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BIOMD0000000126 - Clancy2002_CardiacSodiumChannel_WT

 

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Reference Publication
Publication ID: 11889015
Clancy CE, Rudy Y.
Na(+) channel mutation that causes both Brugada and long-QT syndrome phenotypes: a simulation study of mechanism.
Circulation 2002 Mar; 105(10): 1208-1213
Cardiac Bioelectricity Research and Training Center, Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio 44106-7207, USA.  [more]
Model
Original Model: http://senselab.med.yale.e...
Submitter: Enuo He
Submission ID: MODEL4716238623
Submission Date: 27 Jul 2007 20:21:28 UTC
Last Modification Date: 06 Apr 2014 23:13:46 UTC
Creation Date: 15 Jul 2007 13:35:57 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology heart process
Gene Ontology regulation of sodium ion transport
Gene Ontology sodium channel activity
bqbiol:hasVersion OMIM 601144
OMIM 603830
set #2
bqmodel:isDerivedFrom BioModels Database Clancy2001_Kchannel
PubMed 7514509
PubMed 7788872
PubMed 10318671
PubMed 10533588
set #3
bqbiol:hasTaxon Taxonomy Chordata
set #4
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes

The model is according to the paper Na+ Channel Mutation That Causes Both Brugada and Long-QT Syndrome Phenotypes: A Simulation Study of Mechanism Original model comes from ModelDB with accession number: 62661. This is the wide type model. All the values and reactions obtained from Data Supplement6: Appendix of the paper. Figure3 has been reproduced by MathSBML. The stimulus v=-30mV during the time from 5ms to 20 ms displayed in the event. The meaning for the keyword, C: Close states; O: Open states; IF: Fast inactivation states; IC: Closed-Inactivation states; IM: Intermediat Inactivation states.


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: 11889015 Submission Date: 27 Jul 2007 20:21:28 UTC Last Modification Date: 06 Apr 2014 23:13:46 UTC Creation Date: 15 Jul 2007 13:35:57 UTC
Mathematical expressions
Reactions
IC3=IC2 IC2=IF IF=IM1 IM1=IM2
C3=IC3 C2=C3 C2=IC2 C1=C2
C1=IF IF=O O=C1  
Rules
Assignment Rule (variable: a11) Assignment Rule (variable: a12) Assignment Rule (variable: a13) Assignment Rule (variable: a2)
Assignment Rule (variable: a3) Assignment Rule (variable: b3) Assignment Rule (variable: a4) Assignment Rule (variable: b4)
Assignment Rule (variable: a5) Assignment Rule (variable: b5) Assignment Rule (variable: Ena) Assignment Rule (variable: I_Na)
Assignment Rule (variable: b11) Assignment Rule (variable: b12) Assignment Rule (variable: b13) Assignment Rule (variable: b2)
Events
event_0000001 event_0000002    
Physical entities
Compartments Species
cell C1 C2 C3
IC3 IC2 IM1
IM2 open states IF
Global parameters
[Na]out [Na]in scale v
Ena a11 a12 a13
b11 b12 b13 a2
b2 a3 b3 a4
b4 a5 b5 Gna
Rk Fara Temp I_Na
Reactions (11)
 
 IC3=IC2 [IC3] ↔ [IC2];  
 
 IC2=IF [IC2] ↔ [IF];  
 
 IF=IM1 [IF] ↔ [IM1];  
 
 IM1=IM2 [IM1] ↔ [IM2];  
 
 C3=IC3 [C3] ↔ [IC3];  
 
 C2=C3 [C2] ↔ [C3];  
 
 C2=IC2 [C2] ↔ [IC2];  
 
 C1=C2 [C1] ↔ [C2];  
 
 C1=IF [C1] ↔ [IF];  
 
 IF=O [IF] ↔ [open states];  
 
 O=C1 [open states] ↔ [C1];  
 
Rules (16)
 
 Assignment Rule (name: a11) a11 = 3.802/(0.1027*exp((-v)/17)+0.2*exp((-v)/150))
 
 Assignment Rule (name: a12) a12 = 3.802/(0.1027*exp((-v)/15)+0.23*exp((-v)/150))
 
 Assignment Rule (name: a13) a13 = 3.802/(0.1027*exp((-v)/12)+0.25*exp((-v)/150))
 
 Assignment Rule (name: a2) a2 = 9.178*exp(v/29.68)
 
 Assignment Rule (name: a3) a3 = 3.7933*1E-7*exp((-v)/7.7)
 
 Assignment Rule (name: b3) b3 = 0.0084+2E-5*v
 
 Assignment Rule (name: a4) a4 = a2/100
 
 Assignment Rule (name: b4) b4 = a3
 
 Assignment Rule (name: a5) a5 = a2/(9.5*10000)
 
 Assignment Rule (name: b5) b5 = a3/50
 
 Assignment Rule (name: Ena) Ena = Rk*Temp/Fara*log(nao/nai)
 
 Assignment Rule (name: Ina) I_Na = Gna*O/(IC3+IC2+IF+IM1+IM2+C3+C2+C1+O)*(v-Ena)/scale
 
 Assignment Rule (name: b11) b11 = 0.1917*exp((-v)/20.3)
 
 Assignment Rule (name: b12) b12 = 0.2*exp((-(v-5))/20.3)
 
 Assignment Rule (name: b13) b13 = 0.22*exp((-(v-10))/20.3)
 
 Assignment Rule (name: b2) b2 = a13*a2*a3/(b13*b3)
 
Events (2)
 
 event_0000001
v = -30
 
 event_0000002
v = -80
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 C1
Compartment: cell
Initial concentration: 0.0
 
 C2
Compartment: cell
Initial concentration: 0.0
 
 C3
Compartment: cell
Initial concentration: 1.0
 
 IC3
Compartment: cell
Initial concentration: 0.0
 
 IC2
Compartment: cell
Initial concentration: 0.0
 
 IM1
Compartment: cell
Initial concentration: 0.0
 
 IM2
Compartment: cell
Initial concentration: 0.0
 
 open states
Compartment: cell
Initial concentration: 0.0
 
 IF
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (24)
 
   [Na]out
Value: 140.0
Constant
 
   [Na]in
Value: 15.0
Constant
 
   scale
Value: 1000.0
Constant
 
   v
Value: -80.0
 
   Ena
Value: NaN
 
   a11
Value: NaN
 
   a12
Value: NaN
 
   a13
Value: NaN
 
   b11
Value: NaN
 
   b12
Value: NaN
 
   b13
Value: NaN
 
   a2
Value: NaN
 
   b2
Value: NaN
 
   a3
Value: NaN
 
   b3
Value: NaN
 
   a4
Value: NaN
 
   b4
Value: NaN
 
   a5
Value: NaN
 
   b5
Value: NaN
 
   Gna
Value: 23.5
Constant
 
   Rk
Value: 8314.0
Constant
 
   Fara
Value: 96485.0
Constant
 
   Temp
Value: 310.0
Constant
 
   I_Na
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000126

Curator's comment: (updated: 18 Jul 2007 00:52:55 BST)

Figure3B (wide-type) has been reproduced by MathSBML.

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