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Pathway List for cam

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Entries are color tagged depending on Network  or Pathway 
#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137#137
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticscam statisticsSource
Entry Date
21 CaM
Pathway No. 954
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942948961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 948
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 942
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 936
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 930
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 924
 Ajay_Bhalla_
2007_ReacDiff3

Accession No. 84
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 3
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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
27 CaM
Pathway No. 916
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 910
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 904
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 898
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 892
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 886
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 880
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 874
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 868
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 862
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856868874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 856
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850862868874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 850
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844856862868874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 844
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838850856862868874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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 CaM
Pathway No. 838
 Ajay_Bhalla_
2007_ReacDiff2

Accession No. 83
NetworkMolecule = 5
Enzyme   = 0
Reaction  = 4
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: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832844850856862868874880886892898904910916924930936942948954961967973979
9859919971002100810141021102610321038104410501056106210681094
    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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