03032015123059612m0500
type: Ontology
legacy code URI: /Users/max_neal/Dropbox/Semantic Project/Annotated CellML models/siebert_rode_herzog_till_blickhan_2008/siebert_CC_2008.cellml
sem sim version: 0.2
has cell m ldocumentation: <documentation xmlns="http://cellml.org/tmp-documentation"> <articleinfo> Nonlinearities make a difference: comparison of two common Hill-type models with real muscle <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 represents the [CC] model from the original published paper. Parameter values have been taken from table 2, SOL1 for the [CC] model. The CellML model runs in OpenCell to recreate the published results. The units have been checked and are consistent. The model will not run in COR due to the presence of differential algebraic equations - or "circular arguments". <sect1 id="sec_structure"> Model Structure ABSTRACT: Compared to complex structural Huxley-type models, Hill-type models phenomenologically describe muscle contraction using only few state variables. The Hill-type models dominate in the ever expanding field of musculoskeletal simulations for simplicity and low computational cost. Reasonable parameters are required to gain insight into mechanics of movement. The two most common Hill-type muscle models used contain three components. The series elastic component is connected in series to the contractile component. A parallel elastic component is either connected in parallel to both the contractile and the series elastic component (model [CC+SEC]), or is connected in parallel only with the contractile component (model [CC]). As soon as at least one of the components exhibits substantial nonlinearities, as, e.g., the contractile component by the ability to turn on and off, the two models are mechanically different. We tested which model ([CC+SEC] or [CC]) represents the cat soleus better. Ramp experiments consisting of an isometric and an isokinetic part were performed with an in situ cat soleus preparation using supramaximal nerve stimulation. Hill-type models conta…
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model name: siebert_2008
model id: siebert_2008

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

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.

Contraction of contractile element
type: NamedIndividual
type: Custom physical process
comment: Contraction of the modeled contractile element
has physical property: Tensile velocity

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

UNIT mm
type: NamedIndividual
type: Unit of measurement
has computational code: mm
has unit factor: UNIT meter
unit factor for: UNIT mm per second
unit factor for: UNIT newton per mm
unit factor for: UNIT per mm
unit for: contraction.L 1
unit for: contraction.L 2
unit for: contraction.L 3
unit for: contraction.L 4
unit for: contraction.L cc
unit for: contraction.L m
unit for: contraction.L mtc
unit for: contraction.d LSEC1
unit for: contraction.delta L sec
unit for: contraction.delta L sec1

Axiom
has unit factor prefix: milli
annotated property: hasUnitFactor
annotated target: UNIT meter
annotated source: UNIT mm

UNIT mm per second
type: NamedIndividual
type: Unit of measurement
has computational code: mm_per_second
has unit factor: UNIT mm
has unit factor: UNIT second
unit for: contraction.v cc
unit for: contraction.v max

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated source: UNIT mm per second
annotated target: UNIT second

UNIT newton
type: NamedIndividual
type: Unit of measurement
has computational code: newton
is fundamental unit: true
unit factor for: UNIT newton per mm
unit for: contraction.F 1
unit for: contraction.F im
unit for: contraction.f L
unit for: contraction.f c
unit for: contraction.f sec
unit for: contraction.k 1

UNIT newton per mm
type: NamedIndividual
type: Unit of measurement
has computational code: newton_per_mm
has unit factor: UNIT mm
has unit factor: UNIT newton
unit for: contraction.k

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT mm
annotated source: UNIT newton per mm

UNIT per mm
type: NamedIndividual
type: Unit of measurement
has computational code: per_mm
has unit factor: UNIT mm
unit for: contraction.k 2

Axiom
has unit factor exponent: -1.0
annotated property: hasUnitFactor
annotated target: UNIT mm
annotated source: UNIT per mm

UNIT second
type: NamedIndividual
type: Unit of measurement
has computational code: second
is fundamental unit: true
unit factor for: UNIT mm per second
unit for: contraction.tau
unit for: Time

contraction
type: NamedIndividual
type: Submodel
name: contraction
has associated data structure: contraction.A
has associated data structure: contraction.F 1
has associated data structure: contraction.F im
has associated data structure: contraction.L 1
has associated data structure: contraction.L 2
has associated data structure: contraction.L 3
has associated data structure: contraction.L 4
has associated data structure: contraction.L cc
has associated data structure: contraction.L m
has associated data structure: contraction.L mtc
has associated data structure: contraction.curv
has associated data structure: contraction.d LSEC1
has associated data structure: contraction.delta L sec
has associated data structure: contraction.delta L sec1
has associated data structure: contraction.f L
has associated data structure: contraction.f c
has associated data structure: contraction.f sec
has associated data structure: contraction.f v
has associated data structure: contraction.k
has associated data structure: contraction.k 1
has associated data structure: contraction.k 2
has associated data structure: contraction.k sh
has associated data structure: contraction.tau
has associated data structure: Time
has associated data structure: contraction.v cc
has associated data structure: contraction.v max
has computational component: contraction computation

contraction.A
type: NamedIndividual
type: Decimal
has start value: 1
is solution domain: false
is discrete: false
is declared: true
comment: Activation state
is computational component for: contraction.A property

contraction.F 1
type: NamedIndividual
type: Decimal
has start value: 8.9
is solution domain: false
is discrete: false
is declared: true
comment: Force at which the series elastic component force-elongation relation changes from exponential to linear
has unit: UNIT newton
is computational component for: contraction.F 1 property

contraction.F im
type: NamedIndividual
type: Decimal
has start value: 20.6
is discrete: false
is solution domain: false
is declared: true
comment: The maximum active isometric force of the muscle
has unit: UNIT newton
is computational component for: contraction.F im property

contraction.L 1
type: NamedIndividual
type: Decimal
has start value: -24
is discrete: false
is solution domain: false
is declared: true
comment: Curve-shaping parameter determining width of muscle force-length relationship
has unit: UNIT mm
is computational component for: contraction.L 1 property

contraction.L 2
type: NamedIndividual
type: Decimal
has start value: -14
is discrete: false
is solution domain: false
is declared: true
comment: Muscle length at which the ascending limb changes slope
has unit: UNIT mm
is computational component for: contraction.L 2 property

contraction.L 3
type: NamedIndividual
type: Decimal
has start value: 4
is solution domain: false
is discrete: false
is declared: true
comment: Curve-shaping parameter that sets the length of the force-length plateau
has unit: UNIT mm
is computational component for: contraction.L 3 property

contraction.L 4
type: NamedIndividual
type: Decimal
has start value: 14
is solution domain: false
is discrete: false
is declared: true
comment: Curve-shaping parameter determining width of muscle force-length relationship
has unit: UNIT mm
is computational component for: contraction.L 4 property

contraction.L cc
type: NamedIndividual
type: Decimal
has start value: 0.2
is solution domain: false
is discrete: false
is declared: true
comment: The contractile component length minus the optimal contractile component length
has unit: UNIT mm
is computational component for: contraction.L cc property

contraction.L m
type: NamedIndividual
type: Decimal
has start value: 2.6
is solution domain: false
is discrete: false
is declared: true
comment: The constant sum of the slack length of the series elastic component and the optimal length of the contractile component (used in the [CC] model, but not the [CC+SEC] model)
has unit: UNIT mm
is computational component for: contraction.L m property

contraction.L mtc
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Length of the muscle-tendon complex
has unit: UNIT mm
is computational component for: contraction.L mtc property

contraction.curv
type: NamedIndividual
type: Decimal
has start value: 9.5
is discrete: false
is solution domain: false
is declared: true
comment: Curve-shaping parameter determining relationship between f_v and v_cc
is computational component for: contraction.curv property

contraction.d LSEC1
type: NamedIndividual
type: Decimal
has start value: 2.9
is solution domain: false
is discrete: false
is declared: true
comment: The length at which the force–elongation relation changes from exponential to linear
has unit: UNIT mm
is computational component for: contraction.d LSEC1 property

contraction.delta L sec
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Elongation of series elastic component
has unit: UNIT mm
is computational component for: contraction.delta L sec property

contraction.delta L sec1
type: NamedIndividual
type: Decimal
has start value: 4.1
is solution domain: false
is discrete: false
is declared: true
comment: Length at which the series elastic component force-elongation relation changes from exponential to linear
has unit: UNIT mm
is computational component for: contraction.delta L sec1 property

contraction.f L
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Length-based force factor in overall contractile component force
has unit: UNIT newton
is computational component for: contraction.f L property

contraction.f c
type: NamedIndividual
type: Decimal
has start value: 0.51
is solution domain: false
is discrete: false
is declared: true
comment: The force at which the ascending limb changes slope
has unit: UNIT newton
is computational component for: contraction.f c property

contraction.f sec
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Force generated in series elastic component
has unit: UNIT newton
is computational component for: contraction.f sec property

contraction.f v
type: NamedIndividual
type: Decimal
is solution domain: false
is discrete: false
is declared: true
comment: Velocity-based force factor in overall contractile component force
is computational component for: contraction.f v property

contraction.k
type: NamedIndividual
type: Decimal
has start value: 8.2
is discrete: false
is solution domain: false
is declared: true
comment: Scaling parameter for the series elastic component's force-elongation relationship
has unit: UNIT newton per mm
is computational component for: contraction.k property

contraction.k 1
type: NamedIndividual
type: Decimal
has start value: 0.0064
is solution domain: false
is discrete: false
is declared: true
comment: Curve-shaping parameter for setting the parallel elastic component's force-velocity relationship
has unit: UNIT newton
is computational component for: contraction.k 1 property

contraction.k 2
type: NamedIndividual
type: Decimal
has start value: 0.414
is solution domain: false
is discrete: false
is declared: true
comment: Curve-shaping parameter for setting the parallel elastic component's force-velocity relationship
has unit: UNIT per mm
is computational component for: contraction.k 2 property

contraction.k sh
type: NamedIndividual
type: Decimal
has start value: 2.5
is discrete: false
is solution domain: false
is declared: true
comment: Shaping parameter for the series elastic component's force-elongation relationship
is computational component for: contraction.k sh property

contraction.tau
type: NamedIndividual
type: Decimal
has start value: 0.065
is solution domain: false
is discrete: false
is declared: true
comment: Time constant for muscle activation
has unit: UNIT second
is computational component for: contraction.tau property

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: Time solution domain
has unit: UNIT second
is computational component for: contraction.time property

contraction.v cc
type: NamedIndividual
type: Decimal
is discrete: false
is solution domain: false
is declared: true
comment: Velocity of contractile component
has unit: UNIT mm per second
is computational component for: Tensile velocity

Tensile velocity
type: NamedIndividual
refers to: Tensile velocity
physical property of: Contraction of contractile element
has computational component: contraction.v cc

contraction.v max
type: NamedIndividual
type: Decimal
has start value: -152
is discrete: false
is solution domain: false
is declared: true
comment: Maximal contractile component shortening velocity
has unit: UNIT mm per second
is computational component for: contraction.v max property

contraction computation
type: NamedIndividual
type: Computation
has math ML: <apply> <eq /> <ci>delta_L_sec</ci> <apply> <minus /> <apply> <minus /> <ci>L_mtc</ci> <ci>L_cc</ci> </apply> <ci>L_m</ci> </apply> </apply> <apply> <eq /> <ci>f_sec</ci> <piecewise> <piece> <apply> <times /> <apply> <divide /> <ci>F_1</ci> <apply> <minus /> <apply> <exp /> <ci>k_sh</ci> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> <apply> <minus /> <apply> <exp /> <apply> <divide /> <apply> <times /> <ci>k_sh</ci> <ci>delta_L_sec</ci> </apply> <ci>delta_L_sec1</ci> </apply> </apply> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless">1</cn> </apply> </apply> <apply> <and /> <apply> <gt /> <ci>delta_L_sec</ci> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mm">0</cn> </apply> <apply> <lt /> <ci>delta_L_sec</ci> <ci>delta_L_sec1</ci> </apply> </apply> </piece> <piece> <apply> <plus /> <ci>F_1</ci> <apply> <times /> <ci>k</ci> <apply> <minus /> <ci>delta_L_sec</ci> <ci>delta_L_sec1</ci> </apply> </apply> </apply> <apply> <leq /> <ci>delta_L_sec</ci> <ci>delta_L_sec1</ci> </apply> </piece> </piecewise> </apply> <apply> <eq /> <ci>v_cc</ci> <apply> <times /> <apply> <divide /> <cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="mm_newton_per_second">1</cn> <ci>f_v</ci> </apply> <apply> <divide /> <ci>f_sec</ci> <apply> <times /> <ci>A</ci> <ci>f_L</ci> <ci>F_im</ci> </apply> </apply> </apply> </apply> <apply> <eq /> <apply> <diff /> <bvar> <ci>time</ci> </bvar> <ci>L_cc</ci> </apply> <ci>v_cc</ci> </apply> <apply> <eq /> <ci>f_v</ci> <apply> <divide /> <apply> <minus /> <ci>v_max</ci> <ci>v_cc</ci> </apply> <apply> <plus /> <ci>v_max</ci> <apply> <times /> <ci>v_cc</ci> <ci>curv</ci> </apply> </apply> </apply> </apply> <apply> <eq /> <ci>f_L</ci> <piecewise> <piece> <apply> <times /> <apply> <divide /> <ci>f_c</ci> <apply> <minus /> <ci>L_2</ci> <ci>L_1</ci> </apply> </apply> <apply> <minus /> <ci>L_cc</ci> <ci>L_1</ci> </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
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: Time solution domain
has unit: UNIT second
mapped to: Time
is computational component for: environment.time property