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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.
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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. 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   
2 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   
3 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   
4 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   
5 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   
6 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   
7 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   
8 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   
9 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   
10 MAPK
Pathway No. 965
 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
860866872878884890896902908914921928934940946952958960971977983989995
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   
11 MAPK
Pathway No. 971
 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
860866872878884890896902908914921928934940946952958960965977983989995
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   
12 MAPK
Pathway No. 977
 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
860866872878884890896902908914921928934940946952958960965971983989995
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   
13 MAPK
Pathway No. 983
 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
860866872878884890896902908914921928934940946952958960965971977989995
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. 989
 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
860866872878884890896902908914921928934940946952958960965971977983995
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. 995
 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
860866872878884890896902908914921928934940946952958960965971977983989
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. 1006
 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
860866872878884890896902908914921928934940946952958960965971977983989995
10121018102410301036104210481054106010661103
    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. 1012
 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
860866872878884890896902908914921928934940946952958960965971977983989995
10061018102410301036104210481054106010661103
    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. 1018
 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
860866872878884890896902908914921928934940946952958960965971977983989995
10061012102410301036104210481054106010661103
    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. 1024
 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
860866872878884890896902908914921928934940946952958960965971977983989995
10061012101810301036104210481054106010661103
    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. 1030
 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
860866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241036104210481054106010661103
    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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