(define-module :class "library" :super-classes ("module") :documentation "Superclass for all library elements.") (define-variable :class "var-rate" :super-classes ("variable") :value "100.0d0" :minimum "0.0d0" :maximum "100000.0d0" :unit "1/h") (define-variable :class "concentration" :super-classes ("variable") :unit "mol/l") (define-variable :class "molar-flux" :super-classes ("variable") :minimum "0.0d0" :maximum "1000.0d0" :unit "mol/s") (define-variable :class "mass" :super-classes ("variable") :minimum "0.0d0" :maximum "10000.0d0" :unit "mol") (define-variable :class "scaling-parameter" :super-classes ("variable") :documentation "parameter to perform manual numeric scaling of rate-laws etc. for optimization. It is marked as a help-variable to eventually remove it by the equation-optimizer in Promot." :system-theoretic "help" :value "1.0d0") (define-variable :class "kinetic-parameter" :super-classes ("variable") :system-theoretic "real-parameter") (define-variable :class "stoichiometry" :super-classes ("variable") :documentation "Don't know what is the best solution, but these parameters should not be changed by the user during simulation, therefore I consider them as helps, which means they can be optimized away." :system-theoretic "help" :value "1.0d0" :unit "1") (define-variable :class "volume" :super-classes ("variable") :minimum "0.0d0" :maximum "10.0d0" :unit "l") (define-variable :class "var-output" :super-classes ("variable") :system-theoretic "output") (define-module :class "sbml-model" :super-classes ("module")) (define-variable :class "var-input" :super-classes ("variable") :system-theoretic "input") (define-module :class "compartment" :super-classes ("module") :variables (("v" :is-a "volume" :system-theoretic "real-parameter" :value "1.0d0"))) (define-module :class "reaction" :super-classes ("library") :documentation "Superclass containing all reaction definitions.") (define-module :class "structure" :super-classes ("reaction") :documentation "Superclass containing all possible reaction structures." :variables (("r"))) (define-terminal :class "tsig" :super-classes ("terminal") :icon "icons/term_concentration_in.gif" :link-color "green" :variables (("c" :is-a "concentration" :system-theoretic "state" :value "0.0d0"))) (define-terminal :class "tflux" :super-classes ("tsig") :icon "icons/term_react_blue.gif" :link-color "blue" :variables (("r" :is-a "molar-flux" :system-theoretic "state" :positive-vector-direction "out" :value "0.0d0"))) (define-module :class "s-2-1" :super-classes ("structure") :terminals (("t_p1" :is-a "tflux" :geometry-side "right" :geometry-position "0.5") ("t_r1" :is-a "tflux" :geometry-side "left" :geometry-position "0.33333334") ("t_r2" :is-a "tflux" :geometry-side "left" :geometry-position "0.6666667")) :variables (("gamma_p1" :is-a "stoichiometry" :value "1.0d0") ("gamma_r1" :is-a "stoichiometry" :value "-1.0d0") ("gamma_r2" :is-a "stoichiometry" :value "-1.0d0")) :equations (("e_p1" :relation "t_p1.r == gamma_p1*r") ("e_r1" :relation "t_r1.r == gamma_r1*r") ("e_r2" :relation "t_r2.r == gamma_r2*r"))) (define-variable :class "reaction-rate" :super-classes ("molar-flux") :unit "mol/s") (define-module :class "kinetics" :super-classes ("reaction") :documentation "Superclass containing all kinetics." :variables (("r" :is-a "reaction-rate" :documentation "reaction-rate" :system-theoretic "help" :report "lumped" :unit "umol/g_dw/h") ("skal" :is-a "scaling-parameter"))) (define-terminal :class "tvol" :super-classes ("terminal") :link-color "yellow" :variables (("v" :is-a "volume" :system-theoretic "state"))) (define-module :class "kin-2-1_0_1_k20" :super-classes ("s-2-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k20" :is-a "kinetic-parameter"))) (define-module :class "s-1-1" :super-classes ("structure") :terminals (("t_p1" :is-a "tflux" :geometry-side "right" :geometry-position "0.5") ("t_r1" :is-a "tflux" :geometry-side "left" :geometry-position "0.5")) :variables (("gamma_p1" :is-a "stoichiometry" :value "1.0d0") ("gamma_r1" :is-a "stoichiometry" :value "-1.0d0")) :equations (("e_p1" :relation "t_p1.r == gamma_p1*r") ("e_r1" :relation "t_r1.r == gamma_r1*r"))) (define-module :class "kin-1-1_0_1_k0" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k0" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_1_2_2glc_p2_k2ig6p_k2iig6p_v2r1c7f" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.33333334") ("t_c2" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.6666667") ("t_m1" :is-a "tsig" :geometry-side "top" :geometry-position "0.5")) :variables (("k2glc" :is-a "kinetic-parameter") ("k2ig6p" :is-a "kinetic-parameter") ("k2iig6p" :is-a "kinetic-parameter") ("p2" :is-a "kinetic-parameter") ("v2f" :is-a "kinetic-parameter") ("v2r" :is-a "kinetic-parameter") ("yvol" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_2_k16_yvol" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.33333334") ("t_c2" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.6666667")) :variables (("k16" :is-a "kinetic-parameter") ("yvol" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_2_k13_yvol" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.33333334") ("t_c2" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.6666667")) :variables (("k13" :is-a "kinetic-parameter") ("yvol" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_2_k18_yvol" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.33333334") ("t_c2" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.6666667")) :variables (("k18" :is-a "kinetic-parameter") ("yvol" :is-a "kinetic-parameter"))) (define-module :class "dyn-adapter" :super-classes ("library") :documentation "Superclass containing adapters. Useful for instance for propagating terminals already connected to other elements.") (define-module :class "adapter-vol" :super-classes ("dyn-adapter")) (define-module :class "adapter-volume-pop" :super-classes ("adapter-vol") :parent-type "compartment" :documentation "exports one tvol as volume out of parent" :properties (("abstract" :value "no")) :icon "icons/adapter.gif" :terminals (("out" :is-a "tvol" :geometry-side "RIGHT" :variables (("v" :is-eq-to "parent.v")))) :variables (("v" :is-eq-to "parent.v"))) (define-module :class "compartment-out" :super-classes ("compartment") :terminals (("out" :is-a "tvol" :geometry-side "bottom" :variables (("v" :is-eq-to "parent.v"))))) (define-module :class "kin-1-1_0_1__k7gap_v7r_k7eq199b" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k7dhap" :is-a "kinetic-parameter") ("k7eq" :is-a "kinetic-parameter") ("k7gap" :is-a "kinetic-parameter") ("v7f" :is-a "kinetic-parameter") ("v7r" :is-a "kinetic-parameter"))) (define-module :class "kin-2-1_0_1_k22" :super-classes ("s-2-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k22" :is-a "kinetic-parameter"))) (define-module :class "s-2-2" :super-classes ("structure") :terminals (("t_p1" :is-a "tflux" :geometry-side "right" :geometry-position "0.33333334") ("t_p2" :is-a "tflux" :geometry-side "right" :geometry-position "0.6666667") ("t_r1" :is-a "tflux" :geometry-side "left" :geometry-position "0.33333334") ("t_r2" :is-a "tflux" :geometry-side "left" :geometry-position "0.6666667")) :variables (("gamma_p1" :is-a "stoichiometry" :value "1.0d0") ("gamma_p2" :is-a "stoichiometry" :value "1.0d0") ("gamma_r1" :is-a "stoichiometry" :value "-1.0d0") ("gamma_r2" :is-a "stoichiometry" :value "-1.0d0")) :equations (("e_p1" :relation "t_p1.r == gamma_p1*r") ("e_p2" :relation "t_p2.r == gamma_p2*r") ("e_r1" :relation "t_r1.r == gamma_r1*r") ("e_r2" :relation "t_r2.r == gamma_r2*r"))) (define-module :class "kin-2-2_0_1_v10m_k10pep_k10adp" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k10adp" :is-a "kinetic-parameter") ("k10pep" :is-a "kinetic-parameter") ("v10m" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_k4f6p_v4r_k4eqnpd" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k4eq" :is-a "kinetic-parameter") ("k4f6p" :is-a "kinetic-parameter") ("k4g6p" :is-a "kinetic-parameter") ("v4f" :is-a "kinetic-parameter") ("v4r" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_1_1_v5m_k5_kappa5" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5") ("t_m1" :is-a "tsig" :geometry-side "top" :geometry-position "0.5")) :variables (("k5" :is-a "kinetic-parameter") ("kappa5" :is-a "kinetic-parameter") ("v5m" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_v11m_k11" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k11" :is-a "kinetic-parameter") ("v11m" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_k9f_k9r" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k9f" :is-a "kinetic-parameter") ("k9r" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_ap_k15inadh_k15inad_k15nadhifc" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k15dhap" :is-a "kinetic-parameter") ("k15inad" :is-a "kinetic-parameter") ("k15inadh" :is-a "kinetic-parameter") ("k15nadh" :is-a "kinetic-parameter") ("v15m" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1__k3atp_k3glc1949" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k3atp" :is-a "kinetic-parameter") ("k3dglc" :is-a "kinetic-parameter") ("k3glc" :is-a "kinetic-parameter") ("v3m" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_k8nad_k8bpg_k8nadh_v8r_k8eq155b" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k8bpg" :is-a "kinetic-parameter") ("k8eq" :is-a "kinetic-parameter") ("k8gap" :is-a "kinetic-parameter") ("k8nad" :is-a "kinetic-parameter") ("k8nadh" :is-a "kinetic-parameter") ("v8f" :is-a "kinetic-parameter") ("v8r" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_k23" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k23" :is-a "kinetic-parameter"))) (define-module :class "s-1-2" :super-classes ("structure") :terminals (("t_p1" :is-a "tflux" :geometry-side "right" :geometry-position "0.33333334") ("t_p2" :is-a "tflux" :geometry-side "right" :geometry-position "0.6666667") ("t_r1" :is-a "tflux" :geometry-side "left" :geometry-position "0.5")) :variables (("gamma_p1" :is-a "stoichiometry" :value "1.0d0") ("gamma_p2" :is-a "stoichiometry" :value "1.0d0") ("gamma_r1" :is-a "stoichiometry" :value "-1.0d0")) :equations (("e_p1" :relation "t_p1.r == gamma_p1*r") ("e_p2" :relation "t_p2.r == gamma_p2*r") ("e_r1" :relation "t_r1.r == gamma_r1*r"))) (define-module :class "kin-1-2_0_1_k6dhap_k6eq_ratio6_k6gap_k6igapf7a" :super-classes ("s-1-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k6dhap" :is-a "kinetic-parameter") ("k6eq" :is-a "kinetic-parameter") ("k6fbp" :is-a "kinetic-parameter") ("k6gap" :is-a "kinetic-parameter") ("k6igap" :is-a "kinetic-parameter") ("ratio6" :is-a "kinetic-parameter") ("v6f" :is-a "kinetic-parameter"))) (define-module :class "kin-2-1_0_1_k24f_k24r" :super-classes ("s-2-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k24f" :is-a "kinetic-parameter") ("k24r" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_v12m_k12nadh_k12aca" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("k12aca" :is-a "kinetic-parameter") ("k12nadh" :is-a "kinetic-parameter") ("v12m" :is-a "kinetic-parameter"))) (define-variable :class "var-rate-out" :super-classes ("var-rate" "var-output") :absolute-error "1.0d-8") (define-variable :class "var-concentration" :super-classes ("concentration") :value "1.0d-4" :minimum "0.0d0" :maximum "10.0d0") (define-variable :class "var-concentration-out" :super-classes ("var-concentration" "var-output") :absolute-error "1.0d-8") (define-variable :class "var-state-concentration-out" :super-classes ("var-concentration-out") :system-theoretic "output") (define-variable :class "var-rate-in" :super-classes ("var-rate" "var-input") :absolute-error "1.0d-8") (define-terminal :class "term-storage-flux" :super-classes ("terminal") :documentation "Terminal for a flux in a storage." :icon "icons/term_stor_blue.gif" :link-color "blue" :variables (("c" :is-a "var-concentration-out") ("r" :is-a "var-rate-in" :positive-vector-direction "in" :unit "umol/g_dw/h"))) (define-variable :class "var-concentration-in" :super-classes ("var-concentration" "var-input") :absolute-error "1.0d-8") (define-terminal :class "term-reaction-flux" :super-classes ("terminal") :documentation "Terminal for a flux in a reaction." :icon "icons/term_react_blue.gif" :link-color "blue" :variables (("c" :is-a "var-concentration-in" :unit "umol/g_dw") ("r" :is-a "var-rate-out" :positive-vector-direction "out" :unit "umol/g_dw/h"))) (define-module :class "adapter-flux" :super-classes ("dyn-adapter") :documentation "Flux -> Flux" :properties (("abstract" :value "no")) :icon "icons/adapter.gif" :terminals (("in" :is-a "term-reaction-flux" :geometry-side "LEFT" :geometry-position "0.47333333" :variables (("r" :is-eq-to "parent.r"))) ("out" :is-a "term-storage-flux" :geometry-side "RIGHT" :geometry-position "0.47333333" :variables (("c" :is-eq-to "parent.c")))) :variables (("c" :is-a "var-state-concentration-out") ("r" :is-a "var-rate-out" :positive-vector-direction "out" :value "0.0d0")) :equations (("hurg" :relation "c == in.c") ("rate" :relation "r == out.r"))) (define-module :class "help" :super-classes ("library") :documentation "Superclass containing accessories for making basic operations on signals or converting terminals.") (define-module :class "term-conv" :super-classes ("help") :documentation "Superclass containing elements for converting different terminal types.") (define-terminal :class "term-concentration-out" :super-classes ("terminal") :documentation "Output terminal for a concentration (signal)" :icon "icons/term_concentration_out.gif" :link-color "green" :variables (("c" :is-a "var-concentration-out" :unit "umol/g_dw"))) (define-module :class "cf2co" :super-classes ("term-conv") :documentation "Flux -> Signal. Converts a cf-term to a co-term ." :properties (("abstract" :value "no")) :icon "icons/adapter" :terminals (("cf" :is-a "term-reaction-flux" :geometry-side "LEFT" :geometry-position "0.52666664" :variables (("c" :is-eq-to "parent.c"))) ("co" :is-a "term-concentration-out" :geometry-side "RIGHT" :geometry-position "0.52666664")) :variables (("c" :is-a "var-concentration-in")) :equations (("free" :relation "co.c == c") ("rate" :relation "cf.r == 0.0d0"))) (define-module :class "storage" :super-classes ("library") :documentation "Superclass for species in the network.") (define-module :class "species" :super-classes ("storage") :documentation "Constant species" :icon "icons/species" :parameters (("cf.r" :positive-vector-direction "in" :value "0.0d0")) :terminals (("cf" :is-a "tflux" :variables (("c" :is-eq-to "parent.c")))) :variables (("c" :is-a "concentration" :system-theoretic "help" :report "lumped" :value "n/v") ("n" :is-a "mass" :system-theoretic "real-parameter") ("v" :is-eq-to "parent.v"))) (define-module :class "speciesv" :super-classes ("species") :documentation "Species with molar balance, defined by connected reactions. Concentration calculated using surrounding compartment" :icon "icons/speciesv" :parameters (("n" :system-theoretic "state")) :equations (("balc" :relation ":diff n == cf.r"))) (define-module :class "hynne2001_glycolysis-cytosol" :super-classes ("compartment-out") :rdf-annotation ((:name "BQB_IS_VERSION_OF" :resources ("urn:miriam:obo.go:GO%3A0005829"))) :geometry-width "976" :geometry-height "1154" :parameters (("aca.c" :label "Acetaldehyde" :model-name "ACA") ("aca.n" :value "1.48153d0*v") ("adp.c" :label "ADP" :model-name "ADP") ("adp.n" :value "1.5d0*v") ("amp.c" :label "AMP" :model-name "AMP") ("amp.n" :value "0.33d0*v") ("atp.c" :label "ATP" :model-name "ATP") ("atp.n" :value "2.1d0*v") ("bpg.c" :label "1,3-Bisphosphoglycerate" :model-name "BPG") ("bpg.n" :value "2.7d-4*v") ("dhap.c" :label "Dihydroxyacetone phosphate" :model-name "DHAP") ("dhap.n" :value "2.95d0*v") ("etoh.c" :model-name "EtOH") ("etoh.n" :value "19.2379d0*v") ("f6p.c" :label "Fructose-6-Phosphate" :model-name "F6P") ("f6p.n" :value "0.49d0*v") ("fbp.c" :label "Fructose 1,6-bisphosphate" :model-name "FBP") ("fbp.n" :value "4.64d0*v") ("g6p.c" :label "Glucose-6-Phosphate" :model-name "G6P") ("g6p.n" :value "4.2d0*v") ("gap.c" :label "Glyceraldehyde 3-phosphate" :model-name "GAP") ("gap.n" :value "0.115d0*v") ("glc.c" :label "Cytosolic glucose" :model-name "Glc") ("glc.n" :value "0.573074d0*v") ("glyc.c" :label "Glycerol" :model-name "Glyc") ("glyc.n" :value "4.196d0*v") ("nad.c" :label "NAD" :model-name "NAD") ("nad.n" :value "0.65d0*v") ("nadh.c" :label "NADH" :model-name "NADH") ("nadh.n" :value "0.33d0*v") ("pep.c" :label "Phosphoenolpyruvate" :model-name "PEP") ("pep.n" :value "0.04d0*v") ("pyr.c" :label "Pyruvate" :model-name "Pyr") ("pyr.n" :value "8.7d0*v") ("v" :value "1.0d0" :model-name "cytosol") ("vadh.k12aca" :value "0.71d0") ("vadh.k12nadh" :value "0.1d0") ("vadh.r" :label "Alcohol dehydrogenase" :value "v12m*t_r2.c*t_r1.c/((k12nadh+t_r1.c)*(k12aca+t_r2.c))*t_c1.v" :model-name "vADH") ("vadh.v12m" :value "89.8023d0") ("vak.gamma_p1" :value "2.0d0") ("vak.k24f" :value "432.9d0") ("vak.k24r" :value "133.333d0") ("vak.r" :label "Adenylate kinase" :value "t_c1.v*(k24f*t_r2.c*t_r1.c-k24r*t_p1.c ^ 2)" :model-name "vAK") ("vald.k6dhap" :value "2.0d0") ("vald.k6eq" :value "0.081d0") ("vald.k6fbp" :value "0.3d0") ("vald.k6gap" :value "4.0d0") ("vald.k6igap" :value "10.0d0") ("vald.r" :label "Aldolase" :value "t_c1.v*(v6f*t_r1.c/(k6fbp+t_r1.c+t_p1.c*k6dhap*v6f/(k6eq*v6f*ratio6)+t_p2.c*k6gap*v6f/(k6eq*v6f*ratio6)+t_r1.c*t_p1.c/k6igap+t_p1.c*t_p2.c*v6f/(k6eq*v6f*ratio6))-v6f*t_p1.c*t_p2.c/k6eq/(k6fbp+t_r1.c+t_p1.c*k6dhap*v6f/(k6eq*v6f*ratio6)+t_p2.c*k6gap*v6f/(k6eq*v6f*ratio6)+t_r1.c*t_p1.c/k6igap+t_p1.c*t_p2.c*v6f/(k6eq*v6f*ratio6)))" :model-name "vALD") ("vald.ratio6" :value "5.0d0") ("vald.v6f" :value "2207.82d0") ("vconsum.k23" :value "3.2076d0") ("vconsum.r" :label "ATP consumption" :value "t_c1.v*k23*t_r1.c" :model-name "vconsum") ("vgapdh.k8bpg" :value "0.01d0") ("vgapdh.k8eq" :value "0.0055d0") ("vgapdh.k8gap" :value "0.6d0") ("vgapdh.k8nad" :value "0.1d0") ("vgapdh.k8nadh" :value "0.06d0") ("vgapdh.r" :label "Glyceraldehyde 3-phosphate dehydrogenase" :value "t_c1.v*(v8f*t_r1.c*t_r2.c/k8gap/k8nad/((1+t_r1.c/k8gap+t_p2.c/k8bpg)*(1+t_r2.c/k8nad+t_p1.c/k8nadh))-v8r*t_p2.c*t_p1.c/k8eq/k8gap/k8nad/((1+t_r1.c/k8gap+t_p2.c/k8bpg)*(1+t_r2.c/k8nad+t_p1.c/k8nadh)))" :model-name "vGAPDH") ("vgapdh.v8f" :value "833.858d0") ("vgapdh.v8r" :value "833.858d0") ("vhk.k3atp" :value "0.1d0") ("vhk.k3dglc" :value "0.37d0") ("vhk.k3glc" :value "0.0d0") ("vhk.r" :label "Hexokinase" :value "t_c1.v*v3m*t_r1.c*t_r2.c/(k3dglc*k3atp+k3glc*t_r1.c+k3atp*t_r2.c+t_r2.c*t_r1.c)" :model-name "vHK") ("vhk.v3m" :value "51.7547d0") ("vlpglyc.k15dhap" :value "25.0d0") ("vlpglyc.k15inad" :value "0.13d0") ("vlpglyc.k15inadh" :value "0.034d0") ("vlpglyc.k15nadh" :value "0.13d0") ("vlpglyc.r" :label "Glycerol synthesis" :value "v15m*t_r1.c/(k15dhap*(1+k15inadh/t_r2.c*(1+t_p2.c/k15inad))+t_r1.c*(1+k15nadh/t_r2.c*(1+t_p2.c/k15inad)))*t_c1.v" :model-name "vlpGlyc") ("vlpglyc.v15m" :value "81.4797d0") ("vlppep.k9f" :value "443866.0d0") ("vlppep.k9r" :value "1528.62d0") ("vlppep.r" :label "Phosphoenolpyruvate synthesis" :value "t_c1.v*(k9f*t_r1.c*t_r2.c-k9r*t_p1.c*t_p2.c)" :model-name "vlpPEP") ("vpdc.k11" :value "0.3d0") ("vpdc.r" :label "Pyruvate decarboxylase" :value "v11m*t_r1.c/(k11+t_r1.c)*t_c1.v" :model-name "vPDC") ("vpdc.v11m" :value "53.1328d0") ("vpfk.k5" :value "0.021d0") ("vpfk.kappa5" :value "0.15d0") ("vpfk.r" :label "Phosphofructokinase" :value "v5m*t_r1.c ^ 2/(k5*(1+t_r2.c/t_m1.c*kappa5*t_r2.c/t_m1.c)+t_r1.c ^ 2)*t_c1.v" :model-name "vPFK") ("vpfk.v5m" :value "45.4327d0") ("vpgi.k4eq" :value "0.13d0") ("vpgi.k4f6p" :value "0.15d0") ("vpgi.k4g6p" :value "0.8d0") ("vpgi.r" :label "Phosphoglucoisomerase" :value "t_c1.v*(v4f*t_r1.c/(k4g6p+t_r1.c+k4g6p/k4f6p*t_p1.c)-t_p1.c/k4eq*v4r/(k4g6p+t_r1.c+k4g6p/k4f6p*t_p1.c))" :model-name "vPGI") ("vpgi.v4f" :value "496.042d0") ("vpgi.v4r" :value "496.042d0") ("vpk.k10adp" :value "0.17d0") ("vpk.k10pep" :value "0.2d0") ("vpk.r" :label "Pyruvate kinase" :value "v10m*t_r1.c*t_r2.c/((k10pep+t_r2.c)*(k10adp+t_r1.c))*t_c1.v" :model-name "vPK") ("vpk.v10m" :value "343.096d0") ("vstorage.k22" :value "2.25932d0") ("vstorage.r" :label "Storage" :value "t_c1.v*k22*t_r1.c*t_r2.c" :model-name "vstorage") ("vtim.k7dhap" :value "1.23d0") ("vtim.k7eq" :value "0.055d0") ("vtim.k7gap" :value "1.27d0") ("vtim.r" :label "Triosephosphate isomerase" :value "t_c1.v*(v7f*t_r1.c/(k7dhap+t_r1.c+k7dhap/k7gap*t_p1.c)-t_p1.c/k7eq*v7r/(k7dhap+t_r1.c+k7dhap/k7gap*t_p1.c))" :model-name "vTIM") ("vtim.v7f" :value "116.365d0") ("vtim.v7r" :value "116.365d0")) :terminals (("out" :geometry-side "TOP" :geometry-position "0.07530738") ("t_aca" :is-eq-to "fa_aca.out" :geometry-side "BOTTOM" :geometry-position "0.92469263") ("t_etoh" :is-eq-to "fa_etoh.out" :geometry-side "LEFT" :geometry-position "0.22487001") ("t_g6p" :is-eq-to "fa_g6p.out" :geometry-side "BOTTOM" :geometry-position "0.321209") ("t_glc" :is-eq-to "fa_glc.out" :geometry-side "RIGHT" :geometry-position "0.92504334") ("t_glyc" :is-eq-to "fa_glyc.out" :geometry-side "BOTTOM" :geometry-position "0.92469263")) :modules (("aca" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A15343" "urn:miriam:kegg.compound:C00084"))) :geometry-x "723" :geometry-y "237") ("adp" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16761" "urn:miriam:kegg.compound:C00008"))) :geometry-x "685" :geometry-y "786") ("amp" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16027" "urn:miriam:kegg.compound:C00020"))) :geometry-x "888" :geometry-y "772") ("atp" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A15422" "urn:miriam:kegg.compound:C00002"))) :geometry-x "735" :geometry-y "649") ("bpg" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16001" "urn:miriam:kegg.compound:C00236"))) :geometry-x "544" :geometry-y "345") ("ca_amp" :is-a "cf2co" :geometry-x "716" :geometry-y "741") ("dhap" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16108" "urn:miriam:kegg.compound:C00111"))) :geometry-x "165" :geometry-y "502") ("etoh" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16236" "urn:miriam:kegg.compound:C00469"))) :geometry-x "125" :geometry-y "278") ("f6p" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A20935" "urn:miriam:kegg.compound:C00085"))) :geometry-x "642" :geometry-y "937") ("fa_aca" :is-a "adapter-flux" :geometry-x "796" :geometry-y "261") ("fa_etoh" :is-a "adapter-flux" :geometry-x "65" :geometry-y "340") ("fa_g6p" :is-a "adapter-flux" :geometry-x "272" :geometry-y "893") ("fa_glc" :is-a "adapter-flux" :geometry-x "481" :geometry-y "1073") ("fa_glyc" :is-a "adapter-flux" :geometry-x "447" :geometry-y "78") ("fbp" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16905" "urn:miriam:kegg.compound:C00354"))) :geometry-x "254" :geometry-y "768") ("g6p" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A15954" "urn:miriam:kegg.compound:C00092"))) :geometry-x "371" :geometry-y "898") ("gap" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A29052" "urn:miriam:kegg.compound:C00118"))) :geometry-x "167" :geometry-y "604") ("glc" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17234" "urn:miriam:kegg.compound:C00293"))) :geometry-x "418" :geometry-y "1055") ("glyc" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17754" "urn:miriam:kegg.compound:C00116"))) :geometry-x "379" :geometry-y "96") ("nad" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A15846" "urn:miriam:kegg.compound:C00003"))) :geometry-x "349" :geometry-y "253") ("nadh" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16908" "urn:miriam:kegg.compound:C00004"))) :geometry-x "260" :geometry-y "286") ("pep" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A26055" "urn:miriam:kegg.compound:C00074"))) :geometry-x "747" :geometry-y "429") ("pyr" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A32816" "urn:miriam:kegg.compound:C00022"))) :geometry-x "853" :geometry-y "462") ("va" :is-a "adapter-volume-pop" :geometry-x "435" :geometry-y "564") ("vadh" :is-a "kin-2-2_0_1_v12m_k12nadh_k12aca" :geometry-x "404" :geometry-y "373") ("vak" :is-a "kin-2-1_0_1_k24f_k24r" :geometry-x "653" :geometry-y "677") ("vald" :is-a "kin-1-2_0_1_k6dhap_k6eq_ratio6_k6gap_k6igapf7a" :geometry-x "314" :geometry-y "607") ("vconsum" :is-a "kin-1-1_0_1_k23" :geometry-x "545" :geometry-y "634") ("vgapdh" :is-a "kin-2-2_0_1_k8nad_k8bpg_k8nadh_v8r_k8eq155b" :geometry-x "374" :geometry-y "455") ("vhk" :is-a "kin-2-2_0_1__k3atp_k3glc1949" :geometry-x "499" :geometry-y "757") ("vlpglyc" :is-a "kin-2-2_0_1_ap_k15inadh_k15inad_k15nadhifc" :geometry-x "354" :geometry-y "394") ("vlppep" :is-a "kin-2-2_0_1_k9f_k9r" :geometry-x "562" :geometry-y "561") ("vpdc" :is-a "kin-1-1_0_1_v11m_k11" :geometry-x "659" :geometry-y "432") ("vpfk" :is-a "kin-2-2_1_1_v5m_k5_kappa5" :geometry-x "560" :geometry-y "730") ("vpgi" :is-a "kin-1-1_0_1_k4f6p_v4r_k4eqnpd" :geometry-x "480" :geometry-y "803") ("vpk" :is-a "kin-2-2_0_1_v10m_k10pep_k10adp" :geometry-x "626" :geometry-y "574") ("vstorage" :is-a "kin-2-1_0_1_k22" :geometry-x "505" :geometry-y "694") ("vtim" :is-a "kin-1-1_0_1__k7gap_v7r_k7eq199b" :geometry-x "324" :geometry-y "554")) :links (("cl_amp" :terminals ("ca_amp.co" "vpfk.t_m1")) ("fl_aca" :terminals ("aca.cf" "vpdc.t_p1" "vadh.t_r2" "fa_aca.in") :nodes (("667" "315")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_adp" :terminals ("adp.cf" "vhk.t_p2" "vpfk.t_p2" "vlppep.t_r2" "vpk.t_r1" "vstorage.t_p1" "vconsum.t_p1" "vak.t_p1") :nodes (("592" "688")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil))) ("fl_amp" :terminals ("amp.cf" "ca_amp.cf" "vak.t_r2") :nodes (("779" "749")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_atp" :terminals ("atp.cf" "vhk.t_r1" "vpfk.t_r2" "vlppep.t_p2" "vpk.t_p2" "vstorage.t_r1" "vconsum.t_r1" "vak.t_r1") :nodes (("582" "661")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil))) ("fl_bpg" :terminals ("bpg.cf" "vgapdh.t_p2" "vlppep.t_r1") :nodes (("492" "443")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_dhap" :terminals ("dhap.cf" "vald.t_p2" "vtim.t_r1" "vlpglyc.t_r1") :nodes (("260" "508")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_etoh" :terminals ("etoh.cf" "vadh.t_p2" "fa_etoh.in") :nodes (("166" "335")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_f6p" :terminals ("f6p.cf" "vpgi.t_p1" "vpfk.t_r1") :nodes (("568" "853")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_fbp" :terminals ("fbp.cf" "vpfk.t_p1" "vald.t_r1") :nodes (("336" "715")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_g6p" :terminals ("g6p.cf" "fa_g6p.in" "vhk.t_p1" "vpgi.t_r1" "vstorage.t_r2") :nodes (("406" "824")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil))) ("fl_gap" :terminals ("gap.cf" "vald.t_p1" "vtim.t_p1" "vgapdh.t_r1") :nodes (("267" "560")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_glc" :terminals ("glc.cf" "fa_glc.in" "vhk.t_r2") :nodes (("451" "990")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_glyc" :terminals ("glyc.cf" "vlpglyc.t_p1" "fa_glyc.in") :nodes (("395" "172")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_nad" :terminals ("nad.cf" "vgapdh.t_r2" "vadh.t_p1" "vlpglyc.t_p2") :nodes (("359" "348")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_nadh" :terminals ("nadh.cf" "vgapdh.t_p1" "vadh.t_r1" "vlpglyc.t_r2") :nodes (("313" "364")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_pep" :terminals ("pep.cf" "vlppep.t_p1" "vpk.t_r2") :nodes (("644" "504")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_pyr" :terminals ("pyr.cf" "vpk.t_p1" "vpdc.t_r1") :nodes (("735" "485")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("vl_cytosol" :terminals ("va.out" "vhk.t_c1" "vpgi.t_c1" "vpfk.t_c1" "vald.t_c1" "vtim.t_c1" "vgapdh.t_c1" "vlppep.t_c1" "vpk.t_c1" "vpdc.t_c1" "vadh.t_c1" "vlpglyc.t_c1" "vstorage.t_c1" "vconsum.t_c1" "vak.t_c1") :nodes (("485" "608")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil) ("8" "-1" nil) ("9" "-1" nil) ("10" "-1" nil) ("11" "-1" nil) ("12" "-1" nil) ("13" "-1" nil) ("14" "-1" nil))))) (define-module :class "hynne2001_glycolysis-extracellular" :super-classes ("compartment") :rdf-annotation ((:name "BQB_IS_VERSION_OF" :resources ("urn:miriam:obo.go:GO%3A0005576"))) :geometry-width "850" :geometry-height "741" :parameters (("acax.c" :label "Extracellular acetaldehyde" :model-name "ACAX") ("acax.n" :value "1.28836d0*v") ("cnx.c" :label "Extracellular cyanide" :model-name "CNX") ("cnx.n" :value "5.20358d0*v") ("cnx0.c" :label "Mixed flow cyanide " :model-name "CNX0") ("cnx0.n" :value "5.6d0*v") ("etohx.c" :label "Extracellular ethanol" :model-name "EtOHX") ("etohx.n" :value "16.4514d0*v") ("glcx.c" :label "Extracellular glucose" :model-name "GlcX") ("glcx.n" :value "6.7d0*v") ("glcx0.c" :label "Mixed flow glucose" :model-name "GlcX0") ("glcx0.n" :value "24.0d0*v") ("glycx.c" :label "Extracellular glycerol" :model-name "GlycX") ("glycx.n" :value "1.68478d0*v") ("p.c" :model-name "P") ("p.n" :value "0.0d0") ("v" :value "1.0d0" :model-name "extracellular") ("vdifaca.gamma_r1" :value "-59.0d0") ("vdifaca.k18" :value "24.7d0") ("vdifaca.r" :label "Acetaldehyde out" :value "k18/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)" :model-name "vdifACA") ("vdifaca.yvol" :value "59.0d0") ("vdifetoh.gamma_r1" :value "-59.0d0") ("vdifetoh.k13" :value "16.72d0") ("vdifetoh.r" :label "Ethanol out" :value "k13/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)" :model-name "vdifEtOH") ("vdifetoh.yvol" :value "59.0d0") ("vdifglyc.gamma_r1" :value "-59.0d0") ("vdifglyc.k16" :value "1.9d0") ("vdifglyc.r" :label "Glycerol out" :value "k16/yvol*(t_c2.v*t_r1.c-t_c1.v*t_p1.c)" :model-name "vdifGlyc") ("vdifglyc.yvol" :value "59.0d0") ("vglctrans.gamma_p1" :value "59.0d0") ("vglctrans.k2glc" :value "1.7d0") ("vglctrans.k2ig6p" :value "1.2d0") ("vglctrans.k2iig6p" :value "7.2d0") ("vglctrans.p2" :value "1.0d0") ("vglctrans.r" :label "Glucose uptake" :value "t_c2.v*v2f/yvol*t_r1.c/k2glc/(1+t_r1.c/k2glc+(t_r1.c/k2glc*p2+1)/(t_p1.c/k2glc*p2+1)*(1+t_p1.c/k2glc+t_m1.c/k2ig6p+t_p1.c*t_m1.c/(k2glc*k2iig6p)))-t_c1.v*v2r/yvol*t_p1.c/k2glc/(1+t_p1.c/k2glc+(t_p1.c/k2glc*p2+1)/(t_r1.c/k2glc*p2+1)*(1+t_r1.c/k2glc)+t_m1.c/k2ig6p+t_p1.c*t_m1.c/(k2glc*k2iig6p))" :model-name "vGlcTrans") ("vglctrans.v2f" :value "1014.96d0") ("vglctrans.v2r" :value "1014.96d0") ("vglctrans.yvol" :value "59.0d0") ("vincn.k0" :value "0.048d0") ("vincn.r" :label "Cyanide flow" :value "t_c1.v*k0*(t_r1.c-t_p1.c)" :model-name "vinCN") ("vinglc.k0" :value "0.048d0") ("vinglc.r" :label "Glucose Mixed flow to extracellular medium" :value "t_c1.v*k0*(t_r1.c-t_p1.c)" :model-name "vinGlc") ("vlacto.k20" :value "0.00283828d0") ("vlacto.r" :label "Cyanide-Acetaldehyde flow" :value "t_c1.v*k20*t_r2.c*t_r1.c" :model-name "vlacto") ("voutaca.k0" :value "0.048d0") ("voutaca.r" :label "Acetaldehyde flow" :value "t_c1.v*k0*t_r1.c" :model-name "voutACA") ("voutetoh.k0" :value "0.048d0") ("voutetoh.r" :label "Ethanol flow" :value "t_c1.v*k0*t_r1.c" :model-name "voutEtOH") ("voutglyc.k0" :value "0.048d0") ("voutglyc.r" :label "Glycerol flow" :value "t_c1.v*k0*t_r1.c" :model-name "voutGlyc")) :modules (("acax" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A15343" "urn:miriam:kegg.compound:C00084"))) :geometry-x "529" :geometry-y "160") ("ca_g6p" :is-a "cf2co" :geometry-x "138" :geometry-y "427") ("cnx" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17514" "urn:miriam:kegg.compound:C00177"))) :geometry-x "762" :geometry-y "312") ("cnx0" :is-a "species" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17514" "urn:miriam:kegg.compound:C00177"))) :geometry-x "704" :geometry-y "475") ("cytosol" :is-a "hynne2001_glycolysis-cytosol" :geometry-x "152" :geometry-y "303") ("etohx" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A16236" "urn:miriam:kegg.compound:C000469"))) :geometry-x "295" :geometry-y "88") ("glcx" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17234" "urn:miriam:kegg.compound:C00293"))) :geometry-x "135" :geometry-y "615") ("glcx0" :is-a "species" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17234" "urn:miriam:kegg.compound:C00293"))) :geometry-x "253" :geometry-y "658") ("glycx" :is-a "speciesv" :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.chebi:CHEBI%3A17754" "urn:miriam:kegg.compound:C00116"))) :geometry-x "485" :geometry-y "633") ("p" :is-a "species" :geometry-x "608" :geometry-y "348") ("va" :is-a "adapter-volume-pop" :geometry-x "407" :geometry-y "459") ("vdifaca" :is-a "kin-1-1_0_2_k18_yvol" :geometry-x "340" :geometry-y "342") ("vdifetoh" :is-a "kin-1-1_0_2_k13_yvol" :geometry-x "285" :geometry-y "258") ("vdifglyc" :is-a "kin-1-1_0_2_k16_yvol" :geometry-x "337" :geometry-y "440") ("vglctrans" :is-a "kin-1-1_1_2_2glc_p2_k2ig6p_k2iig6p_v2r1c7f" :geometry-x "235" :geometry-y "444") ("vincn" :is-a "kin-1-1_0_1_k0" :geometry-x "620" :geometry-y "423") ("vinglc" :is-a "kin-1-1_0_1_k0" :geometry-x "262" :geometry-y "565") ("vlacto" :is-a "kin-2-1_0_1_k20" :geometry-x "537" :geometry-y "311") ("voutaca" :is-a "kin-1-1_0_1_k0" :geometry-x "456" :geometry-y "322") ("voutetoh" :is-a "kin-1-1_0_1_k0" :geometry-x "396" :geometry-y "279") ("voutglyc" :is-a "kin-1-1_0_1_k0" :geometry-x "467" :geometry-y "450")) :links (("cl_g6p" :terminals ("ca_g6p.co" "vglctrans.t_m1")) ("fl_aca" :terminals ("cytosol.t_aca" "vdifaca.t_r1")) ("fl_acax" :terminals ("acax.cf" "vdifaca.t_p1" "voutaca.t_r1" "vlacto.t_r2") :nodes (("467" "260")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil))) ("fl_cnx" :terminals ("cnx.cf" "vlacto.t_r1" "vincn.t_p1") :nodes (("662" "338")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_cnx0" :terminals ("cnx0.cf" "vincn.t_r1")) ("fl_etoh" :terminals ("cytosol.t_etoh" "vdifetoh.t_r1")) ("fl_etohx" :terminals ("etohx.cf" "vdifetoh.t_p1" "voutetoh.t_r1") :nodes (("301" "180")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_g6p" :terminals ("cytosol.t_g6p" "ca_g6p.cf")) ("fl_glc" :terminals ("cytosol.t_glc" "vglctrans.t_p1")) ("fl_glcx" :terminals ("glcx.cf" "vinglc.t_p1" "vglctrans.t_r1") :nodes (("187" "553")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_glcx0" :terminals ("glcx0.cf" "vinglc.t_r1")) ("fl_glyc" :terminals ("cytosol.t_glyc" "vdifglyc.t_r1")) ("fl_glycx" :terminals ("glycx.cf" "vdifglyc.t_p1" "voutglyc.t_r1") :nodes (("431" "539")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil))) ("fl_p" :terminals ("p.cf" "voutetoh.t_p1" "voutglyc.t_p1" "voutaca.t_p1" "vlacto.t_p1") :nodes (("510" "355")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil))) ("vl_cytosol" :terminals ("cytosol.out" "vglctrans.t_c1" "vdifetoh.t_c2" "vdifglyc.t_c2" "vdifaca.t_c2") :nodes (("263" "353")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil))) ("vl_extracellular" :terminals ("va.out" "vinglc.t_c1" "vglctrans.t_c2" "vdifetoh.t_c1" "voutetoh.t_c1" "vdifglyc.t_c1" "voutglyc.t_c1" "vdifaca.t_c1" "voutaca.t_c1" "vlacto.t_c1" "vincn.t_c1") :nodes (("391" "403")) :edges (("0" "-1" nil) ("1" "-1" nil) ("2" "-1" nil) ("3" "-1" nil) ("4" "-1" nil) ("5" "-1" nil) ("6" "-1" nil) ("7" "-1" nil) ("8" "-1" nil) ("9" "-1" nil) ("10" "-1" nil))))) (define-module :class "hynne2001_glycolysis" :super-classes ("sbml-model") :documentation "

The model reproduces Fig 6 of the paper. The stoichiometry and rate of reactions involving uptake of metabolites from extracellular medium have been changed corresponding to Yvol (ratio of extracellular volume to cytosolic volume) mentioned in the publication. The extracellular and cytosolic compartments have been set to 1. Concentration of extracellular glucose, GlcX, is set to 6.7 according to the equation for cellular glucose uptake rate in Table 7 of the paper. The model was successfully tested on MathSBML and Jarnac

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SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS

Run this model online at http://jjj.biochem.sun.ac.za

To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online, Bioinformatics, 20:2143-2144

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This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.

For more information see the terms of use.

To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

" :rdf-annotation ((:name "BQM_IS" :resources ("urn:miriam:biomodels.db:BIOMD0000000061")) (:name "BQM_IS_DESCRIBED_BY" :resources ("urn:miriam:pubmed:11744196")) (:name "BQB_IS_HOMOLOG_TO" :resources ("urn:miriam:reactome:REACT_1383")) (:name "BQB_IS_VERSION_OF" :resources ("urn:miriam:obo.go:GO%3A0006096")) (:name "BQB_IS" :resources ("urn:miriam:taxonomy:4932" "urn:miriam:kegg.pathway:sce00010"))) :geometry-width "290" :geometry-height "286" :modules (("extracellular" :is-a "hynne2001_glycolysis-extracellular" :geometry-x "140" :geometry-y "147")))