metaid_0000047
is version of: http://identifiers.org/ec-code/2.7.11.1
reversible: false
is version of: GO:0000186
fast: false
type: Reaction
reactant: 308178
kinetic law: 308202
product: 308190
is version of: GO:0004709
name: Y1p activates X2p

308046
stoichiometry: 1.0
species: species 3
type: SpeciesReference

metaid_0000033
constant: true
value: 1.0
name: Kmyx
type: Parameter

308190
stoichiometry: 1.0
species: species 1
type: SpeciesReference

species 2
is: P16892
constant: false
boundary condition: false
has only substance units: false
initial concentration: 6.271793
initial amount: NaN
in compartment: compartment_0
name: X3p
type: Species

metaid_0000043
kinetic law: 308058
product: 308046
is version of: GO:0000167
is version of: GO:0043575
fast: false
reversible: false
name: S2 activates Y1
type: Reaction

metaid_0000037
constant: true
value: 1.0
name: k12y
type: Parameter

308118
stoichiometry: 1.0
species: species 5
type: SpeciesReference

metaid_0000023
constant: true
value: 10.0
name: Y1T
type: Parameter

BIOMD0000000116
reaction: metaid_0000046
species: species 5
reaction: metaid_0000049
parameter: metaid_0000032
parameter: metaid_0000022
area units: metaid_0000005
species: species_0
name: McClean2007_CrossTalk
occurs in: http://identifiers.org/taxonomy/4932
creator:
  ORG:
    orgname: BNMC
  n:
    given: Enuo
    family: He
parameter: metaid_0000035
parameter: metaid_0000025
parameter: metaid_0000039
parameter: metaid_0000029
volume units: metaid_0000084
parameter: metaid_0000030
parameter: metaid_0000038
reaction: metaid_0000045
creator:
  ORG:
    orgname: Max Planck Institute For Molecular Genetics
  n:
    given: Christian
    family: Waltermann
is described by: http://identifiers.org/pubmed/17259986
reaction: metaid_0000048
curated: true
reaction: metaid_0000041
species: species 1
parameter: metaid_0000031
parameter: metaid_0000021
parameter: metaid_0000034
parameter: metaid_0000024
parameter: metaid_0000028
species: species 2
notes: This model encoded according to the paper Cross-talk and decision making in MAP kinase pathways. Supplementary Figure 2 has been reproduced by COPASI4.0.20 (development) using parameter scan method. You probably need to uncheck "always use initial conditions" in copasi when you simulate for the second run in order to get the figure. S1 scale from 0 to 12. Keep in mind that the y axis is the fractions of excited X3 and Y3, meaning that X3P and Y3P are normalized by total concentration X3T and Y3T. The results from modeling the pathway in Supplementary Figure1a, including both activation and inhibition. According to the paper, the value of ka and kd should in the orange region (ka belongs [0,1], kd belongs [1,10]) so assigned ka=0, kd=1. The author made the simplifying assumption that the interactions between the pathways are symmetric. Thus the k12xy=k12yx=ka, k33xy=k33yx=kd. 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.
reaction: metaid_0000042
reaction: metaid_0000044
created:
  W3 CDTF: Tue May 08 10:29:14 BST 2007
is version of: GO:0000161
parameter: metaid_0000037
reaction: metaid_0000047
modified:
  W3 CDTF: Thu Jul 05 17:32:26 BST 2012
parameter: metaid_0000020
reaction: metaid_0000040
species: species 4
compartment: compartment_0
is: MODEL7321452458
species: species 3
parameter: metaid_0000033
length unit: length
parameter: metaid_0000023
parameter: metaid_0000027
is version of: GO:0019236
parameter: metaid_0000036
parameter: metaid_0000026
type: SBMLModel
substance units: metaid_0000031
reaction: metaid_0000043
time units: metaid_0000048

307950
stoichiometry: 1.0
species: species_0
type: SpeciesReference

308142
stoichiometry: 1.0
species: species_0
type: SpeciesReference

307986
stoichiometry: 1.0
species: species_0
type: SpeciesReference

metaid_0000048
kinetic law: 308238
modifier: 308226
reactant: 308214
is version of: GO:0000188
fast: false
reversible: false
name: X3p inhibited by Y3p
type: Reaction

metaid_0000034
constant: true
value: 5.0
name: S2
type: Parameter

metaid_0000044
kinetic law: 308094
product: 308082
is version of: GO:0000186
reactant: 308070
reversible: false
is version of: GO:0004709
name: Y1p activates Y2p
type: Reaction
fast: false
is version of: http://identifiers.org/ec-code/2.7.11.1

metaid_0000038
constant: true
value: 1.0
name: k23y
type: Parameter

species 3
is: P23561
constant: false
boundary condition: false
has only substance units: false
initial concentration: 3.203692
initial amount: NaN
in compartment: compartment_0
name: Y1p
type: Species

308022
stoichiometry: 1.0
species: species 2
type: SpeciesReference

metaid_0000039
constant: true
value: 1.0
name: Kmxy
type: Parameter

metaid_0000024
constant: true
value: 10.0
name: Y2T
type: Parameter

metaid_0000020
constant: true
value: 10.0
name: X1T
type: Parameter

metaid_0000029
constant: true
value: 1.0
name: k12x
type: Parameter

307962
stoichiometry: 1.0
species: species 1
type: SpeciesReference

metaid_0000031
constant: true
value: 1.0
name: kd
type: Parameter

metaid_0000049
kinetic law: 308274
modifier: 308262
reactant: 308250
is version of: GO:0000188
fast: false
reversible: false
name: Y3p inhibited by X3p
type: Reaction

308154
stoichiometry: 1.0
species: species 4
type: SpeciesReference

metaid_0000035
constant: true
value: 1.0
name: ky
type: Parameter

308106
stoichiometry: 1.0
species: species 4
type: SpeciesReference

metaid_0000045
kinetic law: 308130
fast: false
name: Y2p activates Y3p
is version of: GO:0005078
reactant: 308106
is version of: http://identifiers.org/ec-code/2.7.12.2
is version of: GO:0000187
type: Reaction
product: 308118
reversible: false
is version of: GO:0004708

metaid_0000040
fast: false
is version of: GO:0000186
product: 307962
kinetic law: 307974
is version of: GO:0004709
reversible: false
name: X1 activats X2
is version of: http://identifiers.org/ec-code/2.7.11.1
type: Reaction
reactant: 307950

species_0
is: P23561
in compartment: compartment_0
has only substance units: false
notes: The initial value for each species taken from the original submitted model, they are the concentration of the species when arrived to the steady states.
initial concentration: 1.023667
type: Species
name: X1p
boundary condition: false
constant: false
initial amount: NaN

species 4
is: P08018
constant: false
boundary condition: false
has only substance units: false
initial concentration: 8.232192
initial amount: NaN
in compartment: compartment_0
name: Y2p
type: Species

metaid_0000025
constant: true
value: 10.0
name: Y3T
type: Parameter

metaid_0000028
constant: true
value: 1.0
name: Kmx
type: Parameter

metaid_0000021
constant: true
value: 10.0
name: X2T
type: Parameter

metaid_0000030
constant: true
value: 1.0
name: k23x
type: Parameter

308082
stoichiometry: 1.0
species: species 4
type: SpeciesReference

308214
stoichiometry: 1.0
species: species 2
type: SpeciesReference

metaid_0000032
constant: true
value: 0.0
name: ka
type: Parameter

308010
stoichiometry: 1.0
species: species 1
type: SpeciesReference

metaid_0000036
constant: true
value: 1.0
name: Kmy
type: Parameter

species 1
is: P06784
constant: false
boundary condition: false
has only substance units: false
initial concentration: 2.154231
initial amount: NaN
in compartment: compartment_0
name: X2p
type: Species

metaid_0000046
product: 308154
is version of: GO:0004709
kinetic law: 308166
reversible: false
fast: false
is version of: GO:0000186
reactant: 308142
is version of: http://identifiers.org/ec-code/2.7.11.1
type: Reaction
name: X1p activates Y2p

metaid_0000041
kinetic law: 307998
product: 307986
is version of: GO:0000185
is version of: GO:0005186
fast: false
reversible: false
name: S1 activates X1
type: Reaction

compartment_0
is version of: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell
type: Compartment

metaid_0000042
reversible: false
is version of: http://identifiers.org/ec-code/2.7.12.2
is version of: GO:0000187
name: X2 activates X3
type: Reaction
product: 308022
kinetic law: 308034
reactant: 308010
is version of: GO:0004708
fast: false

species 5
is: P32485
constant: false
boundary condition: false
has only substance units: false
initial concentration: 9.312021
initial amount: NaN
in compartment: compartment_0
name: Y3p
type: Species

308178
stoichiometry: 1.0
species: species 3
type: SpeciesReference

metaid_0000026
constant: true
value: 1.0
name: kx
type: Parameter

metaid_0000027
notes: Use parameter scan value from 0 to 12.
constant: true
value: 8.5
name: S1
type: Parameter

metaid_0000022
constant: true
value: 10.0
name: X3T
type: Parameter

308250
stoichiometry: 1.0
species: species 5
type: SpeciesReference

308070
stoichiometry: 1.0
species: species 3
type: SpeciesReference