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BIOMD0000000060 - Keizer1996_Ryanodine_receptor_adaptation

 

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Reference Publication
Publication ID: 8968617
Keizer J, Levine L.
Ryanodine receptor adaptation and Ca2+(-)induced Ca2+ release-dependent Ca2+ oscillations.
Biophys. J. 1996 Dec; 71(6): 3477-3487
Institute of Theoretical Dynamics, University of California, Davis 95616, USA. jekeizer@ucdavis.edu  [more]
Model
Original Model: BIOMD0000000060.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL0332756009
Submission Date: 23 Jun 2006 16:17:05 UTC
Last Modification Date: 06 Apr 2014 21:39:27 UTC
Creation Date: 01 Oct 2008 17:41:46 UTC
Encoders:  Harish Dharuri
   Lukas Endler
set #1
bqbiol:hasPart Gene Ontology ryanodine-sensitive calcium-release channel activity
Gene Ontology calcium-mediated signaling
Gene Ontology calcium-induced calcium release activity
set #2
bqbiol:is KEGG Pathway map04020
set #3
bqbiol:hasTaxon Taxonomy cellular organisms
set #4
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

The model reproduces the time profile of Open probability of the ryanodine receptor as shown in Fig 2A and 2B of the paper. The model was successfully tested on MathSBML and Jarnac.


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: 8968617 Submission Date: 23 Jun 2006 16:17:05 UTC Last Modification Date: 06 Apr 2014 21:39:27 UTC Creation Date: 01 Oct 2008 17:41:46 UTC
Mathematical expressions
Reactions
Closed_state_1 Open_state_2 Closed State 2  
Rules
Assignment Rule (variable: Open_probability)      
Physical entities
Compartments Species
compartment Pc1 Po2 Po1
Pc2    
Global parameters
Open_probability      
Reactions (3)
 
 Closed_state_1 [Po1] ↔ [Pc1];   {Po1}
 
 Open_state_2 [Po1] ↔ [Po2];   {Po1}
 
 Closed State 2 [Po1] ↔ [Pc2];   {Po1}
 
Rules (1)
 
 Assignment Rule (name: Open_probability) Open_probability = Po1+Po2
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Pc1
Compartment: compartment
Initial amount: 0.963
 
 Po2
Compartment: compartment
Initial amount: 0.0
 
 Po1
Compartment: compartment
Initial amount: 0.0
 
 Pc2
Compartment: compartment
Initial amount: 0.037
 
Global Parameters (1)
 
   Open_probability  
 
Closed_state_1 (4)
 
   ka_minus
Value: 28.8   (Units: per_second)
Constant
 
   ka_plus
Value: 1500.0   (Units: microM-4sec-1)
Constant
 
   Ca
Value: 0.9   (Units: microM)
Constant
 
   n
Value: 4.0   (Units: dimensionless)
Constant
 
Open_state_2 (4)
 
   kb_plus
Value: 1500.0   (Units: microM-3sec-1)
Constant
 
   Ca
Value: 0.9   (Units: microM)
Constant
 
   m
Value: 3.0   (Units: dimensionless)
Constant
 
   kb_minus
Value: 385.9   (Units: per_second)
Constant
 
Closed State 2 (2)
 
   kc_plus
Value: 1.75   (Units: per_second)
Constant
 
   kc_minus
Value: 0.1   (Units: per_second)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000060

Curator's comment: (updated: 01 Oct 2008 19:13:43 BST)

Reproduction of figures 2a and b of the original publication. The simulation was performed using Copasi 4.4.27

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