SBML Model Report
Model name:
“Bagci2008 NO Apoptosis modelA”
2LATEX
May 6, 2016
1 General Overview
This is a document in SBML Level 2 Version 4 format. This model was created by the following
three authors: Wendy Kang1 , Wendy Kang2 and Wendy Kang3 at June 25th 2010 at 1:24 p. m.
and last time modified at June 25th 2010 at 1:24 p. m. Table 1 gives an overview of the quantities
of all components of this model.
Table 1: Number of components in this model, which are described in the following sections.
Element
compartment types
species types
events
reactions
global parameters
rules
Quantity
0
0
0
0
58
30
Element
compartments
species
constraints
function definitions
unit definitions
initial assignments
Quantity
1
0
0
0
5
0
Model Notes
This a model from the article:
Computational insights on the competing effects of nitric oxide in regulatingapoptosis.
Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. PLoS One 2008 May 28;3(5):e2249
1 The
University of Auckland, [email protected]
University of Auckland, [email protected]
3 The University of Auckland, [email protected]
2 The
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1
18509469 ,
Abstract:
Despite the establishment of the important role of nitric oxide (NO) onapoptosis, a molecularlevel understanding of the origin of its dichotomous pro-and anti-apoptotic effects has been
elusive. We propose a new mathematical modelfor simulating the effects of nitric oxide (NO)
on apoptosis. The new modelintegrates mitochondria-dependent apoptotic pathways with NOrelated reactions,to gain insights into the regulatory effect of the reactive NO species N(2)O(3),nonheme iron nitrosyl species (FeL(n)NO), and peroxynitrite (ONOO(-)). Thebiochemical pathways of apoptosis coupled with NO-related reactions aredescribed by ordinary differential equations using mass-action kinetics. In theabsence of NO, the model predicts either cell survival or
apoptosis (a bistablebehavior) with shifts in the onset time of apoptotic response depending on
thestrength of extracellular stimuli. Computations demonstrate that the relativeconcentrations of
anti- and pro-apoptotic reactive NO species, and theirinterplay with glutathione, determine the
net anti- or pro-apoptotic effects atlong time points. Interestingly, transient effects on apoptosis are alsoobserved in these simulations, the duration of which may reach up to hours,despite
the eventual convergence to an anti-apoptotic state. Our computationspoint to the importance
of precise timing of NO production and externalstimulation in determining the eventual pro- or
anti-apoptotic role of NO.
This model was taken from the CellML repository and automatically converted to SBML.
The original model was: Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. (2008) version=1.0
The original CellML model was created by:
Wendy Kang
[email protected]
The University of Auckland
This model originates from BioModels Database: A Database of Annotated Published Models
(http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded
model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain
Dedication for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem
suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it,
commercially or not, in a restricted way or not..
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L,
Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novre N, Laibe C (2010)
BioModels Database: An enhanced, curated and annotated resource for published quantitative
kinetic models. BMC Syst Biol., 4:92.
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2 Unit Definitions
This is an overview of ten unit definitions of which five are predefined by SBML and not mentioned in the model.
2.1 Unit micromolar
Name micromolar
Definition µmol · l−1
2.2 Unit first order rate constant
Name first order rate constant
Definition s−1
2.3 Unit second order rate constant
Name second order rate constant
Definition s−1 · µmol−1 · l
2.4 Unit flux
Name flux
Definition µmol · l−1 · s−1
2.5 Unit rate2
Name rate2
Definition µmol−2 · l2 · s−1
2.6 Unit substance
Notes Mole is the predefined SBML unit for substance.
Definition mol
2.7 Unit volume
Notes Litre is the predefined SBML unit for volume.
Definition l
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3
2.8 Unit area
Notes Square metre is the predefined SBML unit for area since SBML Level 2 Version 1.
Definition m2
2.9 Unit length
Notes Metre is the predefined SBML unit for length since SBML Level 2 Version 1.
Definition m
2.10 Unit time
Notes Second is the predefined SBML unit for time.
Definition s
3 Compartment
This model contains one compartment.
Table 2: Properties of all compartments.
Name SBO
Spatial
Size Unit Constant
Dimensions
Id
3
COMpartment
1
3.1 Compartment COMpartment
Outside
2
3
This is a three dimensional compartment with a constant size of one litre.
4 Parameters
This model contains 58 global parameters.
4
Id
Name
NO
O2
NO 2
CcOX
r 1NO
NO
O2
NO 2
CcOX
r 1NO
Table 3: Properties of each parameter.
SBO
Value
Unit
0.000
35.000
0.000
0.100
0.000
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Constant
2
–
2
3
2
–
2
–
2
–
Id
Name
r 4NO
r 12aNO
r 12bNOp
r 12bNOm
r 14NO
r 15NO
r 16NO
O 2m
SOD
r 2NO
r 5NO
r 10NO
ONOO m
GPX
CO 2
Cyt c
r 6NO
r 7NO
r 8NO
r 9NO
GSH
GSSG
FeLnNO
r 11NO
rm
r 17NO
GSNO
N2O3
r 13NO
FeLn
k 1NO
k 2NO
k 4NO
k 5NO
k 6NO
k 7NO
k 8NO
k 9NO
k 10NO
k 11NO
k 12aNO
k 12bNOm
r 4NO
r 12aNO
r 12bNOp
r 12bNOm
r 14NO
r 15NO
r 16NO
O 2m
SOD
r 2NO
r 5NO
r 10NO
ONOO m
GPX
CO 2
Cyt c
r 6NO
r 7NO
r 8NO
r 9NO
GSH
GSSG
FeLnNO
r 11NO
rm
r 17NO
GSNO
N2O3
r 13NO
FeLn
k 1NO
k 2NO
k 4NO
k 5NO
k 6NO
k 7NO
k 8NO
k 9NO
k 10NO
k 11NO
k 12aNO
k 12bNOm
SBO
Value
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
10.000
0.000
0.000
0.000
0.000
5.800
1000.000
400.000
0.000
0.000
0.000
0.000
10000.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.000
0.050
1.000
0.100
6700.000
2400.000
0.001
2.000
0.058
0.025
6 · 10−4
66.000
6 · 10−6
81000.000
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Unit
Constant
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
3
2
–
2
–
2
–
2
–
2
3
2
3
2
3
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
–
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
5
Id
Name
k 12bNOp
k 13NO
vm
km
k 14NO
k 15NO
k 16NO
k 17NO
k 17bNO
FeLn 0
GSH 0
k 12bNOp
k 13NO
vm
km
k 14NO
k 15NO
k 16NO
k 17NO
k 17bNO
FeLn 0
GSH 0
SBO
Value
Unit
1100.000
1600.000
320.000
50.000
2 · 10−4
100.000
1.210
66.000
2 · 10−4
0.050
10000.000
Constant
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3
5 Rules
This is an overview of 30 rules.
5.1 Rule NO
Rule NO is a rate rule for parameter NO:
d
NO = r 1NO − r 4NO − 2 · r 12aNO − r 12bNOp
dt
+ r 12bNOm + r 14NO − r 15NO − r 16NO
(1)
5.2 Rule CcOX
Rule CcOX is a rate rule for parameter CcOX:
d
CcOX = r 15NO
dt
(2)
5.3 Rule NO 2
Rule NO 2 is a rate rule for parameter NO 2:
d
NO 2 = 2 · r 12aNO − r 12bNOp + r 12bNOm
dt
(3)
5.4 Rule O 2m
Rule O 2m is a rate rule for parameter O 2m:
d
O 2m = r 2NO − r 4NO − r 5NO − r 10NO
dt
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(4)
5.5 Rule ONOO m
Rule ONOO m is a rate rule for parameter ONOO m:
d
ONOO m = r 4NO − r 6NO − r 7NO − r 8NO − r 9NO
dt
(5)
5.6 Rule GSH
Rule GSH is a rate rule for parameter GSH:
d
GSH = r 6NO − r 11NO + 2 · r m − r 17NO
dt
(6)
5.7 Rule GSNO
Rule GSNO is a rate rule for parameter GSNO:
d
GSNO = r 6NO − 2 · r 10NO + r 11NO − r 14NO + r 17NO
dt
(7)
5.8 Rule N2O3
Rule N2O3 is a rate rule for parameter N2O3:
d
N2O3 = r 11NO + r 12bNOp − r 12bNOm − r 13NO
dt
(8)
5.9 Rule FeLn
Rule FeLn is a rate rule for parameter FeLn:
d
FeLn = r 16NO + r 17NO
dt
(9)
5.10 Rule r 1NO
Rule r 1NO is an assignment rule for parameter r 1NO:
r 1NO = k 1NO
(10)
5.11 Rule r 4NO
Rule r 4NO is an assignment rule for parameter r 4NO:
r 4NO = k 4NO · NO · O 2m
(11)
5.12 Rule r 12aNO
Rule r 12aNO is an assignment rule for parameter r 12aNO:
r 12aNO = k 12aNO · NO2 · O 2
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(12)
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5.13 Rule r 12bNOp
Rule r 12bNOp is an assignment rule for parameter r 12bNOp:
r 12bNOp = k 12bNOp · NO 2 · NO
(13)
5.14 Rule r 12bNOm
Rule r 12bNOm is an assignment rule for parameter r 12bNOm:
r 12bNOm = k 12bNOm · N2O3
(14)
5.15 Rule r 14NO
Rule r 14NO is an assignment rule for parameter r 14NO:
r 14NO = k 14NO · GSNO
(15)
5.16 Rule r 15NO
Rule r 15NO is an assignment rule for parameter r 15NO:
r 15NO = k 15NO · CcOX · NO
(16)
5.17 Rule r 16NO
Rule r 16NO is an assignment rule for parameter r 16NO:
r 16NO = k 16NO · FeLn · NO
(17)
5.18 Rule r 2NO
Rule r 2NO is an assignment rule for parameter r 2NO:
r 2NO = k 2NO
(18)
5.19 Rule r 5NO
Rule r 5NO is an assignment rule for parameter r 5NO:
r 5NO = k 5NO · SOD · O 2m
(19)
5.20 Rule r 10NO
Rule r 10NO is an assignment rule for parameter r 10NO:
r 10NO = k 10NO · GSNO2 · O 2m
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(20)
5.21 Rule r 6NO
Rule r 6NO is an assignment rule for parameter r 6NO:
r 6NO = k 6NO · ONOO m · GSH
(21)
5.22 Rule r 7NO
Rule r 7NO is an assignment rule for parameter r 7NO:
r 7NO = k 7NO · ONOO m · GPX
(22)
5.23 Rule r 8NO
Rule r 8NO is an assignment rule for parameter r 8NO:
r 8NO = k 8NO · ONOO m · CO 2
(23)
5.24 Rule r 9NO
Rule r 9NO is an assignment rule for parameter r 9NO:
r 9NO = k 9NO · ONOO m · Cyt c
(24)
5.25 Rule FeLnNO
Rule FeLnNO is an assignment rule for parameter FeLnNO:
FeLnNO = FeLn 0 − FeLn
(25)
5.26 Rule GSSG
Rule GSSG is an assignment rule for parameter GSSG:
GSSG =
GSH 0 − GSH − GSNO
2
(26)
5.27 Rule r 11NO
Rule r 11NO is an assignment rule for parameter r 11NO:
r 11NO = k 11NO · N2O3 · GSH
(27)
5.28 Rule r m
Rule r m is an assignment rule for parameter r m:
rm=
v m · GSSG
k m + GSSG
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(28)
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5.29 Rule r 17NO
Rule r 17NO is an assignment rule for parameter r 17NO:
r 17NO = k 17NO · FeLnNO · GSH
(29)
5.30 Rule r 13NO
Rule r 13NO is an assignment rule for parameter r 13NO:
r 13NO = k 13NO · N2O3
(30)
a
a
a
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for Bioinformatics Tübingen (ZBIT), Germany
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