08032015130337645m0500
type: Ontology
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> A Bifurcation Analysis of Two Coupled Calcium Oscillators <author> <firstname>Catherine</firstname> <surname>Lloyd</surname> <affiliation> <shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil> </affiliation> </author> </articleinfo> Model Status This CellML model runs in both OpenCell and COR to produce an oscillating output similar to that from the original published model. The units have been checked and they are consistent. <sect1 id="sec_structure"> Model Structure ABSTRACT: In many cell types, asynchronous or synchronous oscillations in the concentration of intracellular free calcium occur in adjacent cells that are coupled by gap junctions. Such oscillations are believed to underlie oscillatory intercellular calcium waves in some cell types, and thus it is important to understand how they occur and are modified by intercellular coupling. Using a previous model of intracellular calcium oscillations in pancreatic acinar cells, this article explores the effects of coupling two cells with a simple linear diffusion term. Depending on the concentration of a signal molecule, inositol (1,4,5)-trisphosphate, coupling two identical cells by diffusion can give rise to synchronized in-phase oscillations, as well as different-amplitude in-phase oscillations and same-amplitude antiphase oscillations. Coupling two nonidentical cells leads to more complex behaviors such as cascades of period doubling and multiply periodic solutions. This study is a first step towards understanding the role and significance of the diffusion of calcium through gap junctions in the coordination of oscillatory calcium waves in a variety of cell types. The original paper reference is cited below: A bifurcation analysis of two coupled calcium oscillators, Michael Bindschadler and James Sneyd, 2001, CHAOS , 11, 237-246. PubMed ID: 12779457 <informalfigure float="0" id="fig_cell_diagram"> <media…
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model description: A bifurcation analysis of two coupled calcium oscillators
legacy code URI: C:\Users\thomp_000\Dropbox\Work Related\Annotated Models\Bindschadler_2001\bindschadler_sneyd_2001.cellml
annotator name: Chris Thompson
model id: bindschadler_sneyd_2001
model name: bindschadler_sneyd_2001
cellml URL: https://models.physiomeproject.org/exposure/4542f0f90437cc1d39c0a7130aef110c/bindschadler_sneyd_2001.cellml/view

Chemical concentration
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Chemical concentration

Chemical molar flow rate
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Chemical molar flow rate

calcium ion
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: calcium ion

pancreatic acinar cell
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: pancreatic acinar cell

Endoplasmic reticulum
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Endoplasmic reticulum

Intercellular junction
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Intercellular junction

Plasma membrane
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subclass of: Reference physical entity
subclass of: Restriction
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Portion of cytosol
type: Class
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subclass of: Restriction
  on property: refersTo
  has value: Portion of cytosol

Portion of extracellular matrix
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Portion of extracellular matrix

Composite physical entity
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disjoint with: Reference physical entity
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Computation
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subclass of: Computational model component
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comment: A mathematical and/or logical expression that determines the value of a data structure.

Computational model component
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subclass of: SemSim component
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Custom physical dependency
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subclass of: Physical dependency
disjoint with: Reference physical dependency
comment: A physical dependency defined in a specific SemSim model.

Custom physical entity
type: Class
subclass of: Physical entity
comment: A physical entity defined in a specific SemSim model.

Custom physical process
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subclass of: Physical process
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Custom physical property
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subclass of: Physical property
disjoint with: Reference physical property
comment: A physical property defined in a specific SemSim model.

Data structure
type: Class
subclass of: Computational model component
comment: A computational element that stores numerical and/or logical information related to the model.

Decimal
type: Class
subclass of: Real
disjoint with: Integer
comment: A data structure whose value is limited to decimals.

Integer
type: Class
subclass of: Real
comment: A data structure whose value is limited to the whole numbers.

MMLchoice
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comment: A data structure unique to JSim's Mathematical Modeling Language (MML) used to set one or more model input values at runtime.

Physical dependency
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subclass of: Physical model component
disjoint with: Physical entity
disjoint with: Physical process
disjoint with: Physical property
comment: A quantitative relation between values of physical properties that occurs over a span of time and that determines the time-course of a physical process.

Physical entity
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disjoint with: Physical process
disjoint with: Physical property
comment: A physics analytical entity that represents the material, energy, and/or information content of material or immaterial, space-occupying continuants.

Physical model component
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comment: A SemSim model element used to represent, in whole or in part, the physical meaning of a computational element.

Physical process
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comment: A physical processural entity that is a flow, or the control of a flow, of energy and/or information amongst physical continuants that are participants in the physical process.

Physical property
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subclass of: Physical model component
comment: A physical attribute of an instance of a physical entity, an occurrence of a physical process, or a physical dependency that has a quantitative value that is measurable by a physical device or method, or is computable from such values.

Real
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subclass of: Data structure
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Reference physical dependency
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Reference physical entity
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comment: A physical entity that is defined using a term from an external knowledge resource.

Reference physical process
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subclass of: Physical process
comment: A physical process that is defined using a term in an external knowledge resource.

Reference physical property
type: Class
subclass of: Physical property
comment: A physical property that is defined using a term in an external knowledge resource.

Relational constraint
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subclass of: Computational model component
comment: A logical expression that constrains, but does not define, the value of a data structure. Example: x > 0.

SemSim component
type: Class
comment: A computational or physical element of a SemSim model.

Submodel
type: Class
subclass of: Physical model component
comment: A grouping of one or more data structures that comprise a computationally or physically distinct part of a model or submodel.

Unit of measurement
type: Class
subclass of: Computational model component
comment: A physical quantity chosen as a standard in terms of which other physical quantities may be expressed.

ATPase pumps
type: NamedIndividual
type: Custom physical entity
is index entity for: ATPase pumps part of Plasma membrane part of Second pancreatic acinar cell
part of: Plasma membrane

ATPase pumps
type: NamedIndividual
type: Custom physical entity
is index entity for: ATPase pumps part of Plasma membrane part of First pancreatic acinar cell
part of: Plasma membrane

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Endoplasmic reticulum part of First pancreatic acinar cell
part of: Endoplasmic reticulum

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Portion of cytosol part of First pancreatic acinar cell
part of: Portion of cytosol
has physical property: Chemical concentration

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Portion of cytosol part of Second pancreatic acinar cell
part of: Portion of cytosol
has physical property: Chemical concentration

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Endoplasmic reticulum part of Second pancreatic acinar cell
part of: Endoplasmic reticulum

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Intercellular junction
part of: Intercellular junction

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Portion of extracellular matrix
part of: Portion of extracellular matrix

calcium ion
type: NamedIndividual
refers to: calcium ion
is index entity for: CHEBI 39124 part of Portion of cytosol part of CL 0002064
part of: Portion of cytosol

pancreatic acinar cell
type: NamedIndividual
refers to: pancreatic acinar cell
has part: Plasma membrane
has part: Portion of cytosol

Ca flow from endoplasmic reticulum to cytoplasm in cell 1
type: NamedIndividual
type: Custom physical process
has source: calcium ion
has sink: calcium ion
has mediator: IP3 Ca channel
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 1

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 1
annotated target: IP3 Ca channel

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 1

Ca flow from endoplasmic reticulum to cytoplasm in cell 2
type: NamedIndividual
type: Custom physical process
has sink: calcium ion
has source: calcium ion
has mediator: IP3 Ca channel
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 2
annotated target: IP3 Ca channel

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 2

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Ca flow from endoplasmic reticulum to cytoplasm in cell 2

Ca leakage across cell membrane
type: NamedIndividual
type: Custom physical process
has sink: calcium ion
has source: calcium ion
has mediator: Plasma membrane
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Ca leakage across cell membrane

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Ca leakage across cell membrane

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated source: Ca leakage across cell membrane
annotated target: Plasma membrane

Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps
type: NamedIndividual
type: Custom physical process
has mediator: ATPase pumps
has source: calcium ion
has sink: calcium ion
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated target: ATPase pumps
annotated source: Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps

Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps
type: NamedIndividual
type: Custom physical process
has mediator: ATPase pumps
has source: calcium ion
has sink: calcium ion
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated target: ATPase pumps
annotated source: Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps

Endoplasmic reticulum
type: NamedIndividual
refers to: Endoplasmic reticulum
has part: calcium ion
is index entity for: Endoplasmic reticulum part of First pancreatic acinar cell
part of: First pancreatic acinar cell
has part: IP3 Ca channel

Endoplasmic reticulum
type: NamedIndividual
refers to: Endoplasmic reticulum
has part: calcium ion
is index entity for: Endoplasmic reticulum part of Second pancreatic acinar cell
has part: IP3 Ca channel
part of: Second pancreatic acinar cell

First pancreatic acinar cell
type: NamedIndividual
type: pancreatic acinar cell
type: Custom physical entity
has part: Endoplasmic reticulum
has part: Plasma membrane
has part: Portion of cytosol

IP3 Ca channel
type: NamedIndividual
type: Custom physical entity
part of: Endoplasmic reticulum
is index entity for: IP3 Ca channel part of Endoplasmic reticulum part of First pancreatic acinar cell

IP3 Ca channel
type: NamedIndividual
type: Custom physical entity
part of: Endoplasmic reticulum
is index entity for: IP3 Ca channel part of Endoplasmic reticulum part of Second pancreatic acinar cell

Intercellular diffusion between two pancreatic acinar cells
type: NamedIndividual
type: Custom physical process
has source: calcium ion
has sink: calcium ion
has mediator: calcium ion
has physical property: Chemical molar flow rate

Axiom
has multiplier: 1.0
annotated property: hasMediator
annotated target: calcium ion
annotated source: Intercellular diffusion between two pancreatic acinar cells

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: calcium ion
annotated source: Intercellular diffusion between two pancreatic acinar cells

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: calcium ion
annotated source: Intercellular diffusion between two pancreatic acinar cells

Intercellular junction
type: NamedIndividual
refers to: Intercellular junction
has part: calcium ion

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
has part: ATPase pumps
is index entity for: Plasma membrane part of Second pancreatic acinar cell
part of: Second pancreatic acinar cell

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
part of: pancreatic acinar cell
is index entity for: Plasma membrane part of CL 0002064

Plasma membrane
type: NamedIndividual
refers to: Plasma membrane
has part: ATPase pumps
part of: First pancreatic acinar cell
is index entity for: Plasma membrane part of First pancreatic acinar cell

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: calcium ion
part of: First pancreatic acinar cell
is index entity for: Portion of cytosol part of First pancreatic acinar cell

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: calcium ion
is index entity for: Portion of cytosol part of Second pancreatic acinar cell
part of: Second pancreatic acinar cell

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: calcium ion
part of: pancreatic acinar cell
is index entity for: Portion of cytosol part of CL 0002064

Portion of extracellular matrix
type: NamedIndividual
refers to: Portion of extracellular matrix
has part: calcium ion

Second pancreatic acinar cell
type: NamedIndividual
type: pancreatic acinar cell
type: Custom physical entity
has part: Endoplasmic reticulum
has part: Plasma membrane
has part: Portion of cytosol

UNIT litre
type: NamedIndividual
type: Unit of measurement
has computational code: litre
is fundamental unit: true
unit factor for: UNIT micro molar

UNIT micro molar
type: NamedIndividual
type: Unit of measurement
has computational code: micro_molar
has unit factor: UNIT litre
unit factor for: UNIT micro molar per second
has unit factor: UNIT mole
unit factor for: UNIT second order rate
unit for: c1.c1
unit for: c2.c2
unit for: h1.p
unit for: h2.p
unit for: j diffusion.c1
unit for: j diffusion.c2
unit for: j pump.Kp
unit for: j pump.c1
unit for: j pump.c2
unit for: j receptor.p
unit for: model parameters.Kp
unit for: model parameters.R1
unit for: model parameters.R3
unit for: model parameters.R5
unit for: model parameters.p
unit for: phi.R1
unit for: phi.R3
unit for: phi.R5
unit for: phi.c1
unit for: phi.c2

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT litre
annotated source: UNIT micro molar

Axiom
has unit factor prefix: micro
annotated property: hasUnitFactor
annotated source: UNIT micro molar
annotated target: UNIT mole

UNIT micro molar per second
type: NamedIndividual
type: Unit of measurement
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has unit factor: UNIT micro molar
has unit factor: UNIT per second
unit for: c1.j diffusion
unit for: c1.j leak
unit for: c1.j pump c1
unit for: c1.j receptor c1
unit for: c2.j diffusion
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unit for: c2.j receptor c2
unit for: j diffusion.j diffusion
unit for: j pump.Vp
unit for: j pump.j pump c1
unit for: j pump.j pump c2
unit for: j receptor.j receptor c1
unit for: j receptor.j receptor c2
unit for: j receptor.kf
unit for: model parameters.Vp
unit for: model parameters.j leak
unit for: model parameters.k1
unit for: model parameters.k2
unit for: model parameters.k3
unit for: model parameters.kf
unit for: phi.k1
unit for: phi.k2
unit for: phi.k3

UNIT mole
type: NamedIndividual
type: Unit of measurement
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unit factor for: UNIT micro molar

UNIT per second
type: NamedIndividual
type: Unit of measurement
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unit factor for: UNIT micro molar per second
has unit factor: UNIT second
unit factor for: UNIT second order rate
unit for: h1.phi2 c1
unit for: h1.phi3 c1
unit for: h1.phi 1 c1
unit for: h2.phi2 c2
unit for: h2.phi3 c2
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unit for: j diffusion.D
unit for: j receptor.phi 1 c1
unit for: j receptor.phi 1 c2
unit for: model parameters.D
unit for: model parameters.r4
unit for: phi.phi2 c1
unit for: phi.phi2 c2
unit for: phi.phi3 c1
unit for: phi.phi3 c2
unit for: phi.phi 1 c1
unit for: phi.phi 1 c2
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Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT per second
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
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unit factor for: UNIT per second
unit for: c1.time
unit for: c2.time
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UNIT second order rate
type: NamedIndividual
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has unit factor: UNIT micro molar
has unit factor: UNIT per second
unit for: h1.phi1 c1
unit for: h2.phi1 c2
unit for: j receptor.phi1 c1
unit for: j receptor.phi1 c2
unit for: model parameters.r2
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Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT micro molar
annotated source: UNIT second order rate

c1
type: NamedIndividual
type: Submodel
name: c1
has associated data structure: c1.c1
has associated data structure: c1.j diffusion
has associated data structure: c1.j leak
has associated data structure: c1.j pump c1
has associated data structure: c1.j receptor c1
has associated data structure: c1.time
has computational component: c1 computation

c1.c1
type: NamedIndividual
type: Decimal
has start value: 0.3
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Cell 1 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration
mapped to: j diffusion.c1
mapped to: j pump.c1
mapped to: phi.c1

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: c1.c1

c1.j diffusion
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
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comment: Diffusion of Ca between coupled cells
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Intercellular diffusion between two pancreatic acinar cells
has computational component: c1.j diffusion

c1.j leak
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Ca leakage across the cell membrane
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca leakage across cell membrane
has computational component: c1.j leak

c1.j pump c1
type: NamedIndividual
type: Decimal
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is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Ca flow out of cell 1 via ATPase pumps
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps
has computational component: c1.j pump c1

c1.j receptor c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Ca flow through the IP3 receptor in cell 1
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca flow from endoplasmic reticulum to cytoplasm in cell 1
has computational component: c1.j receptor c1

c1.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
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comment: Time
has unit: UNIT second
is computational component for: c1.time property

c1 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>c1</ci> </apply> <apply> <plus /> <apply> <minus /> <ci>j_receptor_c1</ci> <ci>j_pump_c1</ci> </apply> <ci>j_leak</ci> <ci>j_diffusion</ci> </apply> </apply>
is computational component for: c1

c2
type: NamedIndividual
type: Submodel
name: c2
has associated data structure: c2.c2
has associated data structure: c2.j diffusion
has associated data structure: c2.j leak
has associated data structure: c2.j pump c2
has associated data structure: c2.j receptor c2
has associated data structure: c2.time
has computational component: c2 computation

c2.c2
type: NamedIndividual
type: Decimal
has start value: 0.1
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Cell 2 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration
mapped to: j diffusion.c2
mapped to: j pump.c2
mapped to: phi.c2

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
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c2.j diffusion
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Diffusion of Ca between coupled cells
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Intercellular diffusion between two pancreatic acinar cells
has computational component: c2.j diffusion

c2.j leak
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Ca leakage across the cell membrane
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca leakage across cell membrane
has computational component: c2.j leak

c2.j pump c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Ca flow out of cell 2 via ATPase pumps
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps
has computational component: c2.j pump c2

c2.j receptor c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Ca flow through the IP3 receptor in cell 2
has unit: UNIT micro molar per second
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
has computational component: c2.j receptor c2

c2.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time
has unit: UNIT second
is computational component for: c2.time property

c2 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>c2</ci> </apply> <apply> <plus /> <apply> <minus /> <ci>j_receptor_c2</ci> <ci>j_pump_c2</ci> </apply> <ci>j_leak</ci> <ci>j_diffusion</ci> </apply> </apply>
is computational component for: c2

environment
type: NamedIndividual
type: Submodel
name: environment
has associated data structure: environment.time
has computational component: environment computation

environment.time
type: NamedIndividual
type: Decimal
metadata ID: environment_time
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Time
has unit: UNIT second
mapped to: c1.time
mapped to: c2.time
is computational component for: environment.time property
mapped to: h1.time
mapped to: h2.time

h1
type: NamedIndividual
type: Submodel
name: h1
has associated data structure: h1.h1
has associated data structure: h1.p
has associated data structure: h1.phi1 c1
has associated data structure: h1.phi2 c1
has associated data structure: h1.phi3 c1
has associated data structure: h1.phi 1 c1
has associated data structure: h1.time
has computational component: h1 computation

h1.h1
type: NamedIndividual
type: Decimal
has start value: 0.8
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Cell 1 active IP3 receptors on the endoplasmic reticulum in the open and shut states
is computational component for: h1.h1 property
mapped to: j receptor.h1

h1.p
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: IP3 receptor concentration
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: h1.p

h1.phi1 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 1
has unit: UNIT second order rate
is computational component for: h1.phi1 c1 property

h1.phi2 c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to inactive state in cell 1
has unit: UNIT per second
is computational component for: h1.phi2 c1 property

h1.phi3 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the inactive state to open state in cell 1
has unit: UNIT per second
is computational component for: h1.phi3 c1 property

h1.phi 1 c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 1
has unit: UNIT per second
is computational component for: h1.phi 1 c1 property

h1.time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Time
has unit: UNIT second
is computational component for: h1.time property

h1 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>h1</ci> </apply> <apply> <minus /> <apply> <times /> <ci>phi3_c1</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>h1</ci> </apply> </apply> <apply> <divide /> <apply> <times /> <ci>phi1_c1</ci> <ci>phi2_c1</ci> <ci>h1</ci> <ci>p</ci> </apply> <apply> <plus /> <apply> <times /> <ci>phi1_c1</ci> <ci>p</ci> </apply> <ci>phi_1_c1</ci> </apply> </apply> </apply> </apply>
is computational component for: h1

h2
type: NamedIndividual
type: Submodel
name: h2
has associated data structure: h2.h2
has associated data structure: h2.p
has associated data structure: h2.phi1 c2
has associated data structure: h2.phi2 c2
has associated data structure: h2.phi3 c2
has associated data structure: h2.phi 1 c2
has associated data structure: h2.time
has computational component: h2 computation

h2.h2
type: NamedIndividual
type: Decimal
has start value: 0.1
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Cell 2 active IP3 receptors on the endoplasmic reticulum in the open and shut states
is computational component for: h2.h2 property
mapped to: j receptor.h2

h2.p
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: IP3 receptor concentration
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: h2.p

h2.phi1 c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 2
has unit: UNIT second order rate
is computational component for: h2.phi1 c2 property

h2.phi2 c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to inactive state in cell 2
has unit: UNIT per second
is computational component for: h2.phi2 c2 property

h2.phi3 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the inactive state to open state in cell 2
has unit: UNIT per second
is computational component for: h2.phi3 c2 property

h2.phi 1 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 2
has unit: UNIT per second
is computational component for: h2.phi 1 c2 property

h2.time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Time
has unit: UNIT second
is computational component for: h2.time property

h2 computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>h2</ci> </apply> <apply> <minus /> <apply> <times /> <ci>phi3_c2</ci> <apply> <minus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>h2</ci> </apply> </apply> <apply> <divide /> <apply> <times /> <ci>phi1_c2</ci> <ci>phi2_c2</ci> <ci>h2</ci> <ci>p</ci> </apply> <apply> <plus /> <apply> <times /> <ci>phi1_c2</ci> <ci>p</ci> </apply> <ci>phi_1_c2</ci> </apply> </apply> </apply> </apply>
is computational component for: h2

j diffusion
type: NamedIndividual
type: Submodel
name: j_diffusion
has associated data structure: j diffusion.D
has associated data structure: j diffusion.c1
has associated data structure: j diffusion.c2
has associated data structure: j diffusion.j diffusion
has computational component: j diffusion computation

j diffusion.D
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Intercellular coupling permeability rate constant.
has unit: UNIT per second
is computational component for: j diffusion.D property

j diffusion.c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cell 1 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: j diffusion.c1

j diffusion.c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cell 2 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: j diffusion.c2

j diffusion.j diffusion
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Diffusion of Ca between coupled cells
has unit: UNIT micro molar per second
mapped to: c1.j diffusion
mapped to: c2.j diffusion
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Intercellular diffusion between two pancreatic acinar cells
has computational component: j diffusion.j diffusion

j diffusion computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>j_diffusion</ci> <apply> <times /> <ci>D</ci> <apply> <minus /> <ci>c2</ci> <ci>c1</ci> </apply> </apply> </apply>
is computational component for: j diffusion

j pump
type: NamedIndividual
type: Submodel
name: j_pump
has associated data structure: j pump.Kp
has associated data structure: j pump.Vp
has associated data structure: j pump.c1
has associated data structure: j pump.c2
has associated data structure: j pump.j pump c1
has associated data structure: j pump.j pump c2
has computational component: j pump computation

j pump.Kp
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for calculation of Ca flow via ATPase pumps
has unit: UNIT micro molar
is computational component for: j pump.Kp property

j pump.Vp
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Constant for calculation of Ca flow via ATPase pumps
has unit: UNIT micro molar per second
is computational component for: j pump.Vp property

j pump.c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cell 1 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: j pump.c1

j pump.c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cell 2 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: j pump.c2

j pump.j pump c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
metadata ID: j_pump_j_pump_c1
has cell m lpublic interface: out
is declared: true
comment: Ca flow out of cell 1 via ATPase pumps
has unit: UNIT micro molar per second
mapped to: c1.j pump c1
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca out of cell 1 cytoplasm to extracellular matrix via ATPase pumps
has computational component: j pump.j pump c1

j pump.j pump c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Ca flow out of cell 2 via ATPase pumps
has unit: UNIT micro molar per second
mapped to: c2.j pump c2
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca out of cell 2 cytoplasm to extracellular matrix via ATPase pumps
has computational component: j pump.j pump c2

j pump computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>j_pump_c1</ci> <apply> <divide /> <apply> <times /> <ci>Vp</ci> <apply> <power /> <ci>c1</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> <apply> <plus /> <apply> <power /> <ci>Kp</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <apply> <power /> <ci>c1</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>j_pump_c2</ci> <apply> <divide /> <apply> <times /> <ci>Vp</ci> <apply> <power /> <ci>c2</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> <apply> <plus /> <apply> <power /> <ci>Kp</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <apply> <power /> <ci>c2</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> </apply> </apply>
is computational component for: j pump

j receptor
type: NamedIndividual
type: Submodel
name: j_receptor
has associated data structure: j receptor.h1
has associated data structure: j receptor.h2
has associated data structure: j receptor.j receptor c1
has associated data structure: j receptor.j receptor c2
has associated data structure: j receptor.kf
has associated data structure: j receptor.p
has associated data structure: j receptor.phi1 c1
has associated data structure: j receptor.phi1 c2
has associated data structure: j receptor.phi 1 c1
has associated data structure: j receptor.phi 1 c2
has computational component: j receptor computation

j receptor.h1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Cell 1 active IP3 receptors on the endoplasmic reticulum in the open and shut states
is computational component for: j receptor.h1 property

j receptor.h2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cell 2 active IP3 receptors on the endoplasmic reticulum in the open and shut states
is computational component for: j receptor.h2 property

j receptor.j receptor c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
metadata ID: j_receptor_j_receptor_c1
has cell m lpublic interface: out
is declared: true
comment: Ca flow through the IP3 receptor in cell 1
has unit: UNIT micro molar per second
mapped to: c1.j receptor c1
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca flow from endoplasmic reticulum to cytoplasm in cell 1
has computational component: j receptor.j receptor c1

j receptor.j receptor c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Ca flow through the IP3 receptor in cell 2
has unit: UNIT micro molar per second
mapped to: c2.j receptor c2
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca flow from endoplasmic reticulum to cytoplasm in cell 2
has computational component: j receptor.j receptor c2

j receptor.kf
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Constant for calculation of Ca flow via IP3 receptor channels
has unit: UNIT micro molar per second
is computational component for: j receptor.kf property

j receptor.p
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: IP3 receptor concentration
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: j receptor.p

j receptor.phi1 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 1
has unit: UNIT second order rate
is computational component for: j receptor.phi1 c1 property

j receptor.phi1 c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 2
has unit: UNIT second order rate
is computational component for: j receptor.phi1 c2 property

j receptor.phi 1 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 1
has unit: UNIT per second
is computational component for: j receptor.phi 1 c1 property

j receptor.phi 1 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 2
has unit: UNIT per second
is computational component for: j receptor.phi 1 c2 property

j receptor computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>j_receptor_c1</ci> <apply> <times /> <ci>kf</ci> <apply> <power /> <apply> <divide /> <apply> <times /> <ci>p</ci> <ci>h1</ci> <ci>phi1_c1</ci> </apply> <apply> <plus /> <apply> <times /> <ci>phi1_c1</ci> <ci>p</ci> </apply> <ci>phi_1_c1</ci> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">4</cn> </apply> </apply> </apply> <apply> <eq /> <ci>j_receptor_c2</ci> <apply> <times /> <ci>kf</ci> <apply> <power /> <apply> <divide /> <apply> <times /> <ci>p</ci> <ci>h2</ci> <ci>phi1_c2</ci> </apply> <apply> <plus /> <apply> <times /> <ci>phi1_c2</ci> <ci>p</ci> </apply> <ci>phi_1_c2</ci> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">4</cn> </apply> </apply> </apply>
is computational component for: j receptor

model parameters
type: NamedIndividual
type: Submodel
name: model_parameters
has associated data structure: model parameters.D
has associated data structure: model parameters.Kp
has associated data structure: model parameters.R1
has associated data structure: model parameters.R3
has associated data structure: model parameters.R5
has associated data structure: model parameters.Vp
has associated data structure: model parameters.j leak
has associated data structure: model parameters.k1
has associated data structure: model parameters.k2
has associated data structure: model parameters.k3
has associated data structure: model parameters.kf
has associated data structure: model parameters.p
has associated data structure: model parameters.r2
has associated data structure: model parameters.r4
has computational component: model parameters computation

model parameters.D
type: NamedIndividual
type: Decimal
has start value: 0.01
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Intercellular coupling permeability rate constant.
has unit: UNIT per second
mapped to: j diffusion.D
is computational component for: model parameters.D property

model parameters.Kp
type: NamedIndividual
type: Decimal
has start value: 0.18
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Constant for calculation of Ca flow via ATPase pumps
has unit: UNIT micro molar
mapped to: j pump.Kp
is computational component for: model parameters.Kp property

model parameters.R1
type: NamedIndividual
type: Decimal
has start value: 6
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 1
has unit: UNIT micro molar
is computational component for: model parameters.R1 property
mapped to: phi.R1

model parameters.R3
type: NamedIndividual
type: Decimal
has start value: 50
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT micro molar
is computational component for: model parameters.R3 property
mapped to: phi.R3

model parameters.R5
type: NamedIndividual
type: Decimal
has start value: 1.6
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 3
has unit: UNIT micro molar
is computational component for: model parameters.R5 property
mapped to: phi.R5

model parameters.Vp
type: NamedIndividual
type: Decimal
has start value: 1.2
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for calculation of Ca flow via ATPase pumps
has unit: UNIT micro molar per second
mapped to: j pump.Vp
is computational component for: model parameters.Vp property

model parameters.j leak
type: NamedIndividual
type: Decimal
has start value: 0.2
is solution domain: false
is discrete: false
metadata ID: model_parameters_j_leak
has cell m lpublic interface: out
is declared: true
comment: Ca leakage across the cell membrane
has unit: UNIT micro molar per second
mapped to: c1.j leak
mapped to: c2.j leak
is computational component for: Chemical molar flow rate

Chemical molar flow rate
type: NamedIndividual
refers to: Chemical molar flow rate
physical property of: Ca leakage across cell membrane
has computational component: model parameters.j leak

model parameters.k1
type: NamedIndividual
type: Decimal
has start value: 44
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi -1
has unit: UNIT micro molar per second
is computational component for: model parameters.k1 property
mapped to: phi.k1

model parameters.k2
type: NamedIndividual
type: Decimal
has start value: 26.5
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT micro molar per second
is computational component for: model parameters.k2 property
mapped to: phi.k2

model parameters.k3
type: NamedIndividual
type: Decimal
has start value: 1.6
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 3
has unit: UNIT micro molar per second
is computational component for: model parameters.k3 property
mapped to: phi.k3

model parameters.kf
type: NamedIndividual
type: Decimal
has start value: 28
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for calculation of Ca flow via IP3 receptor channels
has unit: UNIT micro molar per second
mapped to: j receptor.kf
is computational component for: model parameters.kf property

model parameters.p
type: NamedIndividual
type: Decimal
has start value: 0.2778
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: IP3 receptor concentration
has unit: UNIT micro molar
mapped to: h1.p
mapped to: h2.p
mapped to: j receptor.p
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: model parameters.p

model parameters.r2
type: NamedIndividual
type: Decimal
has start value: 100
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 1
has unit: UNIT second order rate
is computational component for: model parameters.r2 property
mapped to: phi.r2

model parameters.r4
type: NamedIndividual
type: Decimal
has start value: 20
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT per second
is computational component for: model parameters.r4 property
mapped to: phi.r4

phi
type: NamedIndividual
type: Submodel
name: phi
has associated data structure: phi.R1
has associated data structure: phi.R3
has associated data structure: phi.R5
has associated data structure: phi.c1
has associated data structure: phi.c2
has associated data structure: phi.k1
has associated data structure: phi.k2
has associated data structure: phi.k3
has associated data structure: phi.phi1 c1
has associated data structure: phi.phi1 c2
has associated data structure: phi.phi2 c1
has associated data structure: phi.phi2 c2
has associated data structure: phi.phi3 c1
has associated data structure: phi.phi3 c2
has associated data structure: phi.phi 1 c1
has associated data structure: phi.phi 1 c2
has associated data structure: phi.r2
has associated data structure: phi.r4
has computational component: phi computation

phi.R1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 1
has unit: UNIT micro molar
is computational component for: phi.R1 property

phi.R3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT micro molar
is computational component for: phi.R3 property

phi.R5
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 3
has unit: UNIT micro molar
is computational component for: phi.R5 property

phi.c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cell 1 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: phi.c1

phi.c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Cell 2 Ca concentration in the cytoplasm
has unit: UNIT micro molar
is computational component for: Chemical concentration

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium ion
has computational component: phi.c2

phi.k1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi -1
has unit: UNIT micro molar per second
is computational component for: phi.k1 property

phi.k2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT micro molar per second
is computational component for: phi.k2 property

phi.k3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 3
has unit: UNIT micro molar per second
is computational component for: phi.k3 property

phi.phi1 c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 1
has unit: UNIT second order rate
mapped to: h1.phi1 c1
mapped to: j receptor.phi1 c1
is computational component for: phi.phi1 c1 property

phi.phi1 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the closed state to open state in cell 2
has unit: UNIT second order rate
mapped to: h2.phi1 c2
mapped to: j receptor.phi1 c2
is computational component for: phi.phi1 c2 property

phi.phi2 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the closed state to inactive state in cell 1
has unit: UNIT per second
mapped to: h1.phi2 c1
is computational component for: phi.phi2 c1 property

phi.phi2 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the closed state to inactive state in cell 2
has unit: UNIT per second
mapped to: h2.phi2 c2
is computational component for: phi.phi2 c2 property

phi.phi3 c1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the inactive state to open state in cell 1
has unit: UNIT per second
mapped to: h1.phi3 c1
is computational component for: phi.phi3 c1 property

phi.phi3 c2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the inactive state to open state in cell 2
has unit: UNIT per second
mapped to: h2.phi3 c2
is computational component for: phi.phi3 c2 property

phi.phi 1 c1
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 1
has unit: UNIT per second
mapped to: h1.phi 1 c1
mapped to: j receptor.phi 1 c1
is computational component for: phi.phi 1 c1 property

phi.phi 1 c2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: out
is declared: true
comment: Rate of change in IP3 receptors from the open state to closed state in cell 2
has unit: UNIT per second
mapped to: h2.phi 1 c2
mapped to: j receptor.phi 1 c2
is computational component for: phi.phi 1 c2 property

phi.r2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 1
has unit: UNIT second order rate
is computational component for: phi.r2 property

phi.r4
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
has cell m lpublic interface: in
is declared: true
comment: Constant for rate equation represented by phi 2
has unit: UNIT per second
is computational component for: phi.r4 property

phi computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>phi1_c1</ci> <apply> <divide /> <apply> <times /> <ci>r2</ci> <ci>c1</ci> </apply> <apply> <plus /> <ci>R1</ci> <ci>c1</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi_1_c1</ci> <apply> <divide /> <ci>k1</ci> <apply> <plus /> <ci>R3</ci> <ci>c1</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi2_c1</ci> <apply> <divide /> <apply> <plus /> <ci>k2</ci> <apply> <times /> <ci>r4</ci> <ci>c1</ci> </apply> </apply> <apply> <plus /> <ci>R3</ci> <ci>c1</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi3_c1</ci> <apply> <divide /> <ci>k3</ci> <apply> <plus /> <ci>R5</ci> <ci>c1</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi1_c2</ci> <apply> <divide /> <apply> <times /> <ci>r2</ci> <ci>c2</ci> </apply> <apply> <plus /> <ci>R1</ci> <ci>c2</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi_1_c2</ci> <apply> <divide /> <ci>k1</ci> <apply> <plus /> <ci>R3</ci> <ci>c2</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi2_c2</ci> <apply> <divide /> <apply> <plus /> <ci>k2</ci> <apply> <times /> <ci>r4</ci> <ci>c2</ci> </apply> </apply> <apply> <plus /> <ci>R3</ci> <ci>c2</ci> </apply> </apply> </apply> <apply> <eq /> <ci>phi3_c2</ci> <apply> <divide /> <ci>k3</ci> <apply> <plus /> <ci>R5</ci> <ci>c2</ci> </apply> </apply> </apply>
is computational component for: phi