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Pathway List for mapk

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Entries are color tagged depending on Network  or Pathway 
#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132#132
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticsmapk statisticsSource
Entry Date
21 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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940952958960965971977983989995
10061012101810241030103610421048105410601066
    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 for just this pathway.
FormatFile
22 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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934946952958960965971977983989995
10061012101810241030103610421048105410601066
    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 for just this pathway.
FormatFile
23 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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928940946952958960965971977983989995
10061012101810241030103610421048105410601066
    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 for just this pathway.
FormatFile
24 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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    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 for just this pathway.
FormatFile
25 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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    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 for just this pathway.
FormatFile
26 MAPK
Pathway No. 914
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
27 MAPK
Pathway No. 908
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
28 MAPK
Pathway No. 902
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
29 MAPK
Pathway No. 896
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
30 MAPK
Pathway No. 890
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
31 MAPK
Pathway No. 884
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
32 MAPK
Pathway No. 878
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
33 MAPK
Pathway No. 872
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
34 MAPK
Pathway No. 866
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
35 MAPK
Pathway No. 860
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
36 MAPK
Pathway No. 854
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848860
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
37 MAPK
Pathway No. 848
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842854860
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
38 MAPK
Pathway No. 842
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836848854860
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
39 MAPK
Pathway No. 836
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830842848854860
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile
40 MAPK
Pathway No. 830
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
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 00:00:00
   Related Pathway: 
62435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
10061012101810241030103610421048105410601066
    This is a 40-compartment reaction-diffusion-transport version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 40 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec In addition, we have a forward (dendrite to soma) transport term of 1 microns/sec. This converts to a rate of 0.1/sec, but applies only to the kf. So the total kf of the diffusion 'reaction' is 0.11 for D = 1 micron^2/sec, and kb is 0.01. If D=0.1 micron^2/sec then kf = 0.101 and kb = 0.001. In addition this model has all molecules buffered in the first and last compartments. This boundary conditions says that the molecules are not drained out of the first compartment, nor do they all pile up in the last one.
The stimulus file pkm_mapk22_transp_endbuf_D1e-13_Fig4CD which was used for the model to replicate Figure 4C and 4D from the paper.
   
This pathway is part of accession 83 and is completely specified in the file acc83.g.
There is no separate for just this pathway.
FormatFile

 
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Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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