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BIOMD0000000114 - Somogyi1990_CaOscillations

 

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Reference Publication
Publication ID: 1904060
Somogyi R, Stucki JW.
Hormone-induced calcium oscillations in liver cells can be explained by a simple one pool model.
J. Biol. Chem. 1991 Jun; 266(17): 11068-11077
Pharmakologisches Institut, Universität Bern, Switzerland.  [more]
Model
Original Model: BIOMD0000000114.xml.origin
Submitter: Enuo He
Submission ID: MODEL8907365389
Submission Date: 05 Jun 2007 21:01:39 UTC
Last Modification Date: 06 Apr 2014 22:01:37 UTC
Creation Date: 10 May 2007 08:46:04 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology hormone-mediated signaling pathway
Gene Ontology regulation of calcium ion transport
Gene Ontology calcium-mediated signaling
bqbiol:hasTaxon Taxonomy Rattus
Notes

This model encoded according to the paper Hormone induced Calcium Oscillations in Liver Cells Can Be Explained by a Simple One Pool Model. The values of parameters a and alpha are varioused inorder to simulate results in different situations. For Figure 3A, a=3.5,alpha=1.2 ; Figure 3B, a=3,alpha=5 ; Figure 3C a= 0.95, alpha=1.5; Figure3D, a=1, alpha=5. Keep in mind that the value for the xy axies are arbitrary value. Figures3 in the paper are reproduced by COPASI 4.0.20(development) , and SBMLodeSolver online.


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: 1904060 Submission Date: 05 Jun 2007 21:01:39 UTC Last Modification Date: 06 Apr 2014 22:01:37 UTC Creation Date: 10 May 2007 08:46:04 UTC
Mathematical expressions
Reactions
Ca flux into the cell Ca translocation between cytoplasm and ER Ca pumped out of the cell InsP3 channel
Rules
Assignment Rule (variable: fy)      
Physical entities
Compartments Species
cytoplasm Ca_Cyt    
endoplasmic reticulum Ca_ER    
extracellular      
Global parameters
k alpha n a
k1 beta fy gamma
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_Cyt
Compartment: cytoplasm
Initial concentration: 1.0
 
 endoplasmic reticulum Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca_ER
Compartment: endoplasmic reticulum
Initial concentration: 1.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
Global Parameters (8)
 
   k
Value: 0.01
Constant
 
 alpha
Value: 5.0
Constant
 
   n
Value: 4.0
Constant
 
 a
Value: 3.0
Constant
 
   k1
Value: 2.0
Constant
 
   beta
Value: 1.0
Constant
 
   fy
Value: NaN
 
   gamma
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000114

Curator's comment: (updated: 11 May 2007 19:26:46 BST)

Figure3A and Figure3B have been simulated using COPASI4.0.20(development).

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