MODEL1006230064
type: SBMLModel
parameter: 684701
parameter: 684739
rule: 684681
parameter: 684735
parameter: 684769
parameter: 684767
parameter: 684727
parameter: 684723
volume units: 290956
parameter: 684729
rule: 684697
rule: 684662
rule: 684665
rule: 684666
rule: 684669
rule: 684674
units def: 492369
parameter: 684720
parameter: 684776
rule: 684678
parameter: 684773
rule: 684686
parameter: 684771
parameter: 684708
notes: This a model from the article: Computational insights on the competing effects of nitric oxide in regulating apoptosis. Bagci EZ, Vodovotz Y, Billiar TR, Ermentrout B, Bahar I. PLoS One 2008 May 28;3(5):e2249 18509469 , Abstract: Despite the establishment of the important role of nitric oxide (NO) on apoptosis, a molecular-level understanding of the origin of its dichotomous pro- and anti-apoptotic effects has been elusive. We propose a new mathematical model for simulating the effects of nitric oxide (NO) on apoptosis. The new model integrates mitochondria-dependent apoptotic pathways with NO-related reactions, to gain insights into the regulatory effect of the reactive NO species N(2)O(3), non-heme iron nitrosyl species (FeL(n)NO), and peroxynitrite (ONOO(-)). The biochemical pathways of apoptosis coupled with NO-related reactions are described by ordinary differential equations using mass-action kinetics. In the absence of NO, the model predicts either cell survival or apoptosis (a bistable behavior) with shifts in the onset time of apoptotic response depending on the strength of extracellular stimuli. Computations demonstrate that the relative concentrations of anti- and pro-apoptotic reactive NO species, and their interplay with glutathione, determine the net anti- or pro-apoptotic effects at long time points. Interestingly, transient effects on apoptosis are also observed in these simulations, the duration of which may reach up to hours, despite the eventual convergence to an anti-apoptotic state. Our computations point to the importance of precise timing of NO production and external stimulation 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 wkan014@aucklanduni.ac.nz The University of Auckland This model ori…
parameter: 684709
parameter: 684761
parameter: 684748
units def: 492333
units def: 492489
rule: 684693
rule: 684661
area units: 291053
rule: 684670
parameter: 684777
rule: 684695
parameter: 684737
rule: 684682
parameter: 684736
rule: 684663
parameter: 684733
units def: 492393
rule: 684699
time units: 483804
parameter: 684731
parameter: 684765
rule: 684667
parameter: 684740
parameter: 684725
rule: 684675
parameter: 684721
rule: 684679
parameter: 684759
rule: 684698
rule: 684687
parameter: 684757
substance units: 178797
parameter: 684717
parameter: 684764
parameter: 684749
parameter: 684747
parameter: 684745
parameter: 684719
parameter: 684705
parameter: 684772
parameter: 684707
rule: 684691
parameter: 684744
parameter: 684704
rule: 684671
rule: 684690
parameter: 684751
parameter: 684752
rule: 684694
rule: 684683
parameter: 684768
parameter: 684728
rule: 684673
parameter: 684724

684701
type: Parameter
constant: false
value: 0.0
name: NO

684739
type: Parameter
constant: false
value: NaN
name: r_11NO

684735
type: Parameter
constant: false
value: 10000.0
name: GSH

684769
type: Parameter
constant: true
value: 2.0E-4
name: k_14NO

684767
type: Parameter
constant: true
value: 320.0
name: v_m

684727
type: Parameter
constant: true
value: 1000.0
name: CO_2

684723
type: Parameter
constant: false
value: NaN
name: r_10NO

684729
type: Parameter
constant: false
value: NaN
name: r_6NO

492369
type: SBMLUnitsDef
unit: 492381
name: first_order_rate_constant

492381
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

684720
type: Parameter
constant: false
value: NaN
name: r_2NO

684776
type: Parameter
constant: true
value: 0.05
name: FeLn_0

684773
type: Parameter
constant: true
value: 66.0
name: k_17NO

684771
type: Parameter
constant: true
value: 100.0
name: k_15NO

684708
type: Parameter
constant: false
value: NaN
name: r_4NO

684709
type: Parameter
constant: false
value: NaN
name: r_12aNO

684761
type: Parameter
constant: true
value: 6.0E-6
name: k_12aNO

684748
type: Parameter
constant: true
value: 1.0
name: k_1NO

492333
type: SBMLUnitsDef
unit: 492357
unit: 492345
name: micromolar

492357
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

492345
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

492489
type: SBMLUnitsDef
unit: 492526
unit: 492513
unit: 492501
name: rate2

492526
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

492513
type: SBMLUnit
exponent: 2.0
scale: 0
multipler: 1.0
kind: LITRE

492501
type: SBMLUnit
exponent: -2.0
scale: -6
multipler: 1.0
kind: MOLE

684777
type: Parameter
constant: true
value: 10000.0
name: GSH_0

684737
type: Parameter
constant: false
value: NaN
name: FeLnNO

684736
type: Parameter
constant: false
value: NaN
name: GSSG

684733
type: Parameter
constant: false
value: NaN
name: r_9NO

492393
type: SBMLUnitsDef
unit: 492429
unit: 492417
unit: 492405
name: second_order_rate_constant

492429
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

492417
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

492405
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

684731
type: Parameter
constant: false
value: NaN
name: r_7NO

684765
type: Parameter
constant: true
value: 1600.0
name: k_13NO

684740
type: Parameter
constant: false
value: NaN
name: r_m

684725
type: Parameter
constant: true
value: 5.8
name: GPX

684721
type: Parameter
constant: false
value: NaN
name: r_5NO

684759
type: Parameter
constant: true
value: 6.0E-4
name: k_10NO

684757
type: Parameter
constant: true
value: 0.025
name: k_9NO

684717
type: Parameter
constant: false
value: 0.0
name: O_2m

684764
type: Parameter
constant: true
value: 1100.0
name: k_12bNOp

684749
type: Parameter
constant: true
value: 0.1
name: k_2NO

684747
type: Parameter
constant: false
value: 0.05
name: FeLn

684745
type: Parameter
constant: false
value: NaN
name: r_13NO

684719
type: Parameter
constant: true
value: 10.0
name: SOD

684705
type: Parameter
constant: false
value: 0.1
name: CcOX

684772
type: Parameter
constant: true
value: 1.21
name: k_16NO

684707
type: Parameter
constant: false
value: NaN
name: r_1NO

684744
type: Parameter
constant: false
value: 0.0
name: N2O3

684704
type: Parameter
constant: false
value: 0.0
name: NO_2

684751
type: Parameter
constant: true
value: 6700.0
name: k_4NO

684752
type: Parameter
constant: true
value: 2400.0
name: k_5NO

684768
type: Parameter
constant: true
value: 50.0
name: k_m

684728
type: Parameter
constant: true
value: 400.0
name: Cyt_c

684724
type: Parameter
constant: false
value: 0.0
name: ONOO_m

ORG:
  orgname: The University of Auckland
n:
  given: Wendy
  family: Kang

684775
type: Parameter
constant: true
value: 2.0E-4
name: k_17bNO

W3 CDTF: Fri Jun 25 14:24:46 BST 2010

684732
type: Parameter
constant: false
value: NaN
name: r_8NO

684763
type: Parameter
constant: true
value: 81000.0
name: k_12bNOm

492441
type: SBMLUnitsDef
unit: 492477
unit: 492465
unit: 492453
name: flux

492477
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

492465
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

492453
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

684755
type: Parameter
constant: true
value: 2.0
name: k_7NO

684756
type: Parameter
constant: true
value: 0.058
name: k_8NO

684753
type: Parameter
constant: true
value: 0.00135
name: k_6NO

684715
type: Parameter
constant: false
value: NaN
name: r_15NO

684658
type: Compartment
constant: true
units: litre
size: 1.0
spatial dimensions: 3.0

684716
type: Parameter
constant: false
value: NaN
name: r_16NO

W3 CDTF: Fri Jun 25 14:24:46 BST 2010

684713
type: Parameter
constant: false
value: NaN
name: r_14NO

684711
type: Parameter
constant: false
value: NaN
name: r_12bNOp

684712
type: Parameter
constant: false
value: NaN
name: r_12bNOm

684760
type: Parameter
constant: true
value: 66.0
name: k_11NO

684743
type: Parameter
constant: false
value: 0.0
name: GSNO

684703
type: Parameter
constant: true
value: 35.0
name: O_2

684741
type: Parameter
constant: false
value: NaN
name: r_17NO

W3 CDTF: Fri Jun 25 14:24:46 BST 2010

W3 CDTF: Fri Jun 25 14:24:46 BST 2010

ORG:
  orgname: The University of Auckland
n:
  given: Wendy
  family: Kang

ORG:
  orgname: The University of Auckland
n:
  given: Wendy
  family: Kang