(define-module :class "library" :super-classes ("module") :documentation "Superclass for all library elements.") (define-module :class "sbml-rules" :super-classes ("module") :documentation "Rules for SBML models.") (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 "sbml-parameter" :super-classes ("variable") :documentation "`Parameters' (can be real-parameters, helps, states read from sbml-files") (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-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-module :class "teusink2000_glycolysis-rules" :super-classes ("sbml-rules") :geometry-width "585" :geometry-height "200" :terminals (("t_adp" :is-a "tsig" :geometry-side "top" :geometry-position "0.5") ("t_amp" :is-a "tsig" :geometry-side "top" :geometry-position "0.8333333") ("t_atp" :is-a "tsig" :geometry-side "top" :geometry-position "0.6666667") ("t_p" :is-a "tsig" :geometry-side "top" :geometry-position "0.33333334") ("t_sum_p" :is-a "tsig" :geometry-side "top" :geometry-position "0.16666667")) :equations (("adp" :relation "0.0d0 == t_adp.c-(t_sum_p.c-(t_p.c ^ 2*(1-4*root.keqak)+2*t_sum_p.c*t_p.c*(4*root.keqak+-1)+t_sum_p.c ^ 2) ^ 0.5d0)/(1-4*root.keqak)") ("amp" :relation "0.0d0 == t_amp.c-t_sum_p.c+t_atp.c+t_adp.c") ("atp" :relation "0.0d0 == t_atp.c-(t_p.c-t_adp.c)/2"))) (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 "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-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-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-module :class "kin-1-1_0_tglco_keqglt_kmgltglci34f" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :variables (("keqglt" :is-a "kinetic-parameter") ("kmgltglci" :is-a "kinetic-parameter") ("kmgltglco" :is-a "kinetic-parameter") ("vmglt" :is-a "kinetic-parameter"))) (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 "dyn-adapter" :super-classes ("library") :documentation "Superclass containing adapters. Useful for instance for propagating terminals already connected to other elements.") (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 "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-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_ktrehalose" :super-classes ("s-2-1" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("ktrehalose" :is-a "kinetic-parameter"))) (define-module :class "s-3-2" :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 "0.25") ("t_r2" :is-a "tflux" :geometry-side "left" :geometry-position "0.5") ("t_r3" :is-a "tflux" :geometry-side "left" :geometry-position "0.75")) :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") ("gamma_r3" :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") ("e_r3" :relation "t_r3.r == gamma_r3*r"))) (define-module :class "kin-3-2_0_1_ksucc" :super-classes ("s-3-2" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("ksucc" :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_2_1_kpep_kmpykadp_keqpyk_kmpykpyr_kmpykatpos3" :super-classes ("s-1-2" "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 "0.33333334") ("t_m2" :is-a "tsig" :geometry-side "top" :geometry-position "0.6666667")) :variables (("keqpyk" :is-a "kinetic-parameter") ("kmpykadp" :is-a "kinetic-parameter") ("kmpykatp" :is-a "kinetic-parameter") ("kmpykpep" :is-a "kinetic-parameter") ("kmpykpyr" :is-a "kinetic-parameter") ("vmpyk" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_mp3g_keqpgm_kmpgmp2g6me" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqpgm" :is-a "kinetic-parameter") ("kmpgmp2g" :is-a "kinetic-parameter") ("kmpgmp3g" :is-a "kinetic-parameter") ("vmpgm" :is-a "kinetic-parameter"))) (define-module :class "kin-1-2_2_1_kp3g_kmpgkatp_keqpgk_kmpgkbpg_kmpgkadp7d8" :super-classes ("s-1-2" "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 "0.33333334") ("t_m2" :is-a "tsig" :geometry-side "top" :geometry-position "0.6666667")) :variables (("keqpgk" :is-a "kinetic-parameter") ("kmpgkadp" :is-a "kinetic-parameter") ("kmpgkatp" :is-a "kinetic-parameter") ("kmpgkbpg" :is-a "kinetic-parameter") ("kmpgkp3g" :is-a "kinetic-parameter") ("vmpgk" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_pgig6p_2_keqpgi_2_kmpgif6p_213yw" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqpgi_2" :is-a "kinetic-parameter") ("kmpgif6p_2" :is-a "kinetic-parameter") ("kmpgig6p_2" :is-a "kinetic-parameter") ("vmpgi_2" :is-a "kinetic-parameter"))) (define-module :class "kin-2-1_3_1_vmpfk" :super-classes ("s-2-1" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5") ("t_m1" :is-a "tsig" :geometry-side "top" :geometry-position "0.25") ("t_m2" :is-a "tsig" :geometry-side "top" :geometry-position "0.5") ("t_m3" :is-a "tsig" :geometry-side "top" :geometry-position "0.75")) :variables (("vmpfk" :is-a "kinetic-parameter"))) (define-module :class "kin-1-2_0_1_vmpdc_npdc_kmpdcpyr" :super-classes ("s-1-2" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("kmpdcpyr" :is-a "kinetic-parameter") ("npdc" :is-a "kinetic-parameter") ("vmpdc" :is-a "kinetic-parameter"))) (define-module :class "kin-2-1_0_1_kglycogen_3" :super-classes ("s-2-1" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("kglycogen_3" :is-a "kinetic-parameter"))) (define-module :class "kin-2-1_2_1_kglci_kmglkatp_keqglk_kmglkg6p_kmglkadpuxj" :super-classes ("s-2-1" "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 "0.33333334") ("t_m2" :is-a "tsig" :geometry-side "top" :geometry-position "0.6666667")) :variables (("keqglk" :is-a "kinetic-parameter") ("kmglkadp" :is-a "kinetic-parameter") ("kmglkatp" :is-a "kinetic-parameter") ("kmglkg6p" :is-a "kinetic-parameter") ("kmglkglci" :is-a "kinetic-parameter") ("vmglk" :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_mgapdhgap_kmgapdhnad_vmgapdhr_kmgapdhbpg_kmgapdhnadh1e35" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("kmgapdhbpg" :is-a "kinetic-parameter") ("kmgapdhgap" :is-a "kinetic-parameter") ("kmgapdhnad" :is-a "kinetic-parameter") ("kmgapdhnadh" :is-a "kinetic-parameter") ("vmgapdhf" :is-a "kinetic-parameter") ("vmgapdhr" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_g3pdhdhap_kmg3pdhnadh_keqg3pdh_kmg3pdhgly_kmg3pdhnad15uq" :super-classes ("s-2-2" "kinetics") :icon "icons/irrev_r" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqg3pdh" :is-a "kinetic-parameter") ("kmg3pdhdhap" :is-a "kinetic-parameter") ("kmg3pdhgly" :is-a "kinetic-parameter") ("kmg3pdhnad" :is-a "kinetic-parameter") ("kmg3pdhnadh" :is-a "kinetic-parameter") ("vmg3pdh" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_op2g_keqeno_kmenopep1e60" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqeno" :is-a "kinetic-parameter") ("kmenop2g" :is-a "kinetic-parameter") ("kmenopep" :is-a "kinetic-parameter") ("vmeno" :is-a "kinetic-parameter"))) (define-module :class "s-1-_" :super-classes ("structure") :terminals (("t_r1" :is-a "tflux" :geometry-side "left" :geometry-position "0.5")) :variables (("gamma_r1" :is-a "stoichiometry" :value "-1.0d0")) :equations (("e_r1" :relation "t_r1.r == gamma_r1*r"))) (define-module :class "kin-1-__1_1_katpase" :super-classes ("s-1-_" "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 (("katpase" :is-a "kinetic-parameter"))) (define-module :class "kin-1-1_0_1_df16p_keqald_kmaldgap_kmalddhap_kmaldgapideg" :super-classes ("s-1-1" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqald" :is-a "kinetic-parameter") ("kmalddhap" :is-a "kinetic-parameter") ("kmaldf16p" :is-a "kinetic-parameter") ("kmaldgap" :is-a "kinetic-parameter") ("kmaldgapi" :is-a "kinetic-parameter") ("vmald" :is-a "kinetic-parameter"))) (define-module :class "kin-2-2_0_1_hnad_kmadhetoh_keqadh_kmadhnad_kmadhnadh_kiadhnadh_kmadhace_kiadhace_kiadhetohcon" :super-classes ("s-2-2" "kinetics") :icon "icons/rev_l" :terminals (("t_c1" :is-a "tvol" :geometry-side "bottom" :geometry-position "0.5")) :variables (("keqadh" :is-a "kinetic-parameter") ("kiadhace" :is-a "kinetic-parameter") ("kiadhetoh" :is-a "kinetic-parameter") ("kiadhnad" :is-a "kinetic-parameter") ("kiadhnadh" :is-a "kinetic-parameter") ("kmadhace" :is-a "kinetic-parameter") ("kmadhetoh" :is-a "kinetic-parameter") ("kmadhnad" :is-a "kinetic-parameter") ("kmadhnadh" :is-a "kinetic-parameter") ("vmadh" :is-a "kinetic-parameter"))) (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 "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 "speciesb" :super-classes ("species") :documentation "Non-constant boundary species, value of c! (not n) is fixed by some external rule. The rule is necessary, n is unused." :icon "icons/speciesb" :parameters (("c" :system-theoretic "state" :value "0") ("n" :system-theoretic "help" :value "c*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 "teusink2000_glycolysis-cytosol" :super-classes ("compartment") :rdf-annotation ((:name "BQB_IS" :resources ("urn:miriam:obo.go:GO%3A0005829"))) :geometry-width "1299" :geometry-height "1194" :parameters (("ace.c" :label "Acetaldehyde" :model-name "ACE") ("ace.n" :value "0.17d0*v") ("bpg.c" :label "1,3-bisphosphoglycerate" :model-name "BPG") ("bpg.n" :value "0.0d0") ("co2.c" :label "CO2" :model-name "CO2") ("co2.n" :value "v") ("etoh.c" :label "Ethanol" :model-name "ETOH") ("etoh.n" :value "50.0d0*v") ("f16p.c" :label "Fructose-1,6 bisphosphate" :model-name "F16P") ("f16p.n" :value "5.51d0*v") ("f26bp.c" :label "F2,6P" :model-name "F26BP") ("f26bp.n" :value "0.02d0*v") ("f6p.c" :label "Fructose 6 Phosphate" :model-name "F6P") ("f6p.n" :value "0.62d0*v") ("g6p.c" :label "Glucose 6 Phosphate" :model-name "G6P") ("g6p.n" :value "2.45d0*v") ("glci.c" :label "Glucose in Cytosol" :model-name "GLCi") ("glci.n" :value "0.087d0*v") ("gly.c" :label "Glycerol" :model-name "GLY") ("gly.n" :value "0.15d0*v") ("glyc.c" :label "Glycogen" :model-name "Glyc") ("glyc.n" :value "0.0d0") ("nad.c" :label "NAD" :model-name "NAD") ("nad.n" :value "1.2d0*v") ("nadh.c" :label "NADH" :model-name "NADH") ("nadh.n" :value "0.39d0*v") ("p.c" :label "High energy phosphates" :model-name "P") ("p.n" :value "6.31d0*v") ("p2g.c" :label "2-phosphoglycerate" :model-name "P2G") ("p2g.n" :value "0.12d0*v") ("p3g.c" :label "3-phosphoglycerate" :model-name "P3G") ("p3g.n" :value "0.9d0*v") ("pep.c" :label "Phosphoenolpyruvate" :model-name "PEP") ("pep.n" :value "0.07d0*v") ("pyr.c" :label "Pyruvate" :model-name "PYR") ("pyr.n" :value "1.85d0*v") ("succ.c" :label "Succinate" :model-name "SUCC") ("succ.n" :value "0.0d0") ("sum_p.c" :label "sum of AXP conc" :model-name "SUM_P") ("sum_p.n" :value "4.1d0*v") ("trh.c" :label "Trehalose" :model-name "Trh") ("trh.n" :value "0.0d0") ("trio.c" :label "Triose-phosphate" :model-name "TRIO") ("trio.n" :value "0.96d0*v") ("v" :value "1.0d0" :model-name "cytosol") ("vadh.keqadh" :value "6.9d-5") ("vadh.kiadhace" :value "1.1d0") ("vadh.kiadhetoh" :value "90.0d0") ("vadh.kiadhnad" :value "0.92d0") ("vadh.kiadhnadh" :value "0.031d0") ("vadh.kmadhace" :value "1.11d0") ("vadh.kmadhetoh" :value "17.0d0") ("vadh.kmadhnad" :value "0.17d0") ("vadh.kmadhnadh" :value "0.11d0") ("vadh.r" :label "Alcohol dehydrogenase" :value "vmadh/(kiadhnad*kmadhetoh)*(t_p1.c*t_p2.c-t_r2.c*t_r1.c/keqadh)/(1+t_p1.c/kiadhnad+kmadhnad*t_p2.c/(kiadhnad*kmadhetoh)+kmadhnadh*t_r1.c/(kiadhnadh*kmadhace)+t_r2.c/kiadhnadh+t_p1.c*t_p2.c/(kiadhnad*kmadhetoh)+kmadhnadh*t_p1.c*t_r1.c/(kiadhnad*kiadhnadh*kmadhace)+kmadhnad*t_p2.c*t_r2.c/(kiadhnad*kmadhetoh*kiadhnadh)+t_r2.c*t_r1.c/(kiadhnadh*kmadhace)+t_p1.c*t_p2.c*t_r1.c/(kiadhnad*kmadhetoh*kiadhace)+t_p2.c*t_r2.c*t_r1.c/(kiadhetoh*kiadhnadh*kmadhace))*(-t_c1.v)" :model-name "vADH") ("vadh.vmadh" :value "810.0d0") ("vald.gamma_p1" :value "2.0d0") ("vald.keqald" :value "0.069d0") ("vald.kmalddhap" :value "2.4d0") ("vald.kmaldf16p" :value "0.3d0") ("vald.kmaldgap" :value "2.0d0") ("vald.kmaldgapi" :value "10.0d0") ("vald.r" :label "Aldolase" :value "t_c1.v*vmald/kmaldf16p*(t_r1.c-root.keqtpi/(1+root.keqtpi)*t_p1.c/(1+root.keqtpi)*t_p1.c/keqald)/(1+t_r1.c/kmaldf16p+root.keqtpi/(1+root.keqtpi)*t_p1.c/kmaldgap+(1/(1+root.keqtpi))*t_p1.c/kmalddhap+root.keqtpi/(1+root.keqtpi)*t_p1.c/(1+root.keqtpi)*t_p1.c/(kmaldgap*kmalddhap)+root.keqtpi/(1+root.keqtpi)*t_r1.c*t_p1.c/(kmaldgapi*kmaldf16p))" :model-name "vALD") ("vald.vmald" :value "322.258d0") ("vatp.katpase" :value "33.7d0") ("vatp.r" :label "ATPase activity" :value "t_c1.v*katpase*t_m1.c" :model-name "vATP") ("veno.keqeno" :value "6.7d0") ("veno.kmenop2g" :value "0.04d0") ("veno.kmenopep" :value "0.5d0") ("veno.r" :label "Enolase" :value "t_c1.v*vmeno/kmenop2g*(t_r1.c-t_p1.c/keqeno)/(1+t_r1.c/kmenop2g+t_p1.c/kmenopep)" :model-name "vENO") ("veno.vmeno" :value "365.806d0") ("vg3pdh.keqg3pdh" :value "4300.0d0") ("vg3pdh.kmg3pdhdhap" :value "0.4d0") ("vg3pdh.kmg3pdhgly" :value "1.0d0") ("vg3pdh.kmg3pdhnad" :value "0.93d0") ("vg3pdh.kmg3pdhnadh" :value "0.023d0") ("vg3pdh.r" :label "Glycerol 3-phosphate dehydrogenase" :value "t_c1.v*vmg3pdh/(kmg3pdhdhap*kmg3pdhnadh)*((1/(1+root.keqtpi))*t_r1.c*t_r2.c-t_p2.c*t_p1.c/keqg3pdh)/((1+(1/(1+root.keqtpi))*t_r1.c/kmg3pdhdhap+t_p2.c/kmg3pdhgly)*(1+t_r2.c/kmg3pdhnadh+t_p1.c/kmg3pdhnad))" :model-name "vG3PDH") ("vg3pdh.reversible" :value "0") ("vg3pdh.vmg3pdh" :value "70.15d0") ("vgapdh.kmgapdhbpg" :value "0.0098d0") ("vgapdh.kmgapdhgap" :value "0.21d0") ("vgapdh.kmgapdhnad" :value "0.09d0") ("vgapdh.kmgapdhnadh" :value "0.06d0") ("vgapdh.r" :label "Glyceraldehyde 3-phosphate dehydrogenase" :value "t_c1.v*(root.keqtpi/(1+root.keqtpi)*vmgapdhf*t_r1.c*t_r2.c/(kmgapdhgap*kmgapdhnad)-vmgapdhr*t_p1.c*t_p2.c/(kmgapdhbpg*kmgapdhnadh))/((1+root.keqtpi/(1+root.keqtpi)*t_r1.c/kmgapdhgap+t_p1.c/kmgapdhbpg)*(1+t_r2.c/kmgapdhnad+t_p2.c/kmgapdhnadh))" :model-name "vGAPDH") ("vgapdh.vmgapdhf" :value "1184.52d0") ("vgapdh.vmgapdhr" :value "6549.8d0") ("vglk.keqglk" :value "3800.0d0") ("vglk.kmglkadp" :value "0.23d0") ("vglk.kmglkatp" :value 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"t_c1.v*vmpfk*root.gr*t_r1.c/root.kmpfkf6p*t_m2.c/root.kmpfkatp*(1+t_r1.c/root.kmpfkf6p+t_m2.c/root.kmpfkatp+t_r1.c/root.kmpfkf6p*root.gr*t_m2.c/root.kmpfkatp)/((1+t_r1.c/root.kmpfkf6p+t_m2.c/root.kmpfkatp+t_r1.c/root.kmpfkf6p*root.gr*t_m2.c/root.kmpfkatp) ^ 2+root.lzero*((1+t_m2.c/root.kipfkatp*root.cipfkatp)/(1+t_m2.c/root.kipfkatp)) ^ 2*((1+t_m1.c/root.kpfkamp*root.cpfkamp)/(1+t_m1.c/root.kpfkamp)) ^ 2*((1+root.cpfkf26bp*t_m3.c/root.kpfkf26bp+root.cpfkf16bp*t_p1.c/root.kpfkf16bp)/(1+t_m3.c/root.kpfkf26bp+t_p1.c/root.kpfkf16bp)) ^ 2*(1+t_m2.c/root.kmpfkatp*root.cpfkatp) ^ 2)" :model-name "vPFK") ("vpfk.reversible" :value "0") ("vpfk.vmpfk" :value "182.903d0") ("vpgi.keqpgi_2" :value "0.314d0") ("vpgi.kmpgif6p_2" :value "0.3d0") ("vpgi.kmpgig6p_2" :value "1.4d0") ("vpgi.r" :label "Glucose-6-phosphate isomerase" :value "t_c1.v*vmpgi_2/kmpgig6p_2*(t_r1.c-t_p1.c/keqpgi_2)/(1+t_r1.c/kmpgig6p_2+t_p1.c/kmpgif6p_2)" :model-name "vPGI") ("vpgi.vmpgi_2" :value "339.677d0") ("vpgk.keqpgk" :value "3200.0d0") ("vpgk.kmpgkadp" :value "0.2d0") ("vpgk.kmpgkatp" :value "0.3d0") ("vpgk.kmpgkbpg" :value "0.003d0") ("vpgk.kmpgkp3g" :value "0.53d0") ("vpgk.r" :label "Phosphoglycerate kinase" :value "t_c1.v*vmpgk/(kmpgkp3g*kmpgkatp)*(keqpgk*t_r1.c*t_m2.c-t_p1.c*t_m1.c)/((1+t_r1.c/kmpgkbpg+t_p1.c/kmpgkp3g)*(1+t_m1.c/kmpgkatp+t_m2.c/kmpgkadp))" :model-name "vPGK") ("vpgk.vmpgk" :value "1306.45d0") ("vpgm.keqpgm" :value "0.19d0") ("vpgm.kmpgmp2g" :value "0.08d0") ("vpgm.kmpgmp3g" :value "1.2d0") ("vpgm.r" :label "Phosphoglycerate mutase" :value "t_c1.v*vmpgm/kmpgmp3g*(t_r1.c-t_p1.c/keqpgm)/(1+t_r1.c/kmpgmp3g+t_p1.c/kmpgmp2g)" :model-name "vPGM") ("vpgm.vmpgm" :value "2525.81d0") ("vpyk.keqpyk" :value "6500.0d0") ("vpyk.kmpykadp" :value "0.53d0") ("vpyk.kmpykatp" :value "1.5d0") ("vpyk.kmpykpep" :value "0.14d0") ("vpyk.kmpykpyr" :value "21.0d0") ("vpyk.r" :label "Pyruvate kinase" :value 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Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

Teusink,B et al.: Eur J Biochem 2000 Sep;267(17):5313-29.

The model reproduces the steady-state fluxes and metabolite concentrations of the branched model as given in Table 4 of the paper. It is derived from the model on JWS online, but has the ATP consumption in the succinate branch with the same stoichiometrie as in the publication. The model was successfully tested on copasi v.4.4(build 26).

For Vmax values, please note that there is a conversion factor of approx. 270 to convert from U/mg-protein as shown in Table 1 of the paper to mmol/(min*L_cytosol). The equilibrium constant for the ADH reaction in the paper is given for the reverse reaction (Keq = 1.45*10 4). The value used in this model is for the forward reaction: 1/Keq = 6.9*10 -5 .

Vmax parameters values used (in [mM/min] except VmGLT):
VmGLT 97.264 mmol/min
VmGLK 226.45
VmPGI 339.667
VmPFK 182.903
VmALD 322.258
VmGAPDH_f 1184.52
VmGAPDH_r 6549.68
VmPGK 1306.45
VmPGM 2525.81
VmENO 365.806
VmPYK 1088.71
VmPDC 174.194
VmG3PDH 70.15
The result of the G6P steady state concentration (marked in red) differs slightly from the one given in table 4. of the publication

Results for steady state:
orig. article this model
Fluxes[mM/min] 
Glucose  88  88 
Ethanol  129  129 
Glycogen  6  6 
Trehalose  4.8  4.8  (G6P flux through trehalose branch)
Glycerol  18.2  18.2 
Succinate  3.6  3.6 
Conc.[mM] 
G6P  1.07  1.03 
F6P  0.11  0.11 
F1,6P  0.6  0.6 
DHAP  0.74  0.74 
3PGA  0.36  0.36 
2PGA  0.04  0.04 
PEP  0.07  0.07 
PYR  8.52  8.52 
AcAld  0.17  0.17 
ATP  2.51  2.51 
ADP  1.29  1.29 
AMP  0.3  0.3 
NAD  1.55  1.55 
NADH  0.04  0.04 
Authors of the publication also mentioned a few misprints in the original article:

in the kinetic law for ADH:

  1. the species a should denote NAD and b Ethanol
  2. the last term in the equation should read bpq/( K ibK iqK p )
in the kinetic law for PFK:
  1. R = 1 + λ 1 + λ 2 + g r λ 1 λ 2
  2. equation L should read: L = L0*(..) 2*(..) 2*(..) 2 not L = L0*(..) 2*(..) 2*(..)
To make the model easier to curate, the species ATP, ADP and AMP were added. These are calculated via assignment rules from the active phosphate species, P, and the sum of all AXP, SUM_P.

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.

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