Model : diauxic_top_flat
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-17 21:17
Modified: 2017-03-17 21:17
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type | FunctionDefinitions [2] | name | math | sbo | cvterm |
---|---|---|---|---|---|
FunctionDefinition | bounds__max | minimum of arguments | |||
FunctionDefinition | bounds__min | maximum of arguments |
type | UnitDefinitions [18] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | h | ||||
UnitDefinition | g | ||||
UnitDefinition | m | ||||
UnitDefinition | m2 | ||||
UnitDefinition | l | ||||
UnitDefinition | mmol | ||||
UnitDefinition | per_h | ||||
UnitDefinition | mmol_per_h | ||||
UnitDefinition | mmol_per_l | ||||
UnitDefinition | l_per_mmol | ||||
UnitDefinition | g_per_l | ||||
UnitDefinition | g_per_mmol | ||||
UnitDefinition | fba__per_h | ||||
UnitDefinition | fba__l_per_mmol | ||||
UnitDefinition | bounds__per_h | ||||
UnitDefinition | bounds__l_per_mmol | ||||
UnitDefinition | update__per_h | ||||
UnitDefinition | update__l_per_mmol |
type | Compartments [2] | name | size | constant | spatial dimensions | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | bioreactor | bioreactor | 1.0 | T | 3 | l | |||
Compartment | fba__bioreactor | bioreactor | 1.0 | T | 3 | l |
type | Species [9] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | Glcxt | glucose |
bioreactor | F | F | 10.8 | mmol | ||||
Species | Ac | acetate |
bioreactor | F | F | 0.4 | mmol | ||||
Species | O2 | oxygen |
bioreactor | F | F | 0.21 | mmol | ||||
Species | X | biomass |
bioreactor | F | F | 0.001 | mmol | ||||
Species | dummy_S | dummy_S |
bioreactor | F | F | 0.0 | mmol | ||||
Species | fba__Glcxt | glucose |
fba__bioreactor | F | F | 10.8 | mmol | ||||
Species | fba__Ac | acetate |
fba__bioreactor | F | F | 0.4 | mmol | ||||
Species | fba__O2 | oxygen |
fba__bioreactor | F | F | 0.21 | mmol | ||||
Species | fba__X | biomass |
fba__bioreactor | F | F | 0.001 | mmol |
type | Parameters [27] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt | fba timestep | 0.01 | h | T | |||
Parameter | Y | biomass [g_per_l] | 1.0 | g_per_l | F | |||
Parameter | O2_ref | O2 reference | 0.21 | mmol_per_l | T | |||
Parameter | kLa | O2 mass transfer | 7.5 | per_h | T | |||
Parameter | EX_Glcxt | 1.0 | mmol_per_h | F | ||||
Parameter | EX_Ac | 1.0 | mmol_per_h | F | ||||
Parameter | EX_O2 | 1.0 | mmol_per_h | F | ||||
Parameter | EX_X | 1.0 | mmol_per_h | F | ||||
Parameter | lb_EX_Ac | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Ac | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_Glcxt | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_Glcxt | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_O2 | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_O2 | 1000.0 | mmol_per_h | F | ||||
Parameter | lb_EX_X | -1000.0 | mmol_per_h | F | ||||
Parameter | ub_EX_X | 1000.0 | mmol_per_h | F | ||||
Parameter | fba__zero | zero bound | 0.0 | mmol_per_h | T | |||
Parameter | fba__lb_default | default lower bound | -1000.0 | mmol_per_h | T | |||
Parameter | fba__ub_default | default upper bound | 1000.0 | mmol_per_h | T | |||
Parameter | bounds__zero | zero bound | 0.0 | mmol_per_h | T | |||
Parameter | bounds__lb_default | default lower bound | -1000.0 | mmol_per_h | T | |||
Parameter | bounds__ub_default | default upper bound | 1000.0 | mmol_per_h | T | |||
Parameter | bounds__lb_kin_EX_Glcxt | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__lb_kin_EX_O2 | -1000.0 | mmol_per_h | F | ||||
Parameter | bounds__Vmax_EX_O2 | 15.0 | mmol_per_h | T | ||||
Parameter | bounds__Vmax_EX_Glcxt | 10.0 | mmol_per_h | T | ||||
Parameter | bounds__Km_EX_Glcxt | Km_vGlcxt | 0.015 | mmol_per_l | T |
type | Rules [11] | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|
Rule | EX_Glcxt | = | ||||
Rule | EX_Ac | = | ||||
Rule | EX_O2 | = | ||||
Rule | EX_X | = | ||||
Rule | Y | = | ||||
Rule | bounds__lb_kin_EX_Glcxt | = | ||||
Rule | bounds__lb_kin_EX_O2 | = | ||||
Rule | lb_EX_Ac | = | ||||
Rule | lb_EX_Glcxt | = | ||||
Rule | lb_EX_O2 | = | ||||
Rule | lb_EX_X | = |
type | Reactions [13] | name | equation | modifiers | formula | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | vO2_transfer | oxygen transfer | ⇆ | ⇆ O2 | |||||
Reaction | dummy_EX_O2 | ➞ | fba__O2 ➞ | ||||||
Reaction | dummy_EX_Glcxt | ➞ | fba__Glcxt ➞ | ||||||
Reaction | dummy_EX_Ac | ⇆ | fba__Ac ⇆ | ||||||
Reaction | dummy_EX_X | ➞ | fba__X ➞ | ||||||
Reaction | fba__v1 | v1 (39.43 Ac + 35 O2 -> X) | ➞ | 39.43 fba__Ac + 35.0 fba__O2 ➞ fba__X | |||||
Reaction | fba__v2 | v2 (9.46 Glcxt + 12.92 O2 -> X) | ➞ | 9.46 fba__Glcxt + 12.92 fba__O2 ➞ fba__X | |||||
Reaction | fba__v3 | v3 (9.84 Glcxt + 12.73 O2 -> 1.24 Ac + X) | ➞ | 9.84 fba__Glcxt + 12.73 fba__O2 ➞ fba__X + 1.24 fba__Ac | |||||
Reaction | fba__v4 | v4 (19.23 Glcxt -> 12.12 Ac + X) | ➞ | 19.23 fba__Glcxt ➞ fba__X + 12.12 fba__Ac | |||||
Reaction | update__update_Glcxt | ⇆ | Glcxt ⇆ |
X |
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Reaction | update__update_Ac | ⇆ | Ac ⇆ |
X |
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Reaction | update__update_O2 | ⇆ | O2 ⇆ |
X |
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Reaction | update__update_X | ⇆ | X ⇆ |
X |