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Accession Type:
Network
Ajay_Bhalla_
2007_ReacDiff2
Shared_Object_
Ajay_Bhalla_
2007_ReacDiff
PKC
MAPK
Ras
CaM
PKM
chain
Shared Object_
Ajay_Bhalla_
2007_ReacDiff2
PKC
MAPK
Ras
CaM
PKM
kinetics[1]
PKC
MAPK
Ras
kinetics[3]
CaM
PKM
kinetics[2]
PKC
MAPK
Ras
CaM
PKM
PKC
MAPK
Ras
CaM
PKM
kinetics[4]
PKC
MAPK
Ras
CaM
PKM
kinetics[5]
PKC
MAPK
Ras
CaM
PKM
kinetics[6]
PKC
MAPK
Ras
CaM
PKM
kinetics[7]
PKC
MAPK
Ras
CaM
PKM
kinetics[8]
PKC
MAPK
Ras
CaM
PKM
kinetics[9]
PKC
MAPK
Ras
CaM
PKM
kinetics[10]
PKC
MAPK
Ras
CaM
PKM
kinetics[11]
PKC
MAPK
Ras
CaM
PKM
kinetics[12]
PKC
MAPK
Ras
CaM
PKM
kinetics[13]
PKC
MAPK
Ras
CaM
PKM
kinetics[14]
PKC
MAPK
Ras
CaM
PKM
kinetics[15]
PKC
MAPK
Ras
CaM
PKM
kinetics[16]
PKC
MAPK
Ras
CaM
PKM
kinetics[17]
PKC
MAPK
Ras
CaM
PKM
kinetics[18]
PKC
MAPK
Ras
CaM
PKM
kinetics[19]
PKC
MAPK
Ras
CaM
PKM
kinetics[20]
PKC
MAPK
Ras
CaM
PKM
kinetics[21]
PKC
MAPK
Ras
CaM
PKM
kinetics[22]
PKC
MAPK
Ras
CaM
PKM
kinetics[23]
PKC
MAPK
Ras
CaM
PKM
kinetics[24]
PKC
MAPK
Ras
CaM
PKM
kinetics[25]
PKC
MAPK
Ras
CaM
PKM
kinetics[26]
PKC
MAPK
Ras
CaM
PKM
kinetics[27]
PKC
MAPK
Ras
CaM
PKM
kinetics[28]
PKC
MAPK
Ras
CaM
PKM
kinetics[29]
PKC
MAPK
Ras
CaM
PKM
kinetics[30]
PKC
MAPK
Ras
CaM
PKM
kinetics[31]
PKC
MAPK
Ras
CaM
PKM
kinetics[32]
PKC
MAPK
Ras
CaM
PKM
kinetics[33]
PKC
MAPK
Ras
CaM
PKM
kinetics[34]
PKC
MAPK
Ras
CaM
PKM
kinetics[35]
PKC
MAPK
Ras
CaM
PKM
kinetics[36]
PKC
MAPK
Ras
CaM
PKM
kinetics[37]
PKC
MAPK
Ras
CaM
PKM
kinetics[38]
PKC
MAPK
Ras
CaM
PKM

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Accession information for Ajay_Bhalla_2007_ReacDiff2 (Accession Number 83)

Reaction Scheme

Accession Basic Parameters

Name Ajay_Bhalla_2007_ReacDiff2
Accession Type Network
Transcriber Upinder S. Bhalla, NCBS
Developer Upinder S. Bhalla, NCBS
Entry Date (YYYY-MM-DD) 2006-12-08
Species Rat
Tissue Hippocampal CA1
Cell Compartment Dendrite
Source Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87
Methodology Semi-Quantitative match to experiments
Model Implementation Exact GENESIS implementation
Model Validation Replicates original data
Notes 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.

Conversion formats

FormatFile
Native Format (GENESIS format)    acc83.g   



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