BIOMD0000000099
type: SBMLModel
species: metaid_0000029
parameter: metaid_0000018
compartment: metaid_0000023
species: metaid_0000030
reaction: metaid_0000038
time units: metaid_0000006
substance units: metaid_0000007
parameter: metaid_0000013
notes: This is model according to the paper "A Molecular Network That Produces Spontaneous Oscillations in Excitalbe Cells of Dictyostelium. Figure 3 has been reproduced by Copasi 4.0.20(development) ". However four of the parameters have been changed , see details in notes. 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 Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
units def: metaid_0000007
reaction: metaid_0000039
reaction: metaid_0000044
parameter: metaid_0000020
parameter: metaid_0000011
reaction: metaid_0000033
species: metaid_0000027
parameter: metaid_0000019
is described by: http://identifiers.org/pubmed/9843585
parameter: metaid_0000017
compartment: metaid_0000022
modified:
  W3 CDTF: Thu Jul 05 17:47:44 BST 2012
parameter: metaid_0000010
reaction: metaid_0000037
length unit: length
reaction: metaid_0000043
parameter: metaid_0000016
parameter: metaid_0000009
is version of: GO:0048511
units def: metaid_0000006
parameter: metaid_0000008
species: metaid_0000024
is: MODEL4515710981
species: metaid_0000025
species: metaid_0000028
reaction: metaid_0000036
reaction: metaid_0000032
created:
  W3 CDTF: Wed Mar 21 13:23:30 GMT 2007
reaction: metaid_0000042
area units: metaid_0000005
reaction: metaid_0000041
parameter: metaid_0000021
parameter: metaid_0000014
occurs in: http://identifiers.org/taxonomy/5782
volume units: metaid_0000004
parameter: metaid_0000015
curated: true
reaction: metaid_0000040
creator:
  ORG:
    orgname: BNMC
  n:
    given: Enuo
    family: He
parameter: metaid_0000012
species: metaid_0000026
reaction: metaid_0000034
name: Laub1998_SpontaneousOscillations
reaction: metaid_0000035
reaction: metaid_0000031

metaid_0000029
type: Species
in compartment: metaid_0000023
constant: false
boundary condition: false
is: P13773
name: CAR1
initial concentration: 1.5
initial amount: NaN
is version of: IPR000848
has only substance units: false

metaid_0000023
type: Compartment
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: Intracellular

metaid_0000018
type: Parameter
notes: The value for this parameters is different from paper (k11=0.3).
constant: true
value: 0.6
name: k11

metaid_0000030
type: Species
initial concentration: 1.6
in compartment: metaid_0000023
has only substance units: false
name: ERK2
initial amount: NaN
boundary condition: false
is version of: IPR008349
constant: false
is homolog to: P28482

metaid_0000038
type: Reaction
kinetic law: 255388
modifier: 255376
reactant: 255364
is version of: GO:0004707
fast: false
reversible: false
name: k8

255364
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000027
type: Species
is version of: IPR000396
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.5
initial amount: NaN
in compartment: metaid_0000023
name: REGA

metaid_0000006
type: SBMLUnitsDef
unit: 255124
name: min

255124
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000007
type: SBMLUnitsDef
unit: 255136
name: micro_Mole

255136
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000013
type: Parameter
constant: true
value: 0.8
name: k6

metaid_0000039
type: Reaction
kinetic law: 255424
modifier: 255412
product: 255400
is version of: GO:0030819
is version of: GO:0004016
fast: false
reversible: false
name: k9

metaid_0000028
type: Species
is version of: IPR008172
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.4
initial amount: NaN
in compartment: metaid_0000023
name: ACA

255400
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000025
type: Species
constant: false
boundary condition: false
initial concentration: 1.0
is: C00575
in compartment: metaid_0000023
name: In_cAMP
initial amount: NaN
has only substance units: false
is: CHEBI:17489

metaid_0000044
type: Reaction
kinetic law: 255592
modifier: 255580
reactant: 255568
is version of: GO:0004672
is version of: http://identifiers.org/ec-code/2.7.11.1
fast: false
reversible: false
name: k14

metaid_0000026
type: Species
is version of: IPR002373
initial amount: NaN
name: PKA
initial concentration: 1.0
constant: false
in compartment: metaid_0000023
boundary condition: false
has only substance units: false
is: P34099

255568
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000020
type: Parameter
notes: In the paper, k13=1.8. This is the most different parameter value between model and paper.
constant: true
value: 33.0
name: k13

metaid_0000011
type: Parameter
constant: true
value: 1.5
name: k4

metaid_0000033
type: Reaction
kinetic law: 255232
modifier: 255220
product: 255208
is version of: GO:0032147
is version of: GO:0001646
fast: false
reversible: false
name: k3

255208
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000019
type: Parameter
constant: true
value: 3.1
name: k12

metaid_0000017
type: Parameter
constant: true
value: 1.0
name: k10

metaid_0000022
type: Compartment
is version of: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: Extracellular

metaid_0000010
type: Parameter
constant: true
value: 2.5
name: k3

metaid_0000037
type: Reaction
kinetic law: 255352
product: 255340
fast: false
reversible: false
name: k7

255340
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000043
type: Reaction
kinetic law: 255556
modifier: 255544
product: 255532
is version of: GO:0001646
fast: false
reversible: false
name: k13

metaid_0000024
type: Species
has only substance units: false
name: Ex_cAMP
boundary condition: false
is: CHEBI:17489
is: C00575
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000022
constant: false

255532
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000016
type: Parameter
notes: The value of the k9 is different from the paper. In the paper k9=0.7.
constant: true
value: 0.29
name: k9

metaid_0000009
type: Parameter
constant: true
value: 0.9
name: k2

metaid_0000008
type: Parameter
constant: true
value: 1.4
name: k1

metaid_0000036
type: Reaction
kinetic law: 255328
modifier: 255316
reactant: 255304
is version of: GO:0004672
fast: false
reversible: false
name: k6

255304
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000032
type: Reaction
kinetic law: 255196
reactant: 255184
is version of: GO:0007194
fast: false
reversible: false
name: k2

255184
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

metaid_0000042
type: Reaction
kinetic law: 255520
reactant: 255508
is version of: GO:0006198
fast: false
reversible: false
name: k12

255508
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

metaid_0000041
type: Reaction
kinetic law: 255496
modifier: 255484
product: 255472
is version of: GO:0004016
fast: false
reversible: false
name: k11

255472
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

metaid_0000021
type: Parameter
notes: In paper this value k14=1.5
constant: true
value: 4.5
name: k14

metaid_0000014
type: Parameter
constant: true
value: 2.0
name: k7

metaid_0000015
type: Parameter
constant: true
value: 1.3
name: k8

metaid_0000040
type: Reaction
kinetic law: 255460
modifier: 255448
reactant: 255436
is version of: GO:0004115
fast: false
reversible: false
name: k10

255436
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

metaid_0000012
type: Parameter
constant: true
value: 0.6
name: k5

metaid_0000034
type: Reaction
kinetic law: 255256
reactant: 255244
is version of: GO:0006469
fast: false
reversible: false
name: k4

255244
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000026

metaid_0000035
type: Reaction
kinetic law: 255292
modifier: 255280
product: 255268
is version of: GO:0045860
fast: false
reversible: false
name: k5

255268
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000031
type: Reaction
kinetic law: 255172
modifier: 255160
product: 255148
is version of: GO:0007190
is version of: GO:0004707
fast: false
reversible: false
name: k1

255148
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028