BIOMD0000000396
type: SBMLModel
parameter: 143692
parameter: 143701
species: 142992
parameter: 143740
curated: true
parameter: 143776
parameter: 143824
parameter: 143815
parameter: 143686
reaction: 143406
reaction: 143340
parameter: 143764
species: 143227
occurs in: CL:0000047
species: 143085
species: 143209
parameter: 143803
parameter: 143674
species: 142687
species: 142902
reaction: 143561
reaction: 143492
parameter: 143839
species: 143282
species: 142957
substance units: 142808
reaction: 143429
parameter: 143710
compartment: 142616
parameter: 143749
reaction: 143320
parameter: 143785
species: 142760
length unit: length
parameter: 143779
parameter: 143695
occurs in: http://identifiers.org/taxonomy/40674
parameter: 143818
species: 143120
species: 143102
reaction: 143451
parameter: 143728
species: 142831
species: 142814
species: 142975
parameter: 143758
parameter: 143713
reaction: 143515
compartment: 142633
parameter: 143794
parameter: 143788
reaction: 143629
volume units: 142784
species: 143048
parameter: 143836
parameter: 143827
parameter: 143698
species: 142921
parameter: 143707
parameter: 143689
species: 142777
parameter: 143833
reaction: 143363
parameter: 143737
species: 143193
parameter: 143743
compartment: 142613
parameter: 143734
species: 142884
parameter: 143773
reaction: 143538
name: Sivakumar2011_NotchSignalingPathway
time units: 949038
species: 142866
species: 142651
species: 142740
parameter: 143770
parameter: 143722
area units: 498119

143692
type: Parameter
constant: true
value: 1.0

143701
type: Parameter
constant: true
value: 2.0

142992
type: Species
initial concentration: NaN
in compartment: 142633
initial amount: 0.0
has only substance units: false
constant: false
notes: Long Name: a46_degraded Synonym: Synonym not specified Accession: U02510
name: a46_degraded
is: CHEBI:36080
boundary condition: false

142633
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus

143740
type: Parameter
constant: true
value: 1.0

143776
type: Parameter
constant: true
value: 1.5

143824
type: Parameter
constant: true
value: 1.95

143815
type: Parameter
constant: true
value: 1.78

143686
type: Parameter
constant: true
value: 1.5

143406
type: Reaction
notes: reversible simple convenience kinetics
reactant: 209648
product: 209672
modifier: 209684
kinetic law: 209696
fast: false
product: 209660
reversible: true

209648
type: SpeciesReference
stoichiometry: 1.0
species: 142866

142866
type: Species
in compartment: 142633
name: Complex_br_(Su(H)/CoR)
notes: Long Name: Long Name: Suppressor of Hairless and Co-repressors Synonym: Synonym not specified Accession: U05412 Heterodimer Member Info: Su(H)#PROTEIN#Suppressor of Hairless [Su(H)]#P01101#C-promoter binding factor 1|CBF1|IKJRB1|Immunoglobulin Kappa J region recombination signal-binding protein 1|LAG-1#;CoR#PROTEIN#Co-repressors#P01112##
constant: false
initial amount: 0.0
boundary condition: false
is version of: GO:0043234
has only substance units: false
initial concentration: NaN

209672
type: SpeciesReference
stoichiometry: 1.0
species: 142849

142849
type: Species
notes: Long Name: Co-repressors Synonym: Synonym not specified Accession: P01112
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 5.0
in compartment: 142633
name: CoR

142902
type: Species
has only substance units: false
notes: Long Name: Notch intracellular soluble fragment Synonym: Synonym not specified Accession: P01120
is version of: GO:0043234
boundary condition: false
initial amount: 0.0
constant: false
initial concentration: NaN
in compartment: 142633
name: NI_sub_c_sub_s

209660
type: SpeciesReference
stoichiometry: 1.0
species: 142831

142831
type: Species
initial concentration: NaN
name: Su(H)
has only substance units: false
in compartment: 142633
constant: false
boundary condition: false
notes: Long Name: Suppressor of Hairless [Su(H)] Synonym: C-promoter binding factor 1,CBF1,IKJRB1,Immunoglobulin Kappa J region recombination signal-binding protein 1,LAG-1 Accession: P01101
initial amount: 5.0
is version of: P28159

143340
type: Reaction
reactant: 209492
product: 209504
kinetic law: 209540
notes: reversible simple convenience kinetics
product: 209516
reversible: true
modifier: 209528
fast: false

209492
type: SpeciesReference
stoichiometry: 1.0
species: 142705

142705
type: Species
initial concentration: NaN
has only substance units: false
is version of: GO:0043234
boundary condition: false
constant: false
name: NI_sub_c_sub_t
in compartment: 142616
notes: Long Name: Notch intracellular tethered fragment Synonym: Synonym not specified Accession: P01119
initial amount: 5.0

142616
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytosol

209504
type: SpeciesReference
stoichiometry: 1.0
species: 142723

142723
type: Species
name: N_sub_tm
constant: false
has only substance units: false
initial concentration: NaN
in compartment: 142616
boundary condition: false
initial amount: 0.0
notes: Long Name: Notch transmembrane domain fragment Synonym: Synonym not specified Accession: P01114
is version of: GO:0043234

209516
type: SpeciesReference
stoichiometry: 1.0
species: 143138

143138
type: Species
in compartment: 142616
is version of: GO:0043234
name: NI_sub_c_sub_s
initial amount: 0.0
boundary condition: false
has only substance units: false
notes: Long Name: Notch intracellular soluble fragment Synonym: Synonym not specified Accession: P01120
initial concentration: NaN
constant: false

143282
type: Species
name: gama secretase
has part: Q9NZ42
has part: Q96BI3
boundary condition: false
has only substance units: false
constant: false
in compartment: 142613
initial concentration: NaN
initial amount: 0.0

142613
type: Compartment
constant: true
size: 1.0
spatial dimensions: 3.0

143764
type: Parameter
constant: true
value: 1.5

143227
type: Species
is version of: CCO:U0000005
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 5.0
in compartment: 142613
name: s76

143085
type: Species
in compartment: 142613
initial amount: 5.0
name: Serrate
has only substance units: false
boundary condition: false
initial concentration: NaN
notes: Long Name: Serrate Synonym: APX-1,F16B12.2,Jagged1,Jagged2 Accession: P01104
is homolog to: Q6SPF9
constant: false

143209
type: Species
initial amount: 0.0
in compartment: 142633
name: E(spl)-C genes
has only substance units: false
notes: Long Name: Enhancer of Split complex genes Synonym: Synonym not specified Accession: G01541
is homolog to: Q5S414
constant: false
boundary condition: false
initial concentration: NaN

143803
type: Parameter
constant: true
value: 1.64

143674
type: Parameter
constant: true
value: 0.5

142687
type: Species
name: Delta
boundary condition: false
has only substance units: false
is version of: O00548
initial amount: 5.0
constant: false
notes: Long Name: Delta Synonym: Delta-like1,Delta-like3,Delta-like4,DeltaC,LAG-2 Accession: P01116
initial concentration: NaN
in compartment: 142613

143561
type: Reaction
kinetic law: 210092
modifier: 210080
product: 210068
reactant: 210056
notes: kinetics of non-modulated unireactant enzymes
fast: false
reversible: true

143174
type: Species
notes: Long Name: LNXp80 Synonym: Ligand of Numb-protein X 80 kDa Accession: P01111
has only substance units: false
initial amount: 0.33
initial concentration: NaN
in compartment: 142616
boundary condition: false
constant: false
name: LNXp80
is homolog to: O70263

210068
type: SpeciesReference
stoichiometry: 1.0
species: 143156

143156
type: Species
notes: Long Name: a25_degraded Synonym: Synonym not specified Accession: U02509
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 142616
name: a25_degraded

210056
type: SpeciesReference
stoichiometry: 1.0
species: 142796

142796
type: Species
has only substance units: false
constant: false
is homolog to: P49757
boundary condition: false
name: Numb
initial concentration: NaN
notes: Long Name: Numb Synonym: Synonym not specified Accession: P01118
initial amount: 0.64
in compartment: 142616

143492
type: Reaction
reversible: true
kinetic law: 209924
modifier: 209912
notes: reversible rapid-equilibrium random order ternary-complex mechanism with one product
reactant: 209888
fast: false
reactant: 209876
product: 209900

143067
type: Species
boundary condition: false
in compartment: 142613
initial concentration: NaN
is homolog to: Q9V6X7
initial amount: 5.0
has only substance units: false
notes: Long Name: Neurotic Synonym: O-fucosyltransferase 1,O-fut1,OFUT1,Ofut1 Accession: P01115
constant: false
name: Neurotic

209888
type: SpeciesReference
stoichiometry: 1.0
species: 142670

142670
type: Species
constant: false
notes: Long Name: Fucose Synonym: Synonym not specified Accession: S01795
has only substance units: false
initial concentration: NaN
name: fucose
is version of: CHEBI:18287
in compartment: 142613
initial amount: 5.0
boundary condition: false

209876
type: SpeciesReference
stoichiometry: 1.0
species: 143012

143012
type: Species
constant: false
in compartment: 142616
notes: Long Name: Notch Synonym: GLP-1,LIN-12,Notch1,Notch2,Notch3,Notch4 Accession: P01099
initial concentration: NaN
is version of: Q6IAD4
initial amount: 5.0
has only substance units: false
boundary condition: false
name: Notch

209900
type: SpeciesReference
stoichiometry: 1.0
species: 143048

143048
type: Species
in compartment: 142616
boundary condition: false
initial amount: 0.0
name: Notch
notes: Long Name: Notch Synonym: GLP-1,LIN-12,Notch1,Notch2,Notch3,Notch4 Accession: P01099
constant: false
has only substance units: false
initial concentration: NaN
is version of: Q6IAD4

143839
type: Parameter
constant: true
value: 0.00594

142957
type: Species
boundary condition: false
is homolog to: Q9UBV2
notes: Long Name: Sel 10 Synonym: Synonym not specified Accession: P01102
name: Sel 10
initial concentration: NaN
in compartment: 142633
initial amount: 0.6
has only substance units: false
constant: false

143429
type: Reaction
product: 209756
reactant: 209708
kinetic law: 209768
reversible: true
reactant: 209720
reactant: 209744
fast: false
reactant: 209732
notes: mass action rate law for , reversible reactions, continuous scheme

209756
type: SpeciesReference
stoichiometry: 1.0
species: 142921

142921
type: Species
initial amount: 0.0
initial concentration: NaN
in compartment: 142633
name: Complex_br_(Mastermind/Su(H)/_br_CoA/NI_sub_c_sub_s)
is version of: GO:0043234
boundary condition: false
notes: Long Name: Long Name: Long name not specified Synonym: Synonym not specified Accession: U05413 Heterodimer Member Info: CoA#PROTEIN#Co-Activators#P01100##;Su(H)#PROTEIN#Suppressor of Hairless [Su(H)]#P01101#C-promoter binding factor 1|CBF1|IKJRB1|Immunoglobulin Kappa J region recombination signal-binding protein 1|LAG-1#;Mastermind#PROTEIN#Mastermind#P01106#MECT-1|Mastermind-like 1 (MAML1)|Mastermind-like2 (MAML2)|Mastermind-like3(MAML3)|mucoepidermoid carcinoma-translocated 1#;NIcs#PROTEIN#Notch intracellular soluble fragment#P01120##
has only substance units: false
constant: false

209708
type: SpeciesReference
stoichiometry: 1.0
species: 142902

209720
type: SpeciesReference
stoichiometry: 1.0
species: 142831

209744
type: SpeciesReference
stoichiometry: 1.0
species: 142884

142884
type: Species
boundary condition: false
is version of: CHEBI:36080
name: CoA
initial concentration: NaN
notes: Long Name: Co-Activators Synonym: Synonym not specified Accession: P01100
constant: false
initial amount: 0.5
in compartment: 142633
has only substance units: false

209732
type: SpeciesReference
stoichiometry: 1.0
species: 142814

142814
type: Species
has only substance units: false
boundary condition: false
name: Mastermind
initial concentration: NaN
constant: false
is version of: Q92585
notes: Long Name: Mastermind Synonym: MECT-1,Mastermind-like 1 (MAML1),Mastermind-like2 (MAML2),Mastermind-like3(MAML3),mucoepidermoid carcinoma-translocated 1 Accession: P01106
in compartment: 142633
initial amount: 0.5

143710
type: Parameter
constant: true
value: 0.5

143749
type: Parameter
constant: true
value: 1.0

143320
type: Reaction
kinetic law: 209480
product: 209468
reactant: 209456
fast: false
reversible: false

209468
type: SpeciesReference
stoichiometry: 1.0
species: 143209

209456
type: SpeciesReference
stoichiometry: 1.0
species: 142921

143785
type: Parameter
constant: true
value: 0.5

142760
type: Species
boundary condition: false
name: a7_degraded
constant: false
initial amount: 0.0
notes: Long Name: a7_degraded Synonym: Synonym not specified Accession: U02511
initial concentration: NaN
is: CHEBI:36080
has only substance units: false
in compartment: 142613

143779
type: Parameter
constant: true
value: 1.25

143695
type: Parameter
constant: true
value: 0.04

143818
type: Parameter
constant: true
value: 0.15

143120
type: Species
in compartment: 142613
initial amount: 0.0
initial concentration: NaN
has only substance units: false
name: Complex_br_(Serrate/N_sub_ext)
boundary condition: false
constant: false
is version of: GO:0043234
notes: Long Name: Long Name: Serrate and Notch extracellular fragment Synonym: Synonym not specified Accession: U05414 Heterodimer Member Info: Next#PROTEIN#Serrate and Notch extracellular fragment#P01103##;Serrate#PROTEIN#Serrate#P01104#APX-1|F16B12.2|Jagged1|Jagged2#

143102
type: Species
notes: Long Name: Long Name: Serrate and Notch (fucosylated) Synonym: Synonym not specified Accession: U05410 Heterodimer Member Info: Notch#PROTEIN#Notch#P01099#GLP-1|LIN-12|Notch1|Notch2|Notch3|Notch4#;Serrate#PROTEIN#Serrate#P01104#APX-1|F16B12.2|Jagged1|Jagged2#
boundary condition: false
initial concentration: NaN
has only substance units: false
name: Complex_br_(Serrate/Notch)
initial amount: 0.0
constant: false
in compartment: 142616
is version of: GO:0043234

143451
type: Reaction
notes: reversible rapid-equilibrium random order ternary-complex mechanism with one product
modifier: 209816
fast: false
product: 209804
reactant: 209780
reversible: true
kinetic law: 209828
reactant: 209792

209804
type: SpeciesReference
stoichiometry: 1.0
species: 142938

142938
type: Species
is version of: GO:0043234
notes: Long Name: Notch intracellular soluble fragment Synonym: Synonym not specified Accession: P01120
constant: false
boundary condition: false
initial amount: 0.0
initial concentration: NaN
has only substance units: false
in compartment: 142633
name: NI_sub_c_sub_s

209780
type: SpeciesReference
stoichiometry: 1.0
species: 142902

209792
type: SpeciesReference
stoichiometry: 1.0
species: 142975

142975
type: Species
boundary condition: false
initial amount: 0.5
notes: Long Name: Ubiquitin Synonym: Synonym not specified Accession: S01796
constant: false
initial concentration: NaN
name: Ub
in compartment: 142633
is: CCO:F0004655
has only substance units: false

143728
type: Parameter
constant: true
value: 2.0

143758
type: Parameter
constant: true
value: 1.5

143713
type: Parameter
constant: true
value: 1.0

143515
type: Reaction
reversible: true
kinetic law: 209984
fast: false
reactant: 209948
reactant: 209936
product: 209960
notes: mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
modifier: 209972

209948
type: SpeciesReference
stoichiometry: 1.0
species: 143085

209936
type: SpeciesReference
stoichiometry: 1.0
species: 143048

209960
type: SpeciesReference
stoichiometry: 1.0
species: 143102

142651
type: Species
is version of: Q8NES3
constant: false
notes: Long Name: Fringe Synonym: Lunatic Fringe,Manic Fringe,Radical Fringe Accession: P01107
in compartment: 142613
initial concentration: NaN
initial amount: 5.0
name: Fringe
boundary condition: false
has only substance units: false

143794
type: Parameter
constant: true
value: 1.61

143788
type: Parameter
constant: true
value: 1.7

143629
type: Reaction
reactant: 210224
modifier: 210260
product: 210248
notes: mass action rate law for second order forward, first order reverse, reversible reactions, two reactants, continuous scheme
reversible: true
fast: false
reactant: 210236
kinetic law: 210272

210224
type: SpeciesReference
stoichiometry: 1.0
species: 143227

143263
type: Species
is version of: CCO:U0000005
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: 142613
name: dapt

210248
type: SpeciesReference
stoichiometry: 1.0
species: 143282

210236
type: SpeciesReference
stoichiometry: 1.0
species: 143245

143245
type: Species
is version of: CCO:U0000005
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: 5.0
in compartment: 142613
name: s77

143836
type: Parameter
constant: true
value: 2.0

143827
type: Parameter
constant: true
value: 0.055

143698
type: Parameter
constant: true
value: 0.05

143707
type: Parameter
constant: true
value: 1.0

143689
type: Parameter
constant: true
value: 1.5

142777
type: Species
boundary condition: false
initial concentration: NaN
notes: Long Name: Neuralized Synonym: Neu Accession: P01117
has only substance units: false
name: Neuralized
initial amount: 0.5
in compartment: 142613
is version of: Q9BR09
constant: false

143833
type: Parameter
constant: true
value: 0.004

143363
type: Reaction
kinetic law: 209588
modifier: 209576
product: 209564
reactant: 209552
notes: kinetics of non-modulated unireactant enzymes
fast: false
reversible: true

209564
type: SpeciesReference
stoichiometry: 1.0
species: 142760

209552
type: SpeciesReference
stoichiometry: 1.0
species: 142687

143737
type: Parameter
constant: true
value: 1.0

143193
type: Species
notes: Long Name: Long Name: Delta and Notch (fucosylated) Synonym: Synonym not specified Accession: U05411 Heterodimer Member Info: Notch#PROTEIN#Notch#P01099#GLP-1|LIN-12|Notch1|Notch2|Notch3|Notch4#;Delta#PROTEIN#Delta#P01116#Delta-like1|Delta-like3|Delta-like4|DeltaC|LAG-2#
constant: false
initial concentration: NaN
name: Complex_br_(Notch/Delta)
is version of: GO:0043234
has only substance units: false
in compartment: 142616
initial amount: 0.0
boundary condition: false

143743
type: Parameter
constant: true
value: 1.5

143734
type: Parameter
constant: true
value: 1.0

143773
type: Parameter
constant: true
value: 1.5

143538
type: Reaction
notes: reversible simple convenience kinetics
reversible: true
fast: false
product: 210008
kinetic law: 210044
modifier: 210032
reactant: 209996
product: 210020

210008
type: SpeciesReference
stoichiometry: 1.0
species: 143120

142740
type: Species
is version of: Q8TE56
initial amount: 0.5
has only substance units: false
initial concentration: NaN
in compartment: 142616
name: TACE
notes: Long Name: TACE Synonym: A disintegrin and metalloproteinase domain 17,ADAM17,Tumor necrosis factor alpha converting enzyme Accession: P01105
boundary condition: false
constant: false

209996
type: SpeciesReference
stoichiometry: 1.0
species: 143102

210020
type: SpeciesReference
stoichiometry: 1.0
species: 142705

143770
type: Parameter
constant: true
value: 1.0

143722
type: Parameter
constant: true
value: 1.0

143680
type: Parameter
constant: true
value: 1.5

143812
type: Parameter
constant: true
value: 1.61

143767
type: Parameter
constant: true
value: 1.5

143797
type: Parameter
constant: true
value: 1.71

143806
type: Parameter
constant: true
value: 1.28

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

143716
type: Parameter
constant: true
value: 0.5

143384
type: Reaction
kinetic law: 209636
modifier: 209624
product: 209612
reactant: 209600
notes: mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
fast: false
reversible: true

209612
type: SpeciesReference
stoichiometry: 1.0
species: 142902

209600
type: SpeciesReference
stoichiometry: 1.0
species: 143138

143473
type: Reaction
kinetic law: 209864
product: 209852
reactant: 209840
notes: mass action rate law for first order forward, first order reverse, reversible reactions, continuous scheme
fast: false
reversible: true

209852
type: SpeciesReference
stoichiometry: 1.0
species: 142992

209840
type: SpeciesReference
stoichiometry: 1.0
species: 142938

143752
type: Parameter
constant: true
value: 1.5

143301
type: Reaction
kinetic law: 209444
product: 209432
reactant: 209420
fast: false
reversible: false

209432
type: SpeciesReference
stoichiometry: 1.0
species: 143209

209420
type: SpeciesReference
stoichiometry: 1.0
species: 142866

143582
type: Reaction
notes: reversible rapid-equilibrium random order ternary-complex mechanism with one product
fast: false
reactant: 210104
modifier: 210140
product: 210128
kinetic law: 210152
reversible: true
reactant: 210116

210104
type: SpeciesReference
stoichiometry: 1.0
species: 142687

210128
type: SpeciesReference
stoichiometry: 1.0
species: 143193

210116
type: SpeciesReference
stoichiometry: 1.0
species: 143048

143606
type: Reaction
modifier: 210200
notes: reversible simple convenience kinetics
product: 210188
reversible: true
fast: false
reactant: 210164
product: 210176
kinetic law: 210212

210188
type: SpeciesReference
stoichiometry: 1.0
species: 142705

210164
type: SpeciesReference
stoichiometry: 1.0
species: 143193

210176
type: SpeciesReference
stoichiometry: 1.0
species: 143030

143030
type: Species
initial amount: 0.0
is version of: GO:0043234
in compartment: 142613
notes: Long Name: Long Name: Delta and Notch extracellular fragment Synonym: Synonym not specified Accession: U05409 Heterodimer Member Info: Next#PROTEIN#Serrate and Notch extracellular fragment#P01103##;Delta#PROTEIN#Delta#P01116#Delta-like1|Delta-like3|Delta-like4|DeltaC|LAG-2#
initial concentration: NaN
boundary condition: false
constant: false
has only substance units: false
name: Complex_br_(Delta/N_sub_ext)

143821
type: Parameter
constant: true
value: 1.87

143683
type: Parameter
constant: true
value: 2.0

143731
type: Parameter
constant: true
value: 1.0

143677
type: Parameter
constant: true
value: 1.0

143809
type: Parameter
constant: true
value: 1.86

143725
type: Parameter
constant: true
value: 0.5

143719
type: Parameter
constant: true
value: 1.5

143761
type: Parameter
constant: true
value: 1.5

143755
type: Parameter
constant: true
value: 1.0

143746
type: Parameter
constant: true
value: 1.5

143791
type: Parameter
constant: true
value: 1.0

143800
type: Parameter
constant: true
value: 1.48

143782
type: Parameter
constant: true
value: 1.5

143704
type: Parameter
constant: true
value: 0.01

143830
type: Parameter
constant: true
value: 2.0

W3 CDTF: Wed Nov 02 14:45:45 GMT 2011

ORG:
  orgname: Rajiv Gandhi Centre for Biotechnology
n:
  given: KC
  family: Sivakumar

W3 CDTF: Fri Apr 20 20:39:34 BST 2012