BIOMD0000000101
type: SBMLModel
species: metaid_0000017
time units: metaid_0000037
parameter: metaid_0000007
area units: metaid_0000005
parameter: metaid_0000004
parameter: metaid_0000010
reaction: metaid_0000021
reaction: metaid_0000027
units def: metaid_0000038
event: metaid_0000035
reaction: metaid_0000024
reaction: metaid_0000032
created:
  W3 CDTF: Tue Nov 28 18:39:38 GMT 2006
modified:
  W3 CDTF: Thu Jul 05 15:45:52 BST 2012
is version of: GO:0007179
curated: true
reaction: metaid_0000022
parameter: metaid_0000003
occurs in: http://identifiers.org/taxonomy/131567
substance units: metaid_0000036
parameter: metaid_0000005
reaction: metaid_0000030
parameter: metaid_0000011
is: MODEL4023382414
reaction: metaid_0000028
notes: The model reproduces Fig 5A of the paper. The ligand concentration is increased from 3E-5 to 0.01 at time t=2500 to ensure that the system reaches steady state. Hence, the time t=0 of the paper corresponds to t=2500 in the model. The peak value of the active ligand receptor complex is off by a value of 1.25, the authors have stated that this discrepancy is due to the fact that the figure in the paper corresponds to a slightly different parameter set. The model was successfully tested on MathSBML. 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.
compartment: metaid_0000012
species: metaid_0000014
species: metaid_0000015
parameter: metaid_0000008
length unit: length
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reaction: metaid_0000025
species: metaid_0000020
reaction: metaid_0000033
has part: REACT 6844.3
volume units: metaid_0000004
parameter: metaid_0000006
has part: hsa04350
reaction: metaid_0000023
units def: metaid_0000037
units def: metaid_0000036
reaction: metaid_0000026
name: Vilar2006_TGFbeta
reaction: metaid_0000031
reaction: metaid_0000029
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
parameter: metaid_0000009
compartment: metaid_0000034
species: metaid_0000013
is described by: http://identifiers.org/pubmed/16446785

metaid_0000017
type: Species
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initial concentration: NaN
has only substance units: true
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in compartment: metaid_0000034
name: ligand receptor complex-endosome
initial amount: 40.0
has part: P01137
boundary condition: false

metaid_0000034
type: Compartment
is: GO:0005768
constant: true
size: 1.0
spatial dimensions: 3.0
name: Endosome

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name: minutes

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multipler: 3600.0
kind: SECOND

metaid_0000007
type: Parameter
constant: true
value: 0.3333333333333

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constant: false
value: 3.0E-5

metaid_0000010
type: Parameter
constant: true
value: 1.0

metaid_0000021
type: Reaction
reversible: false
name: Ligand receptor complex formation
is: GO:0050431
kinetic law: 943645
reactant: 943621
is: GO:0007181
fast: false
reactant: 943609
product: 943633

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name: Receptor 1

metaid_0000012
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product: 943805
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reversible: false
name: RI internalization

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persistant: true
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metaid_0000024
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reactant: 943705
is version of: GO:0030511
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reversible: false
name: Ligand receptor complex internalization

943717
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species: metaid_0000017

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name: Receptor 2 endosome

943965
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metaid_0000022
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name: Ligand receptor complex constitutive degradation

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metaid_0000003
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metaid_0000005
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metaid_0000030
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product: 943915
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fast: false
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name: RII synthesis

943915
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metaid_0000011
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value: 4.0

metaid_0000028
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is version of: GO:0001881
fast: false
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metaid_0000008
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value: 8.0

metaid_0000025
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kinetic law: 943754
product: 943741
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fast: false
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name: RI synthesis

943741
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metaid_0000033
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metaid_0000006
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metaid_0000023
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943681
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metaid_0000026
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943769
type: SpeciesReference
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metaid_0000031
type: Reaction
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is version of: GO:0032801
fast: false
reversible: false
name: RII constitutive degradation

943939
type: SpeciesReference
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species: metaid_0000014

metaid_0000029
type: Reaction
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product: 943891
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is version of: GO:0001881
fast: false
reversible: false
name: Ligand Receptor complex recycling

943891
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943878
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943866
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metaid_0000009
type: Parameter
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