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BIOMD0000000119 - Golomb2006_SomaticBursting_nonzero[Ca]

 

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Reference Publication
Publication ID: 16807352
Golomb D, Yue C, Yaari Y.
Contribution of persistent Na+ current and M-type K+ current to somatic bursting in CA1 pyramidal cells: combined experimental and modeling study.
J. Neurophysiol. 2006 Oct; 96(4): 1912-1926
Department of Physiology and Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University, Be'er-Sheva, Israel. golomb@bgu.ac.il  [more]
Model
Original Model: http://senselab.med.yale.e...
Submitter: Enuo He
Submission ID: MODEL1580005336
Submission Date: 20 Jun 2007 09:26:56 UTC
Last Modification Date: 05 Jul 2012 14:38:05 UTC
Creation Date: 06 Jun 2007 14:28:40 UTC
Encoders:  Enuo He
set #1
bqbiol:isVersionOf Gene Ontology voltage-gated potassium channel activity
Gene Ontology voltage-gated sodium channel activity
Gene Ontology neuronal action potential propagation
bqbiol:occursIn Taxonomy Rattus
Notes

Model is according to the paper Contribution of Persistent Na+ Current and M-Type K+ Current to Somatic Bursting in CA1 Pyramidal Cell: Combined Experimental. This is the second model from this paper for the non-zero [Ca2+] initial value, parameters and the kinetics quations from Table2 in the paper. Figure9Aa has been reproduced by MathSBML. The original model from ModelDB. http://senselab.med.yale.edu/modeldb/


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: 16807352 Submission Date: 20 Jun 2007 09:26:56 UTC Last Modification Date: 05 Jul 2012 14:38:05 UTC Creation Date: 06 Jun 2007 14:28:40 UTC
Mathematical expressions
Reactions
reaction_0000001      
Rules
Assignment Rule (variable: Minfs) Assignment Rule (variable: Pinfs) Assignment Rule (variable: Ainfs) Assignment Rule (variable: IA)
Assignment Rule (variable: Iz) Assignment Rule (variable: INa) Assignment Rule (variable: INaP) Assignment Rule (variable: IKdr)
Rate Rule (variable: zzs) Rate Rule (variable: bbs) Rate Rule (variable: hhs) Rate Rule (variable: nns)
Assignment Rule (variable: mKCa) Assignment Rule (variable: ICa) Assignment Rule (variable: IKC) Assignment Rule (variable: IAHP)
Rate Rule (variable: rrs) Rate Rule (variable: ccs) Rate Rule (variable: qqs) Rate Rule (variable: VVs)
Physical entities
Compartments Species
compartment_0000001 Ca    
Global parameters
Cm pms pns VNa
t_tauh t_taun thetaa sigmaa
thetab sigmab tauBs sigmam
sigmah sigman sigmaz gNa
gKdr gL Iapp gA
gNaP gZ thetaz tauZs
phi thetah thetam thetan
thetap sigmap VK VL
INa INaP IKdr IA
Iz Minfs Pinfs Ainfs
zzs bbs nns hhs
VVs rrs ccs qqs
thetar VCa sigmar sigmac
thetac pwrc pwrq gCa
gKCa gKAHP tauRs aq
ac tauq tauCa uuCa
tauKc mKCa ICa IAHP
IKC      
Reactions (1)
 
 reaction_0000001  → [Ca];  
 
Rules (20)
 
 Assignment Rule (name: Minfs) Minfs = GAMMAF(V, thetam, sigmam)
 
 Assignment Rule (name: Pinfs) Pinfs = GAMMAF(V, thetap, sigmap)
 
 Assignment Rule (name: Ainfs) Ainfs = GAMMAF(V, thetaa, sigmaa)
 
 Assignment Rule (name: IA) IA = gA*Ainfs^3*bbs*(V-VK)
 
 Assignment Rule (name: Iz) Iz = gZ*zzs*(V-VK)
 
 Assignment Rule (name: INa) INa = gNa*Minfs^pms*hhs*(V-VNa)
 
 Assignment Rule (name: INaP) INaP = gNaP*Pinfs*(V-VNa)
 
 Assignment Rule (name: IKdr) IKdr = gKdr*nns^pns*(V-VK)
 
 Rate Rule (name: zzs) d [ zzs] / d t= (GAMMAF(V, thetaz, sigmaz)-zzs)/tauZs
 
 Rate Rule (name: bbs) d [ bbs] / d t= (GAMMAF(V, thetab, sigmab)-bbs)/tauBs
 
 Rate Rule (name: hhs) d [ hhs] / d t= phi*(GAMMAF(V, thetah, sigmah)-hhs)/(1+7.5*GAMMAF(V, t_tauh, -6))
 
 Rate Rule (name: nns) d [ nns] / d t= phi*(GAMMAF(V, thetan, sigman)-nns)/(1+5*GAMMAF(V, t_taun, -15))
 
 Assignment Rule (name: mKCa) mKCa = ZFUNC(ac, Ca, pwrc)
 
 Assignment Rule (name: ICa) ICa = gCa*rrs^2*(V-VCa)
 
 Assignment Rule (name: IKC) IKC = gKCa*mKCa*ccs*(V-VK)
 
 Assignment Rule (name: IAHP) IAHP = gKAHP*qqs*(V-VK)
 
 Rate Rule (name: rrs) d [ rrs] / d t= (GAMMAF(V, thetar, sigmar)-rrs)/tauRs
 
 Rate Rule (name: ccs) d [ ccs] / d t= (GAMMAF(V, thetac, sigmac)-ccs)/tauKc
 
 Rate Rule (name: qqs) d [ qqs] / d t= (ZFUNC(aq, Ca, pwrq)-qqs)/tauq
 
 Rate Rule (name: V) d [ VVs] / d t= ((-gL)*(V-VL)-INa-INaP-IKdr-IA-Iz-ICa-IKC-IAHP+Iapp)/Cm
 
Functions (2)
 
 GAMMAF lambda(VV, theta, sigma, 1/(1+exp((-(VV-theta))/sigma)))
 
 ZFUNC lambda(AA, CA, zz, 1/(1+AA^zz/CA^zz))
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Ca
Compartment: compartment_0000001
Initial concentration: 7.87E-4
 
Global Parameters (69)
 
   Cm
Value: 1.0
Constant
 
   pms
Value: 3.0
Constant
 
   pns
Value: 4.0
Constant
 
   VNa
Value: 55.0
Constant
 
   t_tauh
Value: -40.5
Constant
 
   t_taun
Value: -27.0
Constant
 
   thetaa
Value: -50.0
Constant
 
   sigmaa
Value: 20.0
Constant
 
   thetab
Value: -80.0
Constant
 
   sigmab
Value: -6.0
Constant
 
   tauBs
Value: 15.0
Constant
 
   sigmam
Value: 9.5
Constant
 
   sigmah
Value: -7.0
Constant
 
   sigman
Value: 10.0
Constant
 
   sigmaz
Value: 5.0
Constant
 
   gNa
Value: 35.0
Constant
 
   gKdr
Value: 6.0
Constant
 
   gL
Value: 0.05
Constant
 
   Iapp
Value: 1.0
Constant
 
   gA
Value: 1.4
Constant
 
   gNaP
Value: 0.2
Constant
 
   gZ
Value: 1.0
Constant
 
   thetaz
Value: -39.0
Constant
 
   tauZs
Value: 75.0
Constant
 
   phi
Value: 10.0
Constant
 
   thetah
Value: -45.0
Constant
 
   thetam
Value: -30.0
Constant
 
   thetan
Value: -35.0
Constant
 
   thetap
Value: -41.0
Constant
 
   sigmap
Value: 3.0
Constant
 
   VK
Value: -90.0
Constant
 
   VL
Value: -70.0
Constant
 
   INa
Value: NaN
 
   INaP
Value: NaN
 
   IKdr
Value: NaN
 
   IA
Value: NaN
 
   Iz
Value: NaN
 
   Minfs
Value: NaN
 
   Pinfs
Value: NaN
 
   Ainfs
Value: NaN
 
   zzs
Value: 0.0013689
 
   bbs
Value: 0.207565
 
   nns
Value: 0.0242166
 
   hhs
Value: 0.979199
 
   VVs
Value: -71.962
 
   rrs
Value: 0.005507
 
   ccs
Value: 0.002486
 
   qqs  
 
   thetar
Value: -20.0
Constant
 
   VCa
Value: 120.0
Constant
 
   sigmar
Value: 10.0
Constant
 
   sigmac
Value: 7.0
Constant
 
   thetac
Value: -30.0
Constant
 
   pwrc
Value: 1.0
Constant
 
   pwrq
Value: 4.0
Constant
 
   gCa
Value: 0.08
Constant
 
   gKCa
Value: 10.0
Constant
 
   gKAHP
Value: 5.0
Constant
 
   tauRs
Value: 1.0
Constant
 
   aq
Value: 2.0
Constant
 
   ac
Value: 6.0
Constant
 
   tauq
Value: 450.0
Constant
 
   tauCa
Value: 13.0
Constant
 
   uuCa
Value: 0.13
Constant
 
   tauKc
Value: 2.0
Constant
 
   mKCa
Value: NaN
 
   ICa
Value: NaN
 
   IAHP
Value: NaN
 
   IKC
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000119

Curator's comment: (updated: 15 Aug 2007 19:57:02 BST)

Figure9Aa has been reproduced by MathSBML.

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