BIOMD0000000044
type: SBMLModel
is: MODEL6622948601
species: metaid_0000009
is part of: rno04020
reaction: metaid_0000020
units def: metaid_0000003
notes: Borghans1997 - Calcium Oscillation - Model 2 A theoretical expoloration of possible mechanisms of intracellular calcium oscillations has been studied, considering three hypothesis (see below). This model corresponds to the second hypothesis. This model is described in the article: Complex intracellular calcium oscillations. A theoretical exploration of possible mechanisms. Borghans JM, Dupont G, Goldbeter A. Biophys. Chem. 1997 May; 66(1): 25-41 Abstract: Intracellular Ca(2+) oscillations are commonly observed in a large number of cell types in response to stimulation by an extracellular agonist. In most cell types the mechanism of regular spiking is well understood and models based on Ca(2+)-induced Ca(2+) release (CICR) can account for many experimental observations. However, cells do not always exhibit simple Ca(2+) oscillations. In response to given agonists, some cells show more complex behaviour in the form of bursting, i.e. trains of Ca(2+) spikes separated by silent phases. Here we develop several theoretical models, based on physiologically plausible assumptions, that could account for complex intracellular Ca(2+) oscillations. The models are all based on one- or two-pool models based on CICR. We extend these models by (i) considering the inhibition of the Ca(2+)-release channel on a unique intracellular store at high cytosolic Ca(2+) concentrations, (ii) taking into account the Ca(2+)-activated degradation of inositol 1,4,5-trisphosphate (IP(3)), or (iii) considering explicity the evolution of the Ca(2+) concentration in two different pools, one sensitive and the other one insensitive to IP(3). Besides simple periodic oscillations, these three models can all account for more complex oscillatory behaviour in the form of bursting. Moreover, the model that takes the kinetics of IP(3) into account shows chaotic behaviour. This model is hosted on BioModels Database and identified by: MODEL6622948601 . To cite BioModels Database, please use: BioModels Database: …
substance units: metaid_0000003
reaction: metaid_0000023
created:
  W3 CDTF: Fri Jul 08 14:06:45 BST 2005
is version of: GO:0048016
length unit: length
area units: area
reaction: metaid_0000022
compartment: metaid_0000005
reaction: metaid_0000019
time units: metaid_0000004
parameter: metaid_0000015
reaction: metaid_0000018
volume units: metaid_0000323
creator:
  ORG:
    orgname: Keck Graduate Institute
  n:
    given: Harish
    family: Dharuri
curated: true
compartment: metaid_0000007
species: metaid_0000008
is described by: http://identifiers.org/pubmed/17029867
name: Borghans1997 - Calcium Oscillation - Model 2
compartment: metaid_0000006
modified:
  W3 CDTF: Mon Jun 03 17:03:27 BST 2013
reaction: metaid_0000017
units def: metaid_0000004
species: metaid_0000011
is version of: GO:0019722
reaction: metaid_0000021
reaction: metaid_0000016
species: metaid_0000010
occurs in: http://identifiers.org/taxonomy/10114

metaid_0000009
type: Species
is: CHEBI:29108
in compartment: metaid_0000006
is: C00076
has only substance units: false
is: SBO:0000327
constant: false
initial amount: NaN
initial concentration: 0.0
boundary condition: false

metaid_0000006
type: Compartment
is version of: GO:0005829
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

metaid_0000020
type: Reaction
is version of: GO:0051481
is: SBO:0000185
fast: false
reversible: false

968584
type: LocalParameter
is: SBO:0000035
value: 10.0

http://identifiers.org/biomodels.db/BIOMD0000000044#_849b7746_2e1a_4bfb_9440_2f790ed62491
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000008
type: Species
initial amount: NaN
is: SBO:0000327
initial concentration: 1000.0
boundary condition: false
is: C00076
is: CHEBI:29108
has only substance units: false
constant: false
in compartment: metaid_0000007

metaid_0000007
type: Compartment
is version of: GO:0005615
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

http://identifiers.org/biomodels.db/BIOMD0000000044#facbe4c3_d666_4b18_8b59_aeebeb54f9b7
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000003
type: SBMLUnitsDef
name: micromole (default)

http://identifiers.org/biomodels.db/BIOMD0000000044#caae2b17_bd25_4b5b_baf8_049548b5e054
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000023
type: Reaction
is version of: GO:0019310
is: SBO:0000179
fast: false
reversible: false
name: Ca independent IP3 degradation

968592
type: LocalParameter
is: SBO:0000498
value: 0.1

http://identifiers.org/biomodels.db/BIOMD0000000044#_06ee764c_b812_45d5_b937_53eda70f0f4d
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000010
type: Species
in compartment: metaid_0000006
boundary condition: false
constant: false
is: CHEBI:16595
is: C01245
initial amount: NaN
has only substance units: false
is: SBO:0000327
initial concentration: 0.45

metaid_0000022
type: Reaction
is version of: GO:0019310
is: SBO:0000179
fast: false
reversible: false
name: Ca dependent IP3 degradation

968591
type: LocalParameter
is: SBO:0000190
value: 4.0

968590
type: LocalParameter
is: SBO:0000194
value: 0.4

968588
type: LocalParameter
is: SBO:0000424
value: 1.0

968587
type: LocalParameter
is: SBO:0000324
value: 80.0

http://identifiers.org/biomodels.db/BIOMD0000000044#_080a9679_dd76_4ab0_a157_a3e7f16c643d
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000005
type: Compartment
is version of: GO:0005790
is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

metaid_0000019
type: Reaction
is version of: GO:0007204
is: SBO:0000185
fast: false
reversible: false

968583
type: LocalParameter
is: SBO:0000035
value: 1.0

http://identifiers.org/biomodels.db/BIOMD0000000044#_67774250_bd6c_452b_892c_2f508e1896cd
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

http://identifiers.org/biomodels.db/BIOMD0000000044#ac378bc4_ee6b_40de_a1c2_3cffa06157e2
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
in compartment: metaid_0000005
is: C00076
is: SBO:0000327
initial concentration: 0.36
has only substance units: false
initial amount: NaN
boundary condition: false
constant: false
is: CHEBI:29108

metaid_0000004
type: SBMLUnitsDef
name: minute (default)

http://identifiers.org/biomodels.db/BIOMD0000000044#_844085cc_10ec_4bf3_afd3_5ce889a78a9d
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 60.0
kind: SECOND

metaid_0000015
type: Parameter
is: SBO:0000498
constant: true
value: 0.5

metaid_0000018
type: Reaction
is version of: GO:0051482
reversible: false
fast: false
is version of: GO:0006816
is: SBO:0000185

968582
type: LocalParameter
is: SBO:0000423
value: 0.3

968581
type: LocalParameter
is: SBO:0000424
value: 0.2

968580
type: LocalParameter
is: SBO:0000194
value: 0.2

968579
type: LocalParameter
is: SBO:0000186
value: 19.5

http://identifiers.org/biomodels.db/BIOMD0000000044#bd598d9a_7fee_4183_8c5a_6a70ddcc21a2
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

http://identifiers.org/biomodels.db/BIOMD0000000044#c484780e_569a_4fe2_a0d0_3932c2d10953
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000017
type: Reaction
is version of: GO:0051481
is: SBO:0000185
fast: false
reversible: false

968578
type: LocalParameter
is: SBO:0000424
value: 0.1

968577
type: LocalParameter
is: SBO:0000186
value: 6.5

http://identifiers.org/biomodels.db/BIOMD0000000044#_143d4cd8_9097_4f6a_838b_04a377f6fb9e
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

http://identifiers.org/biomodels.db/BIOMD0000000044#_70a3f13b_355b_436b_a5fa_c16d6c3385eb
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000021
type: Reaction
is version of: GO:0007200
is version of: GO:0006021
is: SBO:0000393
fast: false
reversible: false
name: Agonist stimulated production of IP3

968586
type: LocalParameter
is: SBO:0000048
value: 2.5

http://identifiers.org/biomodels.db/BIOMD0000000044#d7e6d701_8ce4_4a2f_9c52_904a667cb09b
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

metaid_0000016
type: Reaction
is version of: GO:0006816
fast: false
is: SBO:0000185
is version of: GO:0007204
reversible: false

http://identifiers.org/biomodels.db/BIOMD0000000044#a2cd746b_9874_48fa_a0e8_fbff30051500
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

968576
type: LocalParameter
is: SBO:0000162
value: 1.0

968575
type: LocalParameter
is: SBO:0000485
value: 2.0

http://identifiers.org/biomodels.db/BIOMD0000000044#b3d31ee0_175e_4021_b036_d233322ecb1d
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008