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Pathway List for mapk

Default ordering is done according to Pathway Name.Table header can be used for changing the default ordering.
indicates that ordering is done according to ascending or descending order.
Entries are color tagged depending on Network  or Pathway 
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticsmapk statisticsSource
Entry Date
1 MAPK
Pathway No. 75
 Synaptic_
Network

Accession No. 16
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-12-12
   Related Pathway: 
624355661139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by MKP-1. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. For the purposes of this version of the model, MKP-1 is kept at a fixed starting value. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 16 and is completely specified in the file acc16.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc16.g   
GENESIS Format (Annotated version)    Anno_acc16.g   
2 MAPK
Pathway No. 1103
 mTOR_pathway

Accession No. 92
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )/
2009-02-13
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This model consists of various sub-modules. They are as follows: 1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model 5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model.
   
This pathway is part of accession 92 and is completely specified in the file acc92.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc92.g   
3 MAPK
Pathway No. 35
 mkp1_feedback_
effects

Accession No. 4
NetworkMolecule = 16
Enzyme   = 9
Reaction  = 8
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
624566175139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by two forms of MKP. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 4 and is completely specified in the file acc4.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc4.g   
GENESIS Format (Annotated version)    Anno_acc4.g   
MATLAB format    acc4.m   
SBML format    acc4.xml   
4 MAPK
Pathway No. 139
 MAPK_osc

Accession No. 27
PathwayMolecule = 15
Enzyme   = 10
Reaction  = 1
Molecule = 1
Enzyme   = 0
Reaction  = 0
Boris N. Kholodenko Eur J Biochem. (2000) 267(6):1583-8). ( peer-reviewed publication )/
2002-01-22
   Related Pathway: 
62435566175142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is the oscillatory MAPK model from Kholodenko 2000 Eur J. Biochem 267:1583-1588 The original model is formulated in terms of idealized Michaelis-Menten enzymes and the enzyme-substrate complex concentrations are therefore assumed negligible. The current implementation of the model uses explicit enzyme reactions involving substrates and is therefore an approximation to the Kholodenko model. The approximation is greatly improved if the enzyme is flagged as Available which is an option in Kinetikit. This flag means that the enzyme protein concentration is not reduced even when it is involved in a complex. However, the substrate protein continues to participate in enzyme-substrate complexes and its concentration is therefore affected. Overall, this model works almost the same as the Kholodenko model but the peak MAPK-PP amplitudes are a little reduced and the period of oscillations is about 10% longer. If the enzymes are not flagged as Available then the oscillations commence only when the Km for enzyme 1 is set to 0.1 uM.
   
This pathway is part of accession 27 and is completely specified in the file acc27.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc27.g   
GENESIS Format (Annotated version)    Anno_acc27.g   
MATLAB format    acc27.m   
SBML format    acc27.xml   
5 MAPK
Pathway No. 211
 MAPK_network_
2003

Accession No. 50
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/
2003-04-28
   Related Pathway: 
62435566175139142182193230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a network model of many pathways present at the neuronal synapse. The network has properties of temporal tuning as well as steady-state computational properties. In its default form the network is bistable.Bhalla US Biophys J. 2004 Aug;87(2):745-53
   
This pathway is part of accession 50 and is completely specified in the file acc50.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc50.g   
GENESIS Format (Annotated version)    Anno_acc50.g   
MATLAB format    acc50.m   
SBML format    acc50.xml   
6 MAPK
Pathway No. 61
 MAPK_MKP1_
oscillation

Accession No. 9
NetworkMolecule = 15
Enzyme   = 9
Reaction  = 7
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. ( peer-reviewed publication )/
2001-11-08
   Related Pathway: 
624355675139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model relates to figure 5 in Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. It includes the model used for figures 2-4 and also has MKP-1 induction by MAPK activity in the synapse. PP2A is set to 0.16 uM and MKP synthesis is varied from 5x to 40 x basal to get a range of interesting behaviours.
   
This pathway is part of accession 9 and is completely specified in the file acc9.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
MATLAB format    acc9.m   
SBML format    acc9.xml   
7 MAPK
Pathway No. 193
 MAPK_Asthagiri_
adapt_fb

Accession No. 45
PathwayMolecule = 26
Enzyme   = 11
Reaction  = 7
Molecule = 0
Enzyme   = 0
Reaction  = 0
Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication )./
2003-02-22
   Related Pathway: 
62435566175139142182211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a complex model to examine mechanisms that govern MAPK pathway dynamics in Chinese hamster ovary (CHO) cell lines, particularly the role of adapter targeted negative feedback mechanism in generating complete signal adaptation. This model simulates the results as per the figure 7A of the paper by Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39.
   
This pathway is part of accession 45 and is completely specified in the file acc45.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc45.g   
GENESIS Format (Annotated version)    Anno_acc45.g   
MATLAB format    acc45.m   
SBML format    acc45.xml   
8 MAPK
Pathway No. 182
 MAPK-bistability
-fig1c

Accession No. 35
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23 ( peer-reviewed publication )./
2002-11-07
   Related Pathway: 
62435566175139142193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by two forms of MKP. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 35 and is completely specified in the file acc35.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc35.g   
GENESIS Format (Annotated version)    Anno_acc35.g   
MATLAB format    acc35.m   
SBML format    acc35.xml   
9 MAPK
Pathway No. 142
 Huang_Ferrell_
MAPK

Accession No. 30
PathwayMolecule = 14
Enzyme   = 10
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 ( peer-reviewed publication )/
2002-01-31
   Related Pathway: 
62435566175139182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    MAPK model by Huang, C.-Y.F. and Ferrell Jr., J.E. 1996 PNAS USA 93:10078-10083 The parameters are based on the Mathematica code for the model which was kindly supplied by Prof. Ferrell. This simulation very closely replicates figure 2 from the paper.
   
This pathway is part of accession 30 and is completely specified in the file acc30.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc30.g   
GENESIS Format (Annotated version)    Anno_acc30.g   
MATLAB format    acc30.m   
SBML format    acc30.xml   
10 MAPK
Pathway No. 24
 fig4_synapse

Accession No. 3
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
635566175139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is the composite model of 4 kinases: PKC, MAPK, PKA and CaMKII and numerous regulatory pathways involved in synaptic signaling. From Bhalla US and Iyengar R. Science (1999) 283(5400):381-7.This model comes from figure 4 of that paper.
Demonstration script files for generating the figures in the paper, including figure 4, are available here.
   
This pathway is part of accession 3 and is completely specified in the file acc3.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc3.g   
GENESIS Format (Annotated version)    Anno_acc3.g   
11 MAPK
Pathway No. 6
 fig2_egfr

Accession No. 1
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
2435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This network was used to generate figure 2 in Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It consists of the MAPK cascade in a feedback loop with PKC, and receives input from the EGFR in the synapse.
Demonstration script files for generating the figures in the paper, including figure 2, are available here.
   
This pathway is part of accession 1 and is completely specified in the file acc1.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc1.g   
GENESIS Format (Annotated version)    Anno_acc1.g   
12 MAPK
Pathway No. 230
 EGFR_MAPK

Accession No. 58
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US. Biophys J. (2004) 87(2):745-53. ( peer-reviewed publication )/
2004-01-14
   Related Pathway: 
62435566175139142182193211317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    Model of MAPK activation by EGFR in the synapse. Demonstration programs using this model are available here.
Primary citation:Bhalla US. Biophys J. (2004) 87(2):745-53.
   
This pathway is part of accession 58 and is completely specified in the file acc58.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc58.g   
GENESIS Format (Annotated version)    Anno_acc58.g   
MATLAB format    acc58.m   
SBML format    acc58.xml   
13 MAPK
Pathway No. 921
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
14 MAPK
Pathway No. 928
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
15 MAPK
Pathway No. 934
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
16 MAPK
Pathway No. 940
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
17 MAPK
Pathway No. 946
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
18 MAPK
Pathway No. 952
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
19 MAPK
Pathway No. 958
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946952960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   
20 MAPK
Pathway No. 960
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946952958965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_bistable model. The original single-compartment model is repeated 25 times.
In addition, a subset (33 out of 50) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. Here D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) so the kf and kb of this reaction for these 10 micron compartments are both 0.001/sec.
The basal calcium level in this model is held at 95 nM which is rather close to threshold for the flip to the active state. This is necessary to sustain active propagation of activation.
The stimulus file bis6-propgn_D1e-13_FigEF which was used for the model to replicate Figure 4E and 4F from the paper.
   
This pathway is part of accession 84 and is completely specified in the file acc84.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc84.g   

 
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Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
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