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BIOMD0000000047 - Oxhamre2005_Ca_oscillation

 

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Reference Publication
Publication ID: 15596518
Oxhamre C, Richter-Dahlfors A, Zhdanov VP, Kasemo B.
A minimal generic model of bacteria-induced intracellular Ca2+ oscillations in epithelial cells.
Biophys. J. 2005 Apr; 88(4): 2976-2981
Microbiology and Tumor Biology Center, Karolinska Institute, Stockholm, Sweden.  [more]
Model
Original Model: BIOMD0000000047.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL6623415355
Submission Date: 13 Sep 2005 14:57:15 UTC
Last Modification Date: 26 Mar 2014 17:37:13 UTC
Creation Date: 25 Aug 2005 11:00:43 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom PubMed 11874447
set #2
bqbiol:hasTaxon Taxonomy Rattus
bqbiol:is KEGG Pathway rno04020
bqbiol:isVersionOf Gene Ontology inositol phosphate-mediated signaling
Gene Ontology calcium-mediated signaling
Notes

The model should reproduce the figure 1C of the article (successfully reproduced in MathSBML). If your software does not support the variable "time", you can replace the assignmentRule:
n = n0 * [ exp(-kbN*time) + kappa * (1 - exp(-kbN*time))]
by
n = n0 * kappa


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 15596518 Submission Date: 13 Sep 2005 14:57:15 UTC Last Modification Date: 26 Mar 2014 17:37:13 UTC Creation Date: 25 Aug 2005 11:00:43 UTC
Mathematical expressions
Reactions
Jch Jleak Jpump  
Rules
Assignment Rule (variable: n) Assignment Rule (variable: p1) Assignment Rule (variable: p2) Rate Rule (variable: p3)
Physical entities
Compartments Species
Cytosol Ca_Cyt    
Endoplasmic_Reticulum CaER    
Global parameters
n n0 kbN kappa
p1 p11 p12 K1
p2 K2 p3 k31
K3      
Reactions (3)
 
 Jch [CaER] → [Ca_Cyt];  
 
 Jleak [CaER] → [Ca_Cyt];  
 
 Jpump [Ca_Cyt] → [CaER];  
 
Rules (4)
 
 Assignment Rule (name: n) n = n0*(exp((-kbN)*Time)+kappa*(1-exp((-kbN)*Time)))
 
 Assignment Rule (name: p1) p1 = p11+p12*n/(K1+n)
 
 Assignment Rule (name: p2) p2 = Ca_Cyt/(K2+Ca_Cyt)
 
 Rate Rule (name: p3) d [ p3] / d t= -k31*Ca_Cyt*p3+k31*K3*(1-p3)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_Cyt
Compartment: Cytosol
Initial concentration: 0.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 CaER
Compartment: Endoplasmic_Reticulum
Initial concentration: 0.0
 
Global Parameters (13)
 
   n
Value: 1.0
 
   n0
Value: 1.0
Constant
 
   kbN
Value: 0.5
Constant
 
   kappa
Value: 5.0
Constant
 
   p1  
 
   p11
Value: 0.2
Constant
 
   p12
Value: 0.8
Constant
 
   K1
Value: 5.0
Constant
 
   p2  
 
   K2
Value: 0.7
Constant
 
   p3
Value: 0.95
 
   k31
Value: 0.5
Constant
 
   K3
Value: 0.7
Constant
 
Jch (1)
 
   Fch_0
Value: 8.0
Constant
 
Jleak (1)
 
   Fleak
Value: 0.5
Constant
 
Jpump (2)
 
   Fpump_0
Value: 2.0
Constant
 
   Kpump
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000047

Curator's comment: (updated: 17 Dec 2006 13:14:38 GMT)

Simulation result obtained from MathSBML corresponds to Fig 1C of the paper.

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