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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. 1038
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032104410501056106210681094
    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. 1044
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032103810501056106210681094
    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. 1050
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032103810441056106210681094
    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. 1056
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032103810441050106210681094
    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. 1062
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032103810441050105610681094
    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. 1068
 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
832838844850856862868874880886892898904910916924930936942948954961967973
979985991997100210081014102110261032103810441050105610621094
    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. 681
 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
543549555561568573579585591597603609615621627633639645651657663669675688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 688
 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
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 695
 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
688701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 701
 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
688695706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 706
 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
688695701712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 712
 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
688695701706718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 718
 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
688695701706712724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 724
 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
688695701706712718730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 730
 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
688695701706712718724736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 736
 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
688695701706712718724730742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 742
 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
688695701706712718724730736748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 748
 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
688695701706712718724730736742754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 754
 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
688695701706712718724730736742748760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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. 760
 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
688695701706712718724730736742748754766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
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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