03032015130319068m0500
type: Ontology
legacy code URI: /Users/Brian/Desktop/tran_smith_loiselle_crampin_2009/tran_smith_loiselle_crampin_2009.cellml
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca(2+) (SERCA) Pump <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 has been unit checked and is known to run in both OpenCell and COR. This particular version of the CellML model describes the three-state cooperative SERCA model and recreates figure 13. In order to recreate this figure we have had to add an additional equation to the model to define the rate of change in Casr. Please also note there are typographical errors in the original paper and [H+] should be raised to the power of n (n=2) for T_Hi and T_Hsr. Also in figure 12 the concentrations of ADP should be 8uM and 20uM rather than 20uM and 40uM. <sect1 id="sec_structure"> Model Structure ABSTRACT: We present a biophysically based kinetic model of the cardiac SERCA pump that consolidates a range of experimental data into a consistent and thermodynamically constrained framework. The SERCA model consists of a number of sub-states with partial reactions that are sensitive to Ca(2+) and pH, and to the metabolites MgATP, MgADP, and Pi. Optimization of model parameters to fit experimental data favors a fully cooperative Ca(2+)-binding mechanism and predicts a Ca(2+)/H(+) counter-transport stoichiometry of 2. Moreover, the order of binding of the partial reactions, particularly the binding of MgATP, proves to be a strong determinant of the ability of the model to fit the data. A thermodynamic investigation of the model indicates that the binding of MgATP has a large inhibitory effect on the maximal reverse rate of the pump. The model is suitable for integrating into whole-cell models of cardiac electrophysiology and Ca(2+) dynamics to simulate the effects on the cell of compromised metabolis…
has cell m lrdf markup: <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:j.0="http://imc.org/vCard/3.0#"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0#tran_model_2009"> <cmeta:comment> <rdf:Description rdf:about="rdf:#594c54e4-2368-4aba-8dee-bd2175490d26"> <rdf:value></rdf:value> <dc:creator> <rdf:Description rdf:about="rdf:#6b548755-48ec-4433-8329-94c1c0c1c7c3"> <vCard:FN></vCard:FN> </rdf:Description> </dc:creator> </rdf:Description> </cmeta:comment> <bqs:reference rdf:parseType="Resource"> <dc:subject rdf:parseType="Resource"> <rdf:value> <rdf:Bag> <rdf:li>electrophysiology</rdf:li> <rdf:li>cardiac</rdf:li> <rdf:li>SERCA</rdf:li> <rdf:li>calcium dynamics</rdf:li> </rdf:Bag> </rdf:value> <bqs:subject_type>keyword</bqs:subject_type> </dc:subject> </bqs:reference> <bqs:reference> <rdf:Description rdf:about="rdf:#dde09b5f-2570-44e4-b7af-2782b3f4dc03"> <bqs:JournalArticle> <rdf:Description rdf:about="rdf:#1aa7136e-0363-4f6f-8e67-d823ba86d1ab"> <bqs:last_page>2042</bqs:last_page> <dcterms:issued> <rdf:Description rdf:about="rdf:#80797212-992e-4436-9c29-95f80d6ea1d5"> <dcterms:W3CDTF>2009-03-00 00:00</dcterms:W3CDTF> </rdf:Description> </dcterms:issued> <bqs:Journal> <rdf:Description rdf:about="rdf:#dbd53168-2407-4b79-a3da-77beb4f217ab"> <dc:title>Biophysical Journal</dc:title> </rdf:Description> </bqs:Journal> <bqs:first_page>2029</bqs:first_page> <bqs:volume>96</bqs:volume> <dc:title>A Thermodynamic Model of the Cardiac Sarcoplasmic/Endoplasmic Ca(2+) (SERCA) Pump</dc:title> <dc:creator> <rdf:Seq rdf:about="rdf:#277d3fce-1e82-45ea-884f-2e76a89f4a54"> <rdf:li> <bqs:Person rdf:about="rdf:#5a8af88e-79ba-4e3a-a593-38f0298d25aa"> <vCard:N> <rdf:Description rdf:about="rdf:#62cab138-9811-478d-9183-2d5af616ef1e"> <vCard:Family>Tran</vC…
annotator name: Brian Carlson
model description: Model of the cardiac SERCA pump
model id: tran_model_2009
model name: tran_model_2009

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

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

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

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

calcium(2+)
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: calcium(2+)

Cardiac myocyte
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Cardiac myocyte

Cytoplasmic organelle matrix
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Cytoplasmic organelle matrix

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

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

Composite physical entity
type: Class
subclass of: Physical entity
disjoint with: Custom physical entity
disjoint with: Reference physical entity
comment: A physical entity that is defined by linking multiple physical entity terms with structural relations.

Computation
type: Class
subclass of: Computational model component
disjoint with: Data structure
comment: A mathematical and/or logical expression that determines the value of a data structure.

Computational model component
type: Class
subclass of: SemSim component
disjoint with: Physical model component
comment: An element of a SemSim model that relates to the mathematical or logical representation of physical quantities or qualities.

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

Custom physical property
type: Class
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
type: Class
subclass of: Real
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
type: Class
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
type: Class
subclass of: Physical model component
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
type: Class
subclass of: SemSim component
comment: A SemSim model element used to represent, in whole or in part, the physical meaning of a computational element.

Physical process
type: Class
subclass of: Physical model component
disjoint with: Physical property
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
type: Class
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
type: Class
subclass of: Data structure
comment: A data structure whose value is limited to the real numbers.

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

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

Reference physical process
type: Class
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
type: Class
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.

ATP
type: NamedIndividual
refers to: ATP
is index entity for: CHEBI 15422 part of Portion of cytosol part of Cardiac myocyte
part of: Portion of cytosol
has physical property: Chemical concentration

ADP
type: NamedIndividual
refers to: ADP
is index entity for: CHEBI 16761 part of Portion of cytosol part of Cardiac myocyte
part of: Portion of cytosol
has physical property: Chemical concentration

phosphate
type: NamedIndividual
refers to: phosphate
is index entity for: CHEBI 26020 part of Portion of cytosol part of Cardiac myocyte
part of: Portion of cytosol
has physical property: Chemical concentration

calcium(2+)
type: NamedIndividual
refers to: calcium(2+)
is index entity for: CHEBI 29108 part of Cytoplasmic organelle matrix part of Sarcoplasmic reticulum part of Cardiac myocyte
part of: Cytoplasmic organelle matrix
has physical property: Chemical concentration

calcium(2+)
type: NamedIndividual
refers to: calcium(2+)
is index entity for: CHEBI 29108 part of Portion of cytosol part of Cardiac myocyte
part of: Portion of cytosol
has physical property: Chemical concentration

Cardiac myocyte
type: NamedIndividual
refers to: Cardiac myocyte
has part: Portion of cytosol
has part: Sarcoplasmic reticulum

Cytoplasmic organelle matrix
type: NamedIndividual
refers to: Cytoplasmic organelle matrix
has part: calcium(2+)
is index entity for: Cytoplasmic organelle matrix part of Sarcoplasmic reticulum part of Cardiac myocyte
part of: Sarcoplasmic reticulum

Portion of cytosol
type: NamedIndividual
refers to: Portion of cytosol
has part: ATP
has part: ADP
has part: phosphate
has part: calcium(2+)
part of: Cardiac myocyte
is index entity for: Portion of cytosol part of Cardiac myocyte
has part: hydrogen(1+)

SERCA
type: NamedIndividual
type: Submodel
name: SERCA
has associated data structure: SERCA.ADP
has associated data structure: SERCA.ATP
has associated data structure: SERCA.Ca i
has associated data structure: SERCA.Ca sr
has associated data structure: SERCA.H i
has associated data structure: SERCA.P i
has associated data structure: SERCA.T Cai
has associated data structure: SERCA.T Casr
has associated data structure: SERCA.T H
has associated data structure: SERCA.T H1
has associated data structure: SERCA.T Hi
has associated data structure: SERCA.T Hsr
has associated data structure: SERCA.a m1
has associated data structure: SERCA.a m2
has associated data structure: SERCA.a m3
has associated data structure: SERCA.a p1
has associated data structure: SERCA.a p2
has associated data structure: SERCA.a p3
has associated data structure: SERCA.k m1
has associated data structure: SERCA.k m2
has associated data structure: SERCA.k m3
has associated data structure: SERCA.k p1
has associated data structure: SERCA.k p2
has associated data structure: SERCA.k p3
has associated data structure: SERCA.kdcai
has associated data structure: SERCA.kdcasr
has associated data structure: SERCA.kdh
has associated data structure: SERCA.kdh1
has associated data structure: SERCA.kdhi
has associated data structure: SERCA.kdhsr
has associated data structure: SERCA.n
has associated data structure: SERCA.s1
has associated data structure: SERCA.s2
has associated data structure: SERCA.s3
has associated data structure: Time
has associated data structure: SERCA.v cycle
has computational component: SERCA computation

SERCA.ADP
type: NamedIndividual
type: Decimal
has start value: 36.3e-3
metadata ID: SERCA_ADP
is solution domain: false
is discrete: false
is declared: true
comment: Concentration of adenosine diphosphate in the cytosol
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ADP
has computational component: SERCA.ADP

SERCA.ATP
type: NamedIndividual
type: Decimal
has start value: 5
metadata ID: SERCA_ATP
is discrete: false
is solution domain: false
is declared: true
comment: Concentration of adenosine triphosphate in the cytosol
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: ATP
has computational component: SERCA.ATP

SERCA.Ca i
type: NamedIndividual
type: Decimal
has start value: 150e-6
metadata ID: SERCA_Ca_i
is solution domain: false
is discrete: false
is declared: true
comment: Concentration of calcium in the cytosol
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium(2+)
has computational component: SERCA.Ca i

SERCA.Ca sr
type: NamedIndividual
type: Decimal
has start value: 0
metadata ID: SERCA_Ca_sr
is discrete: false
is solution domain: false
is declared: true
comment: Concentration of calcium in the sarcoplasmic reticulum
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: calcium(2+)
has computational component: SERCA.Ca sr

SERCA.H i
type: NamedIndividual
type: Decimal
has start value: 1e-4
metadata ID: SERCA_H_i
is solution domain: false
is discrete: false
is declared: true
comment: Concentration of hydrogen in the cytosol
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
has computational component: SERCA.H i
physical property of: hydrogen(1+)

SERCA.P i
type: NamedIndividual
type: Decimal
has start value: 1
metadata ID: SERCA_P_i
is discrete: false
is solution domain: false
is declared: true
comment: Concentration of phosphate in the cytosol
is computational component for: Chemical concentration
has unit: UNIT millimolar

Chemical concentration
type: NamedIndividual
refers to: Chemical concentration
physical property of: phosphate
has computational component: SERCA.P i

SERCA.T Cai
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.T Cai property

SERCA.T Casr
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.T Casr property

SERCA.T H
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.T H property

SERCA.T H1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.T H1 property

SERCA.T Hi
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.T Hi property

SERCA.T Hsr
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.T Hsr property

SERCA.a m1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.a m1 property
has unit: UNIT first order rate constant

SERCA.a m2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.a m2 property
has unit: UNIT first order rate constant

SERCA.a m3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.a m3 property
has unit: UNIT first order rate constant

SERCA.a p1
type: NamedIndividual
type: Decimal
metadata ID: SERCA_a_p1
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.a p1 property
has unit: UNIT first order rate constant

SERCA.a p2
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.a p2 property
has unit: UNIT first order rate constant

SERCA.a p3
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.a p3 property
has unit: UNIT first order rate constant

SERCA.k m1
type: NamedIndividual
type: Decimal
has start value: 16
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.k m1 property
has unit: UNIT first order rate constant

SERCA.k m2
type: NamedIndividual
type: Decimal
has start value: 67200
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.k m2 property
has unit: UNIT second order rate constant

SERCA.k m3
type: NamedIndividual
type: Decimal
has start value: 149
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.k m3 property
has unit: UNIT second order rate constant

SERCA.k p1
type: NamedIndividual
type: Decimal
has start value: 25900
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.k p1 property
has unit: UNIT second order rate constant

SERCA.k p2
type: NamedIndividual
type: Decimal
has start value: 2540
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.k p2 property
has unit: UNIT first order rate constant

SERCA.k p3
type: NamedIndividual
type: Decimal
has start value: 20.5
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.k p3 property
has unit: UNIT first order rate constant

SERCA.kdcai
type: NamedIndividual
type: Decimal
has start value: 0.9
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.kdcai property
has unit: UNIT millimolar

SERCA.kdcasr
type: NamedIndividual
type: Decimal
has start value: 2.24
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.kdcasr property
has unit: UNIT millimolar

SERCA.kdh
type: NamedIndividual
type: Decimal
has start value: 7.24e-5
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.kdh property
has unit: UNIT millimolar

SERCA.kdh1
type: NamedIndividual
type: Decimal
has start value: 1.09e-5
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.kdh1 property
has unit: UNIT millimolar

SERCA.kdhi
type: NamedIndividual
type: Decimal
has start value: 3.54e-3
is solution domain: false
is discrete: false
is declared: true
is computational component for: SERCA.kdhi property
has unit: UNIT millimolar squared

SERCA.kdhsr
type: NamedIndividual
type: Decimal
has start value: 1.05e-8
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.kdhsr property
has unit: UNIT millimolar squared

SERCA.n
type: NamedIndividual
type: Decimal
has start value: 2
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.n property

SERCA.s1
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.s1 property
has unit: UNIT per second squared

SERCA.s2
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.s2 property
has unit: UNIT per second squared

SERCA.s3
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.s3 property
has unit: UNIT per second squared

Time
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: in
is declared: true
comment: Simulation time domain
is computational component for: SERCA.time property
has unit: UNIT second

SERCA.v cycle
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
is computational component for: SERCA.v cycle property
has unit: UNIT first order rate constant

SERCA computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>T_Cai</ci> <apply> <divide /> <ci>Ca_i</ci> <ci>kdcai</ci> </apply> </apply> <apply> <eq /> <ci>T_Casr</ci> <apply> <divide /> <ci>Ca_sr</ci> <ci>kdcasr</ci> </apply> </apply> <apply> <eq /> <ci>T_H1</ci> <apply> <divide /> <ci>H_i</ci> <ci>kdh1</ci> </apply> </apply> <apply> <eq /> <ci>T_Hi</ci> <apply> <divide /> <apply> <power /> <ci>H_i</ci> <ci>n</ci> </apply> <ci>kdhi</ci> </apply> </apply> <apply> <eq /> <ci>T_Hsr</ci> <apply> <divide /> <apply> <power /> <ci>H_i</ci> <ci>n</ci> </apply> <ci>kdhsr</ci> </apply> </apply> <apply> <eq /> <ci>T_H</ci> <apply> <divide /> <ci>H_i</ci> <ci>kdh</ci> </apply> </apply> <apply> <eq /> <ci>a_p1</ci> <apply> <times /> <ci>k_p1</ci> <ci>ATP</ci> </apply> </apply> <apply> <eq /> <ci>a_p2</ci> <apply> <divide /> <apply> <times /> <ci>k_p2</ci> <apply> <power /> <ci>T_Cai</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> </apply> <apply> <plus /> <apply> <power /> <ci>T_Cai</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <apply> <times /> <apply> <power /> <ci>T_Cai</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <ci>T_Hi</ci> </apply> <apply> <times /> <ci>T_Hi</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>T_H1</ci> </apply> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>a_p3</ci> <apply> <divide /> <apply> <times /> <ci>k_p3</ci> <ci>T_Hsr</ci> </apply> <apply> <plus /> <apply> <times /> <apply> <power /> <ci>T_Casr</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">2</cn> </apply> <ci>T_H</ci> </apply> <ci>T_H</ci> <apply> <times /> <ci>T_Hsr</ci> <apply> <plus /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <ci>T_H</ci> </apply> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>a_m1</…
is computational component for: SERCA

Sarcoplasmic reticulum
type: NamedIndividual
refers to: Sarcoplasmic reticulum
part of: Cardiac myocyte
has part: Cytoplasmic organelle matrix
is index entity for: Sarcoplasmic reticulum part of Cardiac myocyte

UNIT first order rate constant
type: NamedIndividual
type: Unit of measurement
has computational code: first_order_rate_constant
unit for: SERCA.a m1
unit for: SERCA.a m2
unit for: SERCA.a m3
unit for: SERCA.a p1
unit for: SERCA.a p2
unit for: SERCA.a p3
unit for: SERCA.k m1
unit for: SERCA.k p2
unit for: SERCA.k p3
unit for: SERCA.v cycle
has unit factor: UNIT second

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT first order rate constant
annotated target: UNIT second

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

UNIT millimolar
type: NamedIndividual
type: Unit of measurement
has computational code: millimolar
unit for: SERCA.ADP
unit for: SERCA.ATP
unit for: SERCA.Ca i
unit for: SERCA.Ca sr
unit for: SERCA.H i
unit for: SERCA.P i
unit for: SERCA.kdcai
unit for: SERCA.kdcasr
unit for: SERCA.kdh
unit for: SERCA.kdh1
has unit factor: UNIT litre
unit factor for: UNIT millimolar squared
has unit factor: UNIT mole
unit factor for: UNIT second order rate constant

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT millimolar
annotated target: UNIT mole

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

UNIT millimolar squared
type: NamedIndividual
type: Unit of measurement
has computational code: millimolar_squared
unit for: SERCA.kdhi
unit for: SERCA.kdhsr
has unit factor: UNIT millimolar

Axiom
has unit factor exponent: 2.0
annotated property: hasUnitFactor
annotated target: UNIT millimolar
annotated source: UNIT millimolar squared

UNIT mole
type: NamedIndividual
type: Unit of measurement
has computational code: mole
is fundamental unit: true
unit factor for: UNIT millimolar

UNIT per second squared
type: NamedIndividual
type: Unit of measurement
has computational code: per_second_squared
unit for: SERCA.s1
unit for: SERCA.s2
unit for: SERCA.s3
has unit factor: UNIT second

Axiom
has unit factor exponent: -2.0
annotated property: hasUnitFactor
annotated source: UNIT per second squared
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit for: Time
unit factor for: UNIT first order rate constant
unit factor for: UNIT per second squared
unit factor for: UNIT second order rate constant

UNIT second order rate constant
type: NamedIndividual
type: Unit of measurement
has computational code: second_order_rate_constant
unit for: SERCA.k m2
unit for: SERCA.k m3
unit for: SERCA.k p1
has unit factor: UNIT millimolar
has unit factor: UNIT second

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT millimolar
annotated source: UNIT second order rate constant

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT second
annotated source: UNIT second order rate constant

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

Time
type: NamedIndividual
type: Decimal
metadata ID: environment_time
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB_01023
has cell m lpublic interface: out
is declared: true
comment: Simulation time domain
mapped to: Time
has unit: UNIT second
is computational component for: environment.time property

hydrogen(1+)
type: NamedIndividual
type: Custom physical entity
part of: Portion of cytosol
has physical property: Chemical concentration
is index entity for: hydrogen(1+) part of Portion of cytosol part of Cardiac myocyte