BIOMD0000000120
type: SBMLModel
reaction: metaid_0000023
reaction: metaid_0000022
species: metaid_0000019
modified:
  W3 CDTF: Thu Jul 05 15:45:43 BST 2012
parameter: metaid_0000010
units def: metaid_0000039
creator:
  ORG:
    orgname: California Institute of Technology
  n:
    given: Harish
    family: Dharuri
units def: metaid_0000037
time units: metaid_0000066
is version of: hsa04660
parameter: metaid_0000038
reaction: metaid_0000021
area units: metaid_0000005
reaction: metaid_0000028
is version of: GO:0050856
parameter: metaid_0000013
created:
  W3 CDTF: Fri Jun 22 02:48:34 BST 2007
occurs in: http://identifiers.org/taxonomy/131567
parameter: metaid_0000009
parameter: metaid_0000008
substance units: metaid_0000037
reaction: metaid_0000029
event: metaid_0000033
name: Chan2004_TCell_receptor_activation
curated: true
reaction: metaid_0000030
parameter: metaid_0000006
notes: The model reproduces Fig 3a of the paper. Please note that the authors mention that they used a value of 2 for n, n being the power in the positive feedback function for kinase autocatalysis, however the model here has n=1.95 because this results in a simulation that is identical to Fig 3a. 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.
reaction: metaid_0000025
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species: metaid_0000018
parameter: metaid_0000011
compartment: metaid_0000014
parameter: metaid_0000007
length unit: length
volume units: metaid_0000084
is: MODEL2514697386
parameter: metaid_0000036
event: metaid_0000031
is described by: http://identifiers.org/pubmed/15255048
species: metaid_0000017

metaid_0000023
type: Reaction
kinetic law: 935309
product: 935297
reactant: 935285
is version of: GO:0032147
fast: false
reversible: false
name: Basal kinase activation

935297
type: SpeciesReference
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species: metaid_0000017

metaid_0000017
type: Species
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constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000014
name: Active lck

metaid_0000014
type: Compartment
is: GO:0005623
constant: true
size: 1.0
spatial dimensions: 3.0
name: cell

935285
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species: metaid_0000016

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initial amount: 0.0
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name: Inactive lck

metaid_0000022
type: Reaction
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reactant: 935238
kinetic law: 935273
is: http://identifiers.org/ec-code/3.1.3.48
reversible: false
name: Kinase inactivation
modifier: 935261
fast: false
is: GO:0004725

935249
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935238
type: SpeciesReference
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metaid_0000019
type: Species
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constant: false
boundary condition: false
has only substance units: true
initial concentration: NaN
initial amount: 0.6
in compartment: metaid_0000014
name: Active phosphatase

metaid_0000010
type: Parameter
constant: true
units: metaid_0000039
value: 0.01

metaid_0000039
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metaid_0000038
type: Parameter
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unit: 935153
name: items_per_time

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type: Reaction
kinetic law: 935225
product: 935213
is version of: GO:0042605
fast: false
reversible: false
name: Kinase recruitment to T-cell receptor

935213
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000028
type: Reaction
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is version of: GO:0032516
fast: false
reversible: false
name: Catalyzed phosphatase activation

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name: Inactive phosphatase

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metaid_0000009
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value: 0.15

metaid_0000008
type: Parameter
constant: true
units: metaid_0000039
value: 0.15

metaid_0000029
type: Reaction
kinetic law: 935514
product: 935502
reactant: 935490
is version of: GO:0032515
fast: false
reversible: false
name: Phosphatase inactivation

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type: SpeciesReference
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type: SpeciesReference
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species: metaid_0000019

metaid_0000033
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use values from trigger time: true
name: Resetting r(l) to 0

935574
type: Trigger
persistant: true
initial value: true

metaid_0000030
type: Reaction
kinetic law: 935538
reactant: 935526
fast: false
reversible: false
name: Active phosphatase diffusion

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species: metaid_0000019

metaid_0000006
type: Parameter
constant: true
units: metaid_0000039
value: 0.01

metaid_0000025
type: Reaction
kinetic law: 935370
reactant: 935358
is version of: GO:0050868
fast: false
reversible: false
name: Inactive kinase diffusion

935358
type: SpeciesReference
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species: metaid_0000016

metaid_0000027
type: Reaction
kinetic law: 935430
product: 935418
reactant: 935406
is version of: GO:0032516
fast: false
reversible: false
name: Basal phosphatase activation

935418
type: SpeciesReference
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species: metaid_0000019

935406
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species: metaid_0000018

metaid_0000024
type: Reaction
kinetic law: 935346
product: 935333
reactant: 935321
is version of: GO:0032147
fast: false
reversible: false
name: Catalytic kinase activation

935333
type: SpeciesReference
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type: SpeciesReference
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species: metaid_0000016

metaid_0000032
type: Species
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initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000014
name: Total kinase

metaid_0000026
type: Reaction
kinetic law: 935394
reactant: 935382
is version of: GO:0050868
fast: false
reversible: false
name: Active kinase diffusion

935382
type: SpeciesReference
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metaid_0000012
type: Parameter
constant: true
units: metaid_0000039
value: 0.02

metaid_0000005
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value: 1.0

metaid_0000011
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metaid_0000007
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value: 1.0

metaid_0000036
type: Parameter
constant: true
units: dimensionless
value: 1.95

metaid_0000031
type: Event
event assignment: 935562
trigger: 935550
use values from trigger time: true
name: Setting r(l) to 1

935550
type: Trigger
persistant: true
initial value: true