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Pathway List for cam

Default ordering is done according to Pathway Name.Table header can be used for changing the default ordering.
indicates that ordering is done according to ascending or descending order.
Entries are color tagged depending on Network  or Pathway 
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticscam statisticsSource
Entry Date
1 CaM
Pathway No. 1094
 CaMKIII

Accession No. 90
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 4
Molecule = 1
Enzyme   = 0
Reaction  = 0
Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )/
2009-02-12
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942948954961967973
9799859919971002100810141021102610321038104410501056106210681109
    CaMKIII is activated by Ca2+ and inactivated by S6K. Since CaMKIII inhibits eEF2, the net effect of Ca2+ on elongation is inhibitory and of S6K is excitatory
   
This pathway is part of accession 90 and is completely specified in the file acc90.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc90.g   
2 CaM
Pathway No. 1109
 mTOR_pathway

Accession No. 92
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 4
Molecule = 1
Enzyme   = 0
Reaction  = 0
Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )/
2009-02-13
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942948954961967973
9799859919971002100810141021102610321038104410501056106210681094
    This model consists of various sub-modules. They are as follows: 1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model 5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model.
   
This pathway is part of accession 92 and is completely specified in the file acc92.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc92.g   
3 CaM
Pathway No. 14
 fig3_CaMKII

Accession No. 2
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 5
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
2781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942948954961967973
97998599199710021008101410211026103210381044105010561062106810941109
    This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse.
Demonstration script files for generating the figures in the paper, including figure 3, are available here.
   
This pathway is part of accession 2 and is completely specified in the file acc2.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc2.g   
GENESIS Format (Annotated version)    Anno_acc2.g   
4 CaM
Pathway No. 27
 fig4_synapse

Accession No. 3
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 5
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
1481107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452458464470476482488494500506512518524530537
543549555561568573579585591597603609615621627633639645651657663669675681
688695701706712718724730736742748754760766772778784790796802808814820826
832838844850856862868874880886892898904910916924930936942948954961967973
97998599199710021008101410211026103210381044105010561062106810941109
    This is the composite model of 4 kinases: PKC, MAPK, PKA and CaMKII and numerous regulatory pathways involved in synaptic signaling. From Bhalla US and Iyengar R. Science (1999) 283(5400):381-7.This model comes from figure 4 of that paper.
Demonstration script files for generating the figures in the paper, including figure 4, are available here.
   
This pathway is part of accession 3 and is completely specified in the file acc3.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc3.g   
GENESIS Format (Annotated version)    Anno_acc3.g   
5 CaM
Pathway No. 368
 Ajay_Bhalla_
2007_Bistable

Accession No. 79
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358373379386392398
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a model of ERKII signaling which is bistable due to feedback. The feedback occurs through ERKII phosphorylation of phospholipase A2 (PLA2), leading to increased production of arachidonic acid (AA), which activates protein kinase C (PKC) which activates c-Raf which is upstream of ERKII.
The model is a highly simplified variant of more detailed bistable models of MAPK signaling (Bhalla US, Iyengar R. Science. 1999 Jan 15;283(5400):381-7, Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80)
   
This pathway is part of accession 79 and is completely specified in the file acc79.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc79.g   
MATLAB format    acc79.m   
SBML format    acc79.xml   
6 CaM
Pathway No. 373
 Ajay_Bhalla_
2007_PKM

Accession No. 80
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368379386392398
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a non-bistable model of ERKII signaling that also incorporates PKM synthesis triggered by Ca influx. It is a simplified variant of the model of Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80.
   
This pathway is part of accession 80 and is completely specified in the file acc80.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc80.g   
MATLAB format    acc80.m   
SBML format    acc80.xml   
7 CaM
Pathway No. 379
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373386392398
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
8 CaM
Pathway No. 386
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379392398
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
9 CaM
Pathway No. 392
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386398
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
10 CaM
Pathway No. 398
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
405411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
11 CaM
Pathway No. 405
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398411418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
12 CaM
Pathway No. 411
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405418423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
13 CaM
Pathway No. 418
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411423428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
14 CaM
Pathway No. 423
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418428434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
15 CaM
Pathway No. 428
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423434440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
16 CaM
Pathway No. 434
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428440446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
17 CaM
Pathway No. 440
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434446452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
18 CaM
Pathway No. 446
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440452458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
19 CaM
Pathway No. 452
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446458464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
20 CaM
Pathway No. 458
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
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
   Related Pathway: 
142781107122146160173203217236246259265273283323340358368373379386392
398405411418423428434440446452464470476482488494500506512518524530537543
549555561568573579585591597603609615621627633639645651657663669675681688
695701706712718724730736742748754760766772778784790796802808814820826832
838844850856862868874880886892898904910916924930936942948954961967973979
98599199710021008101410211026103210381044105010561062106810941109
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 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. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   

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