm.y5_node.c = nucleus.y5_node.c; cytoplasm.y6_node.V = nucleus.y6_node.V; cytoplasm.y6_node.c = nucleus.y6_node.c; cytoplasm.y2_node.V = nucleus.y2_node.V; cytoplasm.y2_node.c = nucleus.y2_node.c; cytoplasm.y3_node.V = nucleus.y3_node.V; cytoplasm.y3_node.c = nucleus.y3_node.c; end BioChem_Examples_CircadianOscillator_Container; " "[flattening/libraries/biochem/ContainerTotal.mo:867:9-867:145:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. [flattening/libraries/biochem/ContainerTotal.mo:868:9-868:144:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. [flattening/libraries/biochem/ContainerTotal.mo:869:9-869:144:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. [flattening/libraries/biochem/ContainerTotal.mo:870:9-870:145:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. " "Check of BioChem_Examples_CircadianOscillator_Container completed successfully. Class BioChem_Examples_CircadianOscillator_Container has 252 equation(s) and 252 variable(s). 180 of these are trivial equation(s)." "[flattening/libraries/biochem/ContainerTotal.mo:867:9-867:145:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. [flattening/libraries/biochem/ContainerTotal.mo:868:9-868:144:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. [flattening/libraries/biochem/ContainerTotal.mo:869:9-869:144:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. [flattening/libraries/biochem/ContainerTotal.mo:870:9-870:145:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. " true true "" "class BioChem_Examples_CaOscillations_Cytosol Real V(quantity = \"Volume\", unit = \"l\", start = 1.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real Endoplasmic_Reticulum.V(quantity = \"Volume\", unit = \"l\", start = 1.0, stateSelect = StateSelect.prefer) \"Compartment volume\"; Real Endoplasmic_Reticulum.Endoplasmic_Reticulum_V = Endoplasmic_Reticulum.V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real Endoplasmic_Reticulum.CaER.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real Endoplasmic_Reticulum.CaER.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real Endoplasmic_Reticulum.CaER.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real Endoplasmic_Reticulum.CaER.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.CaER.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.CaER.n1.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.p1_sbml = p1_sbml; Real Endoplasmic_Reticulum.p2_sbml = p2_sbml; Real Endoplasmic_Reticulum.p3_sbml = p3_sbml; Real Endoplasmic_Reticulum.Ca_Cyt_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.Ca_Cyt_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.Ca_Cyt_node.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.Jch.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real Endoplasmic_Reticulum.Jch.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.Jch.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.Jch.s1.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.Jch.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.Jch.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.Jch.p1.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.Jch.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real Endoplasmic_Reticulum.Jch.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real Endoplasmic_Reticulum.Jch.Fch_0 = 8.0; Real Endoplasmic_Reticulum.Jch.p1_sbml = Endoplasmic_Reticulum.p1_sbml; Real Endoplasmic_Reticulum.Jch.p2_sbml = Endoplasmic_Reticulum.p2_sbml; Real Endoplasmic_Reticulum.Jch.p3_sbml = Endoplasmic_Reticulum.p3_sbml; Real Endoplasmic_Reticulum.Jleak.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real Endoplasmic_Reticulum.Jleak.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.Jleak.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.Jleak.s1.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.Jleak.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.Jleak.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.Jleak.p1.V(quantity = \"Volume\", unit = \"l\"); Real Endoplasmic_Reticulum.Jleak.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real Endoplasmic_Reticulum.Jleak.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real Endoplasmic_Reticulum.Jleak.Fleak = 0.5; Real Endoplasmic_Reticulum.CaER_node.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Endoplasmic_Reticulum.CaER_node.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Endoplasmic_Reticulum.CaER_node.V(quantity = \"Volume\", unit = \"l\"); Real Cytosol_V = V \"Variable used to make the compartment volume accessible for inner components. Do not edit.\"; Real Endoplasmic_Reticulum_V = Endoplasmic_Reticulum.V \"Variable used to make the compartment volume of inner compartments accessible. Do not edit.\"; Real Ca_Cyt.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0, start = 0.0, stateSelect = StateSelect.prefer) \"Current concentration of substance (mM)\"; Real Ca_Cyt.rNet(quantity = \"Molar flow rate\", unit = \"mol/s\") \"Net flow rate of substance into the node\"; Real Ca_Cyt.n(quantity = \"AmountOfSubstance\", unit = \"mol\", min = 0.0, stateSelect = StateSelect.prefer) \"Number of moles of substance in pool (mol)\"; Real Ca_Cyt.n1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Ca_Cyt.n1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Ca_Cyt.n1.V(quantity = \"Volume\", unit = \"l\"); Real n_sbml(start = 1.0); parameter Real n0 = 1.0; parameter Real kbN = 0.5; parameter Real kappa = 5.0; Real p1_sbml(start = 0.0); parameter Real p11 = 0.2; parameter Real p12 = 0.8; parameter Real K1 = 5.0; Real p2_sbml(start = 0.0); parameter Real K2 = 0.7; Real p3_sbml(start = 0.95); parameter Real k31 = 0.5; parameter Real K3 = 0.7; Real Jpump.rr(quantity = \"Reaction rate\", unit = \"mol/s\") \"Rate of the reaction\"; Real Jpump.s1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Jpump.s1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Jpump.s1.V(quantity = \"Volume\", unit = \"l\"); Real Jpump.p1.c(quantity = \"Concentration\", unit = \"mol/l\", min = 0.0); Real Jpump.p1.r(quantity = \"Molar flow rate\", unit = \"mol/s\"); Real Jpump.p1.V(quantity = \"Volume\", unit = \"l\"); Real Jpump.nS1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the substrate\"; Real Jpump.nP1(quantity = \"Stoichiometric coefficient\", unit = \"1\") = 1.0 \"Stoichiometric coefficient for the product\"; parameter Real Jpump.Fpump_0 = 2.0; parameter Real Jpump.Kpump = 0.1; equation der(Endoplasmic_Reticulum.CaER.n) = Endoplasmic_Reticulum.CaER.rNet; Endoplasmic_Reticulum.CaER.rNet = Endoplasmic_Reticulum.CaER.n1.r; Endoplasmic_Reticulum.CaER.c = Endoplasmic_Reticulum.CaER.n1.c; Endoplasmic_Reticulum.V = Endoplasmic_Reticulum.CaER.n1.V; Endoplasmic_Reticulum.CaER.c = Endoplasmic_Reticulum.CaER.n / Endoplasmic_Reticulum.V; Endoplasmic_Reticulum.Jch.rr = Endoplasmic_Reticulum.Jch.Fch_0 * Endoplasmic_Reticulum.Jch.p1_sbml * Endoplasmic_Reticulum.Jch.p2_sbml * Endoplasmic_Reticulum.Jch.p3_sbml; Endoplasmic_Reticulum.Jch.s1.r = Endoplasmic_Reticulum.Jch.nS1 * Endoplasmic_Reticulum.Jch.rr; Endoplasmic_Reticulum.Jch.p1.r = (-Endoplasmic_Reticulum.Jch.nP1) * Endoplasmic_Reticulum.Jch.rr; Endoplasmic_Reticulum.Jleak.rr = Endoplasmic_Reticulum.Jleak.Fleak; Endoplasmic_Reticulum.Jleak.s1.r = Endoplasmic_Reticulum.Jleak.nS1 * Endoplasmic_Reticulum.Jleak.rr; Endoplasmic_Reticulum.Jleak.p1.r = (-Endoplasmic_Reticulum.Jleak.nP1) * Endoplasmic_Reticulum.Jleak.rr; der(Endoplasmic_Reticulum.V) = 0.0 \"Compartment volume is constant\"; der(Ca_Cyt.n) = Ca_Cyt.rNet; Ca_Cyt.rNet = Ca_Cyt.n1.r; Ca_Cyt.c = Ca_Cyt.n1.c; V = Ca_Cyt.n1.V; Ca_Cyt.c = Ca_Cyt.n / V; Jpump.rr = Jpump.Fpump_0 * Jpump.s1.c / (Jpump.Kpump + Jpump.s1.c); Jpump.s1.r = Jpump.nS1 * Jpump.rr; Jpump.p1.r = (-Jpump.nP1) * Jpump.rr; n_sbml = n0 * (exp((-kbN) * time) + kappa * (1.0 - exp((-kbN) * time))); p1_sbml = p11 + p12 * n_sbml / (K1 + n_sbml); p2_sbml = Ca_Cyt.c / (K2 + Ca_Cyt.c); der(p3_sbml) = k31 * (K3 * (1.0 - p3_sbml) - Ca_Cyt.c * p3_sbml); der(V) = 0.0 \"Compartment volume is constant\"; Ca_Cyt.n1.r + Jpump.s1.r + Endoplasmic_Reticulum.Ca_Cyt_node.r = 0.0; Jpump.p1.r + Endoplasmic_Reticulum.CaER_node.r = 0.0; Endoplasmic_Reticulum.CaER.n1.r + Endoplasmic_Reticulum.Jleak.s1.r + (-Endoplasmic_Reticulum.CaER_node.r) + Endoplasmic_Reticulum.Jch.s1.r = 0.0; (-Endoplasmic_Reticulum.Ca_Cyt_node.r) + Endoplasmic_Reticulum.Jleak.p1.r + Endoplasmic_Reticulum.Jch.p1.r = 0.0; Endoplasmic_Reticulum.Ca_Cyt_node.V = Endoplasmic_Reticulum.Jch.p1.V; Endoplasmic_Reticulum.Ca_Cyt_node.V = Endoplasmic_Reticulum.Jleak.p1.V; Endoplasmic_Reticulum.Ca_Cyt_node.c = Endoplasmic_Reticulum.Jch.p1.c; Endoplasmic_Reticulum.Ca_Cyt_node.c = Endoplasmic_Reticulum.Jleak.p1.c; Endoplasmic_Reticulum.CaER.n1.V = Endoplasmic_Reticulum.CaER_node.V; Endoplasmic_Reticulum.CaER.n1.V = Endoplasmic_Reticulum.Jch.s1.V; Endoplasmic_Reticulum.CaER.n1.V = Endoplasmic_Reticulum.Jleak.s1.V; Endoplasmic_Reticulum.CaER.n1.c = Endoplasmic_Reticulum.CaER_node.c; Endoplasmic_Reticulum.CaER.n1.c = Endoplasmic_Reticulum.Jch.s1.c; Endoplasmic_Reticulum.CaER.n1.c = Endoplasmic_Reticulum.Jleak.s1.c; Ca_Cyt.n1.V = Endoplasmic_Reticulum.Ca_Cyt_node.V; Ca_Cyt.n1.V = Jpump.s1.V; Ca_Cyt.n1.c = Endoplasmic_Reticulum.Ca_Cyt_node.c; Ca_Cyt.n1.c = Jpump.s1.c; Endoplasmic_Reticulum.CaER_node.V = Jpump.p1.V; Endoplasmic_Reticulum.CaER_node.c = Jpump.p1.c; end BioChem_Examples_CaOscillations_Cytosol; " "[flattening/libraries/biochem/CytosolTotal.mo:862:9-862:228:writable] Warning: Connecting two signal sources while connecting Ca_Cyt.n1.V to Endoplasmic_Reticulum.Ca_Cyt_node.V. " "Check of BioChem_Examples_CaOscillations_Cytosol completed successfully. Class BioChem_Examples_CaOscillations_Cytosol has 60 equation(s) and 60 variable(s). 44 of these are trivial equation(s)." "[flattening/libraries/biochem/CytosolTotal.mo:862:9-862:228:writable] Warning: Connecting two signal sources while connecting Ca_Cyt.n1.V to Endoplasmic_Reticulum.Ca_Cyt_node.V. " true false "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.InsulinSignaling_Sedaghat not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.Glycolysis not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.EnzMM not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GMO.cell not found in scope <TOP>. " "" "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.centralMetabolism not found in scope <TOP>. Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.centralMetabolism.cytosol not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CircadianOscillator.Container not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CircadianOscillator.Nucleus not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CircadianOscillator.Cytoplasm not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CellDivison.cell not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CaOscillations.Cytosol not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.CaOscillations.Endoplasmic_Reticulum not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.GlucoseInsulinModel not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.UtilizationReaction not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.U_ii_reaction not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.MM_insulin not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.GlucoseUptakeReaction not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MassAction.UniUni not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MassAction.UniBi not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MultiCompartments.GlucoseMetabolism not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MultiCompartments.BigCompartmentReversible not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MultiCompartments.BigCompartmentIrreversible not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MultiCompartments.Utilities.TCA not found in scope <TOP>. " "" "Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. Error: Class BioChem.Examples.MultiCompartments.Utilities.SmallCompartment not found in scope <TOP>. " Equation mismatch: diff says: --- /tmp/omc-rtest-unknown/flattening/libraries/biochem/BiochemModels.mos_temp7898/equations-expected2018-12-19 23:05:56.959016002 +0000 +++ /tmp/omc-rtest-unknown/flattening/libraries/biochem/BiochemModels.mos_temp7898/equations-got2018-12-19 23:05:59.507011145 +0000 @@ -1931,134 +1931,115 @@ Class BioChem_Examples_CaOscillations_Cytosol has 60 equation(s) and 60 variable(s). 44 of these are trivial equation(s)." "[flattening/libraries/biochem/CytosolTotal.mo:862:9-862:228:writable] Warning: Connecting two signal sources while connecting Ca_Cyt.n1.V to Endoplasmic_Reticulum.Ca_Cyt_node.V. " true -true +false +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +" "" -"Check of BioChem.Examples.InsulinSignaling_Sedaghat completed successfully. -Class BioChem.Examples.InsulinSignaling_Sedaghat has 141 equation(s) and 141 variable(s). -96 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.Glycolysis completed successfully. -Class BioChem.Examples.Glycolysis has 170 equation(s) and 170 variable(s). -117 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.EnzMM completed successfully. -Class BioChem.Examples.EnzMM has 22 equation(s) and 22 variable(s). -17 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GMO.cell completed successfully. -Class BioChem.Examples.GMO.cell has 96 equation(s) and 96 variable(s). -65 of these are trivial equation(s)." -"" -"" -"Check of BioChem.Examples.centralMetabolism.cytosol completed successfully. -Class BioChem.Examples.centralMetabolism.cytosol has 320 equation(s) and 320 variable(s). -229 of these are trivial equation(s)." -"Error: Cannot instantiate BioChem.Examples.centralMetabolism due to class specialization PACKAGE. -" -"Check of BioChem.Examples.CircadianOscillator.Container completed successfully. -Class BioChem.Examples.CircadianOscillator.Container has 252 equation(s) and 252 variable(s). -180 of these are trivial equation(s)." -"[BioChem 1.0.1/Examples/package.mo:1086:7-1086:129:writable] Warning: Connecting two signal sources while connecting cytoplasm.y5_node.V to nucleus.y5_node.V. -[BioChem 1.0.1/Examples/package.mo:1087:7-1087:128:writable] Warning: Connecting two signal sources while connecting nucleus.y6_node.V to cytoplasm.y6_node.V. -[BioChem 1.0.1/Examples/package.mo:1088:7-1088:128:writable] Warning: Connecting two signal sources while connecting cytoplasm.y2_node.V to nucleus.y2_node.V. -[BioChem 1.0.1/Examples/package.mo:1089:7-1089:129:writable] Warning: Connecting two signal sources while connecting nucleus.y3_node.V to cytoplasm.y3_node.V. -" -"Check of BioChem.Examples.CircadianOscillator.Nucleus completed successfully. -Class BioChem.Examples.CircadianOscillator.Nucleus has 99 equation(s) and 101 variable(s). -70 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.CircadianOscillator.Cytoplasm completed successfully. -Class BioChem.Examples.CircadianOscillator.Cytoplasm has 140 equation(s) and 142 variable(s). -100 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.CellDivison.cell completed successfully. -Class BioChem.Examples.CellDivison.cell has 148 equation(s) and 148 variable(s). -101 of these are trivial equation(s)." +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.InsulinSignaling_Sedaghat not found in scope <TOP>. +" "" -"Check of BioChem.Examples.CaOscillations.Cytosol completed successfully. -Class BioChem.Examples.CaOscillations.Cytosol has 60 equation(s) and 60 variable(s). -44 of these are trivial equation(s)." -"[BioChem 1.0.1/Examples/package.mo:2195:7-2195:211:writable] Warning: Connecting two signal sources while connecting Ca_Cyt.n1.V to endoplasmicReticulum.Ca_Cyt_node.V. +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.Glycolysis not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.EnzMM not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GMO.cell not found in scope <TOP>. +" +"" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.centralMetabolism not found in scope <TOP>. +Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.centralMetabolism.cytosol not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CircadianOscillator.Container not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CircadianOscillator.Nucleus not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CircadianOscillator.Cytoplasm not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CellDivison.cell not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CaOscillations.Cytosol not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.CaOscillations.Endoplasmic_Reticulum not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.GlucoseInsulinModel not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.UtilizationReaction not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.U_ii_reaction not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.MM_insulin not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.GlucoseUptakeReaction not found in scope <TOP>. " -"Check of BioChem.Examples.CaOscillations.Endoplasmic_Reticulum completed successfully. -Class BioChem.Examples.CaOscillations.Endoplasmic_Reticulum has 34 equation(s) and 35 variable(s). -26 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.GlucoseInsulinModel completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.GlucoseInsulinModel has 687 equation(s) and 687 variable(s). -530 of these are trivial equation(s)." -"[BioChem 1.0.1/Examples/package.mo:2450:11-2450:101:writable] Warning: Connecting two signal sources while connecting Ra_calc.n1.V to Ra_connector.V. -[BioChem 1.0.1/Examples/package.mo:2666:11-2666:131:writable] Warning: Connecting two signal sources while connecting G_t.n1.V to U_idm_connector.V. -[BioChem 1.0.1/Examples/package.mo:2667:11-2667:130:writable] Warning: Connecting two signal sources while connecting G_t.n1.V to U_idf_connector.V. -[BioChem 1.0.1/Examples/package.mo:2668:11-2668:96:writable] Warning: Connecting two signal sources while connecting G_t.n1.V to G_connector.V. -[BioChem 1.0.1/Examples/package.mo:2640:11-2640:105:writable] Warning: connect(G_p_connector, G_p_connector) connects the same connector instance! The connect equation will be ignored. -[BioChem 1.0.1/Examples/package.mo:2560:11-2560:127:writable] Warning: Connecting two signal sources while connecting G_p.n1.V to E_connector.V. -[BioChem 1.0.1/Examples/package.mo:2561:11-2561:95:writable] Warning: Connecting two signal sources while connecting G_p.n1.V to G_connector.V. -[BioChem 1.0.1/Examples/package.mo:2562:11-2562:120:writable] Warning: Connecting two signal sources while connecting G_p_signal.n1.V to G_p_connector.V. -[BioChem 1.0.1/Examples/package.mo:2563:11-2563:110:writable] Warning: Connecting two signal sources while connecting G_signal.n1.V to G_signal_connector.V. -[BioChem 1.0.1/Examples/package.mo:2525:11-2525:109:writable] Warning: Connecting two signal sources while connecting I_signal.n1.V to I_signal_connector.V. -[BioChem 1.0.1/Examples/package.mo:2526:11-2526:135:writable] Warning: Connecting two signal sources while connecting I_p_signal.n1.V to I_p_connector.V. -[BioChem 1.0.1/Examples/package.mo:2527:11-2527:96:writable] Warning: Connecting two signal sources while connecting I_p.n1.V to I_connector.V. -[BioChem 1.0.1/Examples/package.mo:2584:11-2584:138:writable] Warning: Connecting two signal sources while connecting I_connector.V to I_l.n1.V. -[BioChem 1.0.1/Examples/package.mo:2621:11-2621:103:writable] Warning: Connecting two signal sources while connecting EGP_calc.n1.V to EGP_connector.V. -[BioChem 1.0.1/Examples/package.mo:2499:11-2499:108:writable] Warning: Connecting two signal sources while connecting I_po_connector.V to I_po_signal.n1.V. -[BioChem 1.0.1/Examples/package.mo:2502:11-2502:132:writable] Warning: Connecting two signal sources while connecting S_calc.n1.V to S_connector.V. -" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.FlowReaction has 7 equation(s) and 7 variable(s). -4 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.UtilizationReaction completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.UtilizationReaction has 11 equation(s) and 11 variable(s). -6 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.signaltosubstance has 7 equation(s) and 7 variable(s). -5 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.U_ii_reaction completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.U_ii_reaction has 7 equation(s) and 7 variable(s). -5 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.ActivationReaction has 9 equation(s) and 9 variable(s). -6 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.MM_insulin completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.MM_insulin has 9 equation(s) and 9 variable(s). -6 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.GlucoseUptakeReaction completed successfully. -Class BioChem.Examples.GlucoseInsulinModel.Utilities.Reactions.GlucoseUptakeReaction has 9 equation(s) and 9 variable(s). -6 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MassAction.UniUni completed successfully. -Class BioChem.Examples.MassAction.UniUni has 745 equation(s) and 745 variable(s). -609 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MassAction.UniBi completed successfully. -Class BioChem.Examples.MassAction.UniBi has 945 equation(s) and 945 variable(s). -769 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MultiCompartments.GlucoseMetabolism completed successfully. -Class BioChem.Examples.MultiCompartments.GlucoseMetabolism has 385 equation(s) and 385 variable(s). -278 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MultiCompartments.BigCompartmentReversible completed successfully. -Class BioChem.Examples.MultiCompartments.BigCompartmentReversible has 26 equation(s) and 26 variable(s). -20 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MultiCompartments.BigCompartmentIrreversible completed successfully. -Class BioChem.Examples.MultiCompartments.BigCompartmentIrreversible has 26 equation(s) and 26 variable(s). -20 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MultiCompartments.Utilities.TCA completed successfully. -Class BioChem.Examples.MultiCompartments.Utilities.TCA has 206 equation(s) and 206 variable(s). -155 of these are trivial equation(s)." -"" -"Check of BioChem.Examples.MultiCompartments.Utilities.SmallCompartment completed successfully. -Class BioChem.Examples.MultiCompartments.Utilities.SmallCompartment has 10 equation(s) and 10 variable(s). -8 of these are trivial equation(s)." "" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MassAction.UniUni not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MassAction.UniBi not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MultiCompartments.GlucoseMetabolism not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MultiCompartments.BigCompartmentReversible not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MultiCompartments.BigCompartmentIrreversible not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MultiCompartments.Utilities.TCA not found in scope <TOP>. +" +"" +"Error: Failed to load package BioChem (default) using MODELICAPATH /var/lib/jenkins/workspace/OpenModelica_maintenance_v1.13/build/lib/omlibrary. +Error: Class BioChem.Examples.MultiCompartments.Utilities.SmallCompartment not found in scope <TOP>. +" Equation mismatch: omc-diff says: Failed 't' 'f' Line 1936: Text differs: expected: true got: false == 1 out of 1 tests failed [flattening/libraries/biochem/BiochemModels.mos_temp7898, time: 3]