Model : toy_top
CreatorMatthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-17 16:49
Modified: 2017-03-17 16:49
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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 [9] | name | units | sbo | cvterm |
---|---|---|---|---|---|
UnitDefinition | s | ||||
UnitDefinition | kg | ||||
UnitDefinition | m | ||||
UnitDefinition | m2 | ||||
UnitDefinition | m3 | ||||
UnitDefinition | mM | ||||
UnitDefinition | per_s | ||||
UnitDefinition | item_per_s | ||||
UnitDefinition | item_per_m3 |
type | Compartments [5] | name | size | constant | spatial dimensions | unit | derived unit | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|
Compartment | extern | external compartment | 1.0 | T | 3 | m3 | |||
Compartment | cell | cell | 1.0 | T | 3 | m3 | |||
Compartment | fba__extern | external compartment | 1.0 | T | 3 | m3 | |||
Compartment | fba__cell | cell | 1.0 | T | 3 | m3 | |||
Compartment | fba__membrane | membrane | 1.0 | T | 2 | m2 |
type | Species [8] | name | compartment | boundary condition | constant | initial amount | initial concentration | substance units | derived units | sbo | cvterm |
---|---|---|---|---|---|---|---|---|---|---|---|
Species | dummy_S | extern | F | F | 0.0 | item | |||||
Species | A | extern | F | F | 0.0 | item | |||||
Species | C | extern | F | F | 0.0 | item | |||||
Species | D | extern | F | F | 0.0 | item | |||||
Species | fba__A | A |
fba__extern | F | F | 10.0 | item | ||||
Species | fba__C | C |
fba__extern | F | F | 0.0 | item | ||||
Species | fba__B1 | B1 |
fba__cell | F | F | 0.0 | item | ||||
Species | fba__B2 | B2 |
fba__cell | F | F | 0.0 | item |
type | Parameters [14] | name | value | unit | derived unit | constant | sbo | cvterm |
---|---|---|---|---|---|---|---|---|
Parameter | dt | 0.1 | s | F | ||||
Parameter | EX_A | 1.0 | item_per_s | F | ||||
Parameter | EX_C | 1.0 | item_per_s | F | ||||
Parameter | k_R4 | k R4 | 0.1 | per_s | T | |||
Parameter | lb_EX_A | -1000.0 | item_per_s | F | ||||
Parameter | ub_EX_A | 1000.0 | item_per_s | F | ||||
Parameter | lb_EX_C | -1000.0 | item_per_s | F | ||||
Parameter | ub_EX_C | 1000.0 | item_per_s | F | ||||
Parameter | bounds__lb_default | -1000.0 | item_per_s | T | ||||
Parameter | bounds__ub_R1 | 1.0 | item_per_s | F | ||||
Parameter | bounds__k1 | k1 | -0.2 | per_s | F | |||
Parameter | fba__ub_R1 | ub R1 | 1.0 | item_per_s | T | |||
Parameter | fba__lb | lower bound | 0.0 | item_per_s | T | |||
Parameter | fba__ub | upper bound | 1000.0 | item_per_s | T |
type | Rules [5] | assignment | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|
Rule | EX_A | = | ||||
Rule | EX_C | = | ||||
Rule | d bounds__ub_R1/dt | = | ||||
Rule | lb_EX_A | = | ||||
Rule | lb_EX_C | = |
type | Reactions [8] | name | equation | modifiers | formula | derived units | sbo | cvterm | |
---|---|---|---|---|---|---|---|---|---|
Reaction | R4 | C -> D | ➞ | C ➞ D | |||||
Reaction | fba__R1 | A import (R1) | ⇆ | fba__A ⇆ fba__B1 | |||||
Reaction | fba__R2 | B1 <-> B2 (R2) | ⇆ | fba__B1 ⇆ fba__B2 | |||||
Reaction | fba__R3 | B2 export (R3) | ⇆ | fba__B2 ⇆ fba__C | |||||
Reaction | dummy_EX_A | ⇆ | fba__A ⇆ | ||||||
Reaction | dummy_EX_C | ⇆ | fba__C ⇆ | ||||||
Reaction | update__update_A | ⇆ | A ⇆ | ||||||
Reaction | update__update_C | ⇆ | C ⇆ |