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Model : toy_top

Creator
Matthias, Koenig, Humboldt University Berlin, konigmatt@googlemail.com
Created: 2017-03-17 16:49
Modified: 2017-03-17 16:49

SBML model


idtoy_top
nametoy (TOP model)
versionL3V1
times
substanceitem
extentitem
volumem3
aream2
lengthm
FunctionDefinitions [2] name math sbo cvterm
bounds__max minimum of arguments x y x x y y
bounds__min maximum of arguments x y x x y y

UnitDefinitions [9] name units sbo cvterm
s s
kg kg
m m
m2 m 2
m3 m 3
mM mole m 3
per_s 1 s
item_per_s item s
item_per_m3 item m 3

Compartments [5] name size constant spatial dimensions unit derived unit sbo cvterm
extern external compartment 1.0 3 m3 m 3
cell cell 1.0 3 m3 m 3
fba__extern external compartment 1.0 3 m3 m 3
fba__cell cell 1.0 3 m3 m 3
fba__membrane membrane 1.0 2 m2 m 2

Species [8] name compartment boundary condition constant initial amount initial concentration substance units derived units sbo cvterm
dummy_S
extern 0.0 item item
A
extern 0.0 item item
C
extern 0.0 item item
D
extern 0.0 item item
fba__A A
fba__extern 10.0 item item
fba__C C
fba__extern 0.0 item item
fba__B1 B1
fba__cell 0.0 item item
fba__B2 B2
fba__cell 0.0 item item

Parameters [14] name value unit derived unit constant sbo cvterm
dt 0.1 s s
EX_A 1.0 item_per_s item s
EX_C 1.0 item_per_s item s
k_R4 k R4 0.1 per_s 1 s
lb_EX_A -1000.0 item_per_s item s
ub_EX_A 1000.0 item_per_s item s
lb_EX_C -1000.0 item_per_s item s
ub_EX_C 1000.0 item_per_s item s
bounds__lb_default -1000.0 item_per_s item s
bounds__ub_R1 1.0 item_per_s item s
bounds__k1 k1 -0.2 per_s 1 s
fba__ub_R1 ub R1 1.0 item_per_s item s
fba__lb lower bound 0.0 item_per_s item s
fba__ub upper bound 1000.0 item_per_s item s

Rules [5]   assignment derived units sbo cvterm
EX_A = dummy_EX_A item s
EX_C = dummy_EX_C item s
d bounds__ub_R1/dt = bounds__k1 bounds__ub_R1 item s 2
lb_EX_A = bounds__max bounds__lb_default A dt item s
lb_EX_C = bounds__max bounds__lb_default C dt item s

Reactions [8] name equation modifiers formula derived units sbo cvterm
R4 C -> D C ➞ D k_R4 C item s
fba__R1 A import (R1) fba__A ⇆ fba__B1
fba__R2 B1 <-> B2 (R2) fba__B1 ⇆ fba__B2
fba__R3 B2 export (R3) fba__B2 ⇆ fba__C
dummy_EX_A fba__A ⇆
dummy_EX_C fba__C ⇆
update__update_A A ⇆ EX_A item s
update__update_C C ⇆ EX_C item s