04032015124909013m0600
type: Ontology
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> Teaching from classic papers: Hill's model of muscle contraction <author> <firstname>Catherine</firstname> <surname>Lloyd</surname> <affiliation> <shortaffil>Auckland Bioengineering Institute, University of Auckland</shortaffil> </affiliation> </author> </articleinfo> Model Status This CellML model runs in both PCEnv and COR to reproduce the published results. The units have been checked and they are consistent. <sect1 id="sec_structure"> Model Structure ABSTRACT: A. V. Hill's 1938 paper "The heat of shortening and the dynamic constants of muscle" is an enduring classic, presenting detailed methods, meticulous experiments, and the model of muscle contraction that now bears Hill's name. Pairing a simulation based on Hill's model with a reading of his paper allows students to follow his thought process to discover key principles of muscle physiology and gain insight into how to develop quantitative models of physiological processes. In this article, the experience of the author using this approach in a graduate biomedical engineering course is outlined, along with suggestions for adapting this approach to other audiences. Teaching from classic papers: Hill's model of muscle contraction, J.W. Holmes, 2006, Advances in Physiology Education , 30, 67-72. PubMed ID: 16709736 <informalfigure float="0" id="diagram"> <mediaobject> <imageobject> <objectinfo> diagram </objectinfo> <imagedata fileref="holmes_2006.png" /> </imageobject> </mediaobject> A schematic diagram of the two component muscle model. Force in the muscle = F_SE = F_CE. By specifying Lm, Fm is calculated from the force velocity properties of CE and the force-length relationship of SE. </informalfigure> </sect1> </documentation>
has cell m lrdf markup: <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.cellml.org/metadata/simulation/1.0#"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0#holmes_2006"> <simulation rdf:parseType="Resource"> <boundIntervals rdf:parseType="Resource"> <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/> <rdf:first rdf:parseType="Resource"> <endingValue xml:lang="en">10</endingValue> <maximumStepSize xml:lang="en">0.1</maximumStepSize> </rdf:first> </boundIntervals> </simulation> </rdf:Description> </rdf:RDF>
legacy code URI: C:\Users\chthompson\Dropbox\Work Related\Annotated Models\Holmes_2006\holmes_2006.cellml
annotator name: Chris Thompson
model id: holmes_2006
model name: holmes_2006

Surface normal tensile stress
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Surface normal tensile stress

Tensile velocity
type: Class
subclass of: Reference physical property
subclass of: Restriction
  on property: refersTo
  has value: Tensile velocity

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

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

Set of skeletal muscle cells
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Set of skeletal muscle cells

Skeletal muscle tissue
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Skeletal muscle tissue

Striated muscle tissue
type: Class
subclass of: Reference physical entity
subclass of: Restriction
  on property: refersTo
  has value: Striated muscle tissue

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.

Elastic tissue
type: NamedIndividual
refers to: Elastic tissue
is index entity for: Elastic tissue part of Striated muscle tissue
part of: Striated muscle tissue
has physical property: Span of spatial entity

Set of skeletal muscle cells
type: NamedIndividual
refers to: Set of skeletal muscle cells
is index entity for: Set of skeletal muscle cells part of Striated muscle tissue
part of: Striated muscle tissue
has physical property: Span of spatial entity

Skeletal muscle contraction
type: NamedIndividual
type: Custom physical process
comment: Contraction of skeletal muscle
has sink: Elastic tissue
has source: Set of skeletal muscle cells
has physical property: Tensile velocity

Axiom
has multiplier: 1.0
annotated property: hasSink
annotated target: Elastic tissue
annotated source: Skeletal muscle contraction

Axiom
has multiplier: 1.0
annotated property: hasSource
annotated target: Set of skeletal muscle cells
annotated source: Skeletal muscle contraction

Skeletal muscle tissue
type: NamedIndividual
refers to: Skeletal muscle tissue
has physical property: Surface normal tensile stress

Striated muscle tissue
type: NamedIndividual
refers to: Striated muscle tissue
has part: Elastic tissue
has part: Set of skeletal muscle cells

UNIT mNpermmsq
type: NamedIndividual
type: Unit of measurement
has computational code: mNpermmsq
has unit factor: UNIT metre
has unit factor: UNIT newton
unit for: contraction.P
unit for: contraction.Po
unit for: contraction.a
unit for: contraction.alpha

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT mNpermmsq
annotated target: UNIT newton

Axiom
has unit factor exponent: -2.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT mNpermmsq
annotated target: UNIT metre

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

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

UNIT pms
type: NamedIndividual
type: Unit of measurement
has computational code: pms
has unit factor: UNIT second
unit for: contraction.b
unit for: contraction.v

Axiom
has unit factor exponent: -1.0
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated source: UNIT pms
annotated target: UNIT second

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit factor for: UNIT pms
unit for: Time

contraction
type: NamedIndividual
type: Submodel
name: contraction
has associated data structure: contraction.L
has associated data structure: contraction.L ce
has associated data structure: contraction.L se
has associated data structure: contraction.L se o
has associated data structure: contraction.P
has associated data structure: contraction.Po
has associated data structure: contraction.a
has associated data structure: contraction.alpha
has associated data structure: contraction.b
has associated data structure: Time
has associated data structure: contraction.v
has computational component: contraction computation

contraction.L
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Fraction of muscle length
is computational component for: contraction.L property

contraction.L ce
type: NamedIndividual
type: Decimal
has start value: 0.7
metadata ID: contraction_L_ce
is discrete: false
is solution domain: false
is declared: true
comment: Contribution of muscle contractile elements to fraction of muscle length
is computational component for: Span of spatial entity

Span of spatial entity
type: NamedIndividual
refers to: Span of spatial entity
physical property of: Set of skeletal muscle cells
has computational component: contraction.L ce

contraction.L se
type: NamedIndividual
type: Decimal
metadata ID: contraction_L_se
is solution domain: false
is discrete: false
is declared: true
comment: Contribution of muscle elastic elements to fraction of muscle length
is computational component for: Span of spatial entity

contraction.L se o
type: NamedIndividual
type: Decimal
has start value: 0.3
is solution domain: false
is discrete: false
is declared: true
comment: Initial contribution of muscle elastic elements to fraction of muscle length
is computational component for: contraction.L se o property

Span of spatial entity
type: NamedIndividual
refers to: Span of spatial entity
physical property of: Elastic tissue
has computational component: contraction.L se

contraction.P
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Steady-state force
has unit: UNIT mNpermmsq
is computational component for: Surface normal tensile stress

Surface normal tensile stress
type: NamedIndividual
refers to: Surface normal tensile stress
physical property of: Skeletal muscle tissue
has computational component: contraction.P

contraction.Po
type: NamedIndividual
type: Decimal
has start value: 144.9
is discrete: false
is solution domain: false
is declared: true
comment: Maximal isometric tetanic force
has unit: UNIT mNpermmsq
is computational component for: contraction.Po property

contraction.a
type: NamedIndividual
type: Decimal
has start value: 37.24
is solution domain: false
is discrete: false
is declared: true
comment: Slope of the relationship between the change in muscle length and excess heat.
has unit: UNIT mNpermmsq
is computational component for: contraction.a property

contraction.alpha
type: NamedIndividual
type: Decimal
has start value: 1449.027
is discrete: false
is solution domain: false
is declared: true
comment: Spring constant for series elastic element
has unit: UNIT mNpermmsq
is computational component for: contraction.alpha property

contraction.b
type: NamedIndividual
type: Decimal
has start value: 0.325
is solution domain: false
is discrete: false
is declared: true
comment: Slope excess energy rate and steady-state force relationship
has unit: UNIT pms
is computational component for: contraction.b property

Time
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
refers to: http://bhi.washington.edu/OPB#OPB01023
has cell m lpublic interface: in
is declared: true
comment: Time Domain
has unit: UNIT second
is computational component for: contraction.time property

contraction.v
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Shortening velocity
has unit: UNIT pms
is computational component for: Tensile velocity

Tensile velocity
type: NamedIndividual
refers to: Tensile velocity
physical property of: Skeletal muscle contraction
has computational component: contraction.v

contraction computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>v</ci> <apply> <divide /> <apply> <times /> <apply> <minus /> <ci>b</ci> </apply> <apply> <minus /> <ci>Po</ci> <ci>P</ci> </apply> </apply> <apply> <plus /> <ci>P</ci> <ci>a</ci> </apply> </apply> </apply> <apply> <eq /> <ci>L_se</ci> <apply> <minus /> <ci>L</ci> <ci>L_ce</ci> </apply> </apply> <apply> <eq /> <ci>L</ci> <piecewise> <piece> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> <apply> <leq /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">1</cn> </apply> </piece> <piece> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.92</cn> <apply> <and /> <apply> <gt /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">1</cn> </apply> <apply> <lt /> <ci>time</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="second">5</cn> </apply> </apply> </piece> <otherwise> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">0.9</cn> </otherwise> </piecewise> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>L_ce</ci> </apply> <ci>v</ci> </apply> <apply> <eq /> <ci>P</ci> <apply> <times /> <ci>alpha</ci> <apply> <minus /> <ci>L_se</ci> <ci>L_se_o</ci> </apply> </apply> </apply>
is computational component for: contraction

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#OPB01023
has cell m lpublic interface: out
is declared: true
comment: Time Domain
has unit: UNIT second
mapped to: Time
is computational component for: environment.time property