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BIOMD0000000184 - Lavrentovich2008_Ca_Oscillations

 

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Reference Publication
Publication ID: 18275973
Lavrentovich M, Hemkin S.
A mathematical model of spontaneous calcium(II) oscillations in astrocytes.
J. Theor. Biol. 2008 Apr; 251(4): 553-560
Department of Chemistry, Kenyon College, Gambier, OH 43022, USA.  [more]
Model
Original Model: BIOMD0000000184.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL9223106020
Submission Date: 20 Aug 2008 17:12:50 UTC
Last Modification Date: 11 Jul 2012 17:45:28 UTC
Creation Date: 21 Aug 2008 11:36:22 UTC
Encoders:  Harish Dharuri
   Lukas Endler
set #1
bqbiol:hasPart Gene Ontology calcium-mediated signaling
set #2
bqbiol:occursIn Taxonomy Mammalia
Notes

The model reproduces the time profile of cytoplasmic Calcium as depicted in Fig 3 of the paper. Model successfully reproduced using Jarnac and MathSBML.


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: 18275973 Submission Date: 20 Aug 2008 17:12:50 UTC Last Modification Date: 11 Jul 2012 17:45:28 UTC Creation Date: 21 Aug 2008 11:36:22 UTC
Mathematical expressions
Reactions
vin Calcium export from cell CICR serca
Leak flux PLC IP3 degradation  
Physical entities
Compartments Species
Cytoplasm Cytoplasmic Calcium IP3  
Endoplasmic Reticulum Calcium in ER    
Global parameters
vin kout vM3 k_CaA
n k_CaI m kip3
vM2 k2 kf vp
kp kdeg    
Reactions (7)
 
 vin  → [Cytoplasmic Calcium];  
 
 Calcium export from cell [Cytoplasmic Calcium] → ;  
 
 CICR [Calcium in ER] → [Cytoplasmic Calcium];   {IP3}
 
 serca [Cytoplasmic Calcium] → [Calcium in ER];  
 
 Leak flux [Calcium in ER] → [Cytoplasmic Calcium];  
 
 PLC  → [IP3];   {Cytoplasmic Calcium}
 
 IP3 degradation [IP3] → ;  
 
 Cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 Cytoplasmic Calcium
Compartment: Cytoplasm
Initial concentration: 0.1
 
 IP3
Compartment: Cytoplasm
Initial concentration: 0.1
 
 Endoplasmic Reticulum Spatial dimensions: 3.0  Compartment size: 1.0
 
 Calcium in ER
Compartment: Endoplasmic Reticulum
Initial concentration: 1.5
 
Global Parameters (14)
 
   vin
Value: 0.05   (Units: uM_sec_1)
Constant
 
   kout
Value: 0.5   (Units: sec_1)
Constant
 
   vM3
Value: 40.0   (Units: sec_1)
Constant
 
   k_CaA
Value: 0.15   (Units: uM)
Constant
 
   n
Value: 2.02   (Units: dimensionless)
Constant
 
   k_CaI
Value: 0.15   (Units: uM)
Constant
 
   m
Value: 2.2   (Units: dimensionless)
Constant
 
   kip3
Value: 0.1   (Units: uM)
Constant
 
   vM2
Value: 15.0   (Units: uM_sec_1)
Constant
 
   k2
Value: 0.1   (Units: uM)
Constant
 
   kf
Value: 0.5   (Units: sec_1)
Constant
 
   vp
Value: 0.05   (Units: uM_sec_1)
Constant
 
   kp
Value: 0.3   (Units: uM)
Constant
 
   kdeg
Value: 0.08   (Units: sec_1)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000184

Curator's comment: (updated: 20 Aug 2008 11:17:44 BST)

The plot corresponds to Fig 3 of the paper. Result obtained using MathSBML.

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