/Users/max_neal/Dropbox/Semantic Project/Annotated CellML models/cooling_hunter_crampin_2007/cooling_hunter_crampin_2007.cellml
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:j.0="http://www.cellml.org/bqs/1.0#" xmlns:j.1="http://imc.org/vCard/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:j.2="http://purl.org/dc/terms/" xmlns:j.3="http://www.cellml.org/metadata/simulation/1.0#"> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0"> <dc:creator rdf:parseType="Resource"> <ORG rdf:parseType="Resource"> <Orgunit xml:lang="en">Auckland Bioengineering Institute</Orgunit> <Orgname xml:lang="en">The University of Auckland</Orgname> </ORG> <EMAIL> <j.1:internet> <rdf:value xml:lang="en">m.cooling@auckland.ac.nz</rdf:value> </j.1:internet> </EMAIL> <N rdf:parseType="Resource"> <Given xml:lang="en">Mike</Given> <Family xml:lang="en">Cooling</Family> </N> </dc:creator> </rdf:Description> <rdf:Description rdf:about="http://www.cellml.org/cellml/1.0#cooling_2007"> <j.0:reference rdf:parseType="Resource"> <j.0:JournalArticle rdf:parseType="Resource"> <j.0:last_page xml:lang="en">3433</j.0:last_page> <j.0:first_page xml:lang="en">3421</j.0:first_page> <j.2:issued rdf:parseType="Resource"> <j.2:W3CDTF xml:lang="en">2007-00-00 00:00</j.2:W3CDTF> </j.2:issued> <j.0:Journal rdf:parseType="Resource"> <dc:title xml:lang="en">Biophysical Journal</dc:title> </j.0:Journal> <dc:title xml:lang="en">Modeling hypertrophic IP3 transients in the cardiac myocyte</dc:title> <j.0:volume xml:lang="en">93</j.0:volume> <dc:creator> <rdf:Seq> <rdf:li rdf:parseType="Resource"> <ORG rdf:parseType="Resource"> <Orgunit xml:lang="en">University of Auckland</Orgunit> <Orgname xml:lang="en">Auckland Bioengineering Institute</Orgname> </ORG> <EMAIL> <j.1:internet> <rdf:value xml:lang="en">m.cooling@auckland.ac.nz</rdf:value> </j.1:internet> </EMAIL> <N rdf:parseType="Resource"> <Given xml:lang="en">Mike</Given> <Family xml:lang="en">Cooling</Family> </N> </rdf:li> <rdf:li rdf:parseType="Resource"> <ORG rdf:parseType="Resource"> <Orgunit xml:lang="en">University of Auckland</Orgunit> <Orgname xml:lang="en">Auckland Bioengineering Institute</Orgname> </ORG> <EMAIL> <j.1:internet> <rdf:value xml:lang="en">p.hunter@auckland.ac.nz</rdf:value> </j.1:internet> </EMAIL> <N rdf:parseType="Resource"> <Given xml:lang="en">Peter</Given> <Family xml:lang="en">Hunter</Family> </N> </rdf:li> <rdf:li rdf:parseType="Resource"> <ORG rdf:parseType="Resource"> <Orgunit xml:lang="en">University of Auckland</Orgunit> <Orgname xml:lang="en">Auckland Bioengineering Institute</Orgname> </ORG> <EMAIL> <j.1:internet> <rdf:value xml:lang="en">e.crampin@auckland.ac.nz</rdf:value> </j.1:internet> </EMAIL> <N rdf:parseType="Resource"> <Given xml:lang="en">Edmund</Given> <Family xml:lang="en">Crampin</Family> </N> </rdf:li> </rdf:Seq> </dc:creator> </j.0:JournalArticle> </j.0:reference> <j.0:reference rdf:parseType="Resource"> <dc:subject rdf:parseType="Resource"> <j.0:subject_type xml:lang="en">keyword</j.0:subject_type> <rdf:value> <rdf:Bag> <rdf:li xml:lang="en">Signal Transduction</rdf:li> </rdf:Bag> </rdf:value> </dc:subject> </j.0:reference> <j.3:simulation rdf:parseType="Resource"> <j.3:boundIntervals rdf:parseType="Collection"> <rdf:Description> <j.3:endingValue xml:lang="en">100</j.3:endingValue> <j.3:nonstandard-pointDensity xml:lang="en">10000</j.3:nonstandard-pointDensity> <j.3:maximumStepSize xml:lang="en">.1</j.3:maximumStepSize> </rdf:Description> </j.3:boundIntervals> </j.3:simulation> </rdf:Description> </rdf:RDF>
Fluid volume
Chemical flow rate
Chemical concentration
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 (EC 3.1.4.11) (PLC-154) (Phosphoinositide phospholipase C-beta-1) (Phospholipase C-beta-1) (PLC-beta-1)
1D-myo-inositol 1,4,5-trisphosphate
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
calcium(2+)
Extracellular space
Plasma membrane
Portion of cytosol
Regular atrial cardiac myocyte
A physical entity that is defined by linking multiple physical entity terms with structural relations.
A mathematical and/or logical expression that determines the value of a data structure.
An element of a SemSim model that relates to the mathematical or logical representation of physical quantities or qualities.
A physical dependency defined in a specific SemSim model.
A physical entity defined in a specific SemSim model.
A physical process defined in a specific SemSim model.
A physical property defined in a specific SemSim model.
A computational element that stores numerical and/or logical information related to the model.
A data structure whose value is limited to decimals.
A data structure whose value is limited to the whole numbers.
A data structure unique to JSim's Mathematical Modeling Language (MML) used to set one or more model input values at runtime.
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.
A physics analytical entity that represents the material, energy, and/or information content of material or immaterial, space-occupying continuants.
A SemSim model element used to represent, in whole or in part, the physical meaning of a computational element.
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.
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.
A data structure whose value is limited to the real numbers.
A physical dependency that is defined using a term in an external knowledge resource.
A physical entity that is defined using a term from an external knowledge resource.
A physical process that is defined using a term in an external knowledge resource.
A physical property that is defined using a term in an external knowledge resource.
A logical expression that constrains, but does not define, the value of a data structure. Example: x > 0.
A computational or physical element of a SemSim model.
A grouping of one or more data structures that comprise a computationally or physically distinct part of a model or submodel.
A physical quantity chosen as a standard in terms of which other physical quantities may be expressed.
Binding of G-alpha-GDP to receptor
Binding of G-alpha-GTP to calcium-bound PLC-beta
Binding of PLC-beta to G-alpha-GTP
Binding of calcium to G-alpha-GTP-bound PLC-beta
Binding of calcium to PLC-beta
Binding of ligand and receptor to G-alpha-GDP
Binding of ligand to receptor
Binding of ligand to receptor and G-alpha-GDP
Degradation of G-alpha-GTP
Degradation of free IP3
Dissociation of G-alpha-GTP from PLC-beta and degradation
Dissociation of G-alpha-GTP from activated receptor
Dissociation of G-alpha-GTP from calcium-bound PLC-beta and degradation
G-alpha-GDP
G-alpha-GTP
Hydrolysis of PIP2 by calcium-bound PLC-beta
Hydrolysis of PIP2 by calcium-bound PLC-beta and G-alpha-GTP complex
Ligand
Ligand bound to phosphorylated receptor and G-alpha-GDP
Ligand bound to receptor
Ligand bound to receptor and G-alpha-GDP
PLC-beta bound to G-alpha-GTP
PLC-beta bound to calcium (2+)
PLC-beta bound to calcium (2+) and G-alpha-GTP
Phosphorylation of ligand-bound receptor
Receptor bound to G-alpha-GDP
Receptor not bound to G-alpha-GDP
Cytosolic calcium (2+) concentration
Factor for converting from number of particles to cytosolic concentration
Factor for converting number of particles to a density on the cell’s plasma membrane
Factor for converting between density fluxes and concentration fluxes
Area density of free inactive G-protein. "...represents the densities of a species required to form that mobile messenger—the amount of free G-alpha-GDP."
G-alpha-GTP density
IP3 concentration in cytosol
Reaction R1 flux
Reaction R10 flux
Reaction R11 flux
Reaction R12 flux
Reaction R13 flux
Reaction R14 flux
Reaction R15 flux
Reaction R16 flux
Reaction R2 flux
Reaction R3 flux
Reaction R4 flux
Reaction R5 flux
Reaction R6 flux
Reaction R7 flux
Reaction R8 flux
Reaction R9 flux
Dissociation constant for the binding of ligand to the receptor with no attached G-protein
Reaction R11 dissociation rate constant
Dissociation constant for the binding of unbound receptor to G-protein
Dissociation constant for the binding of ligand to the receptor with attached G-protein
Reaction R14 Km value
Reaction R15 Km value
Extracellular ligand concentration for unstimulated condition
Full-strength ligand concentration during stimulation
PLC-beta density
PIP2 density
Density of PLC-beta bound to calcium (2+)
Density of PLC-beta bound to calcium (2+) and G-alpha-GTP
Density of PLC-beta bound to G-alpha-GTP
Area density of noncoupled receptors
Density of receptors coupled with G-proteins
Ligand-bound receptor density
Active receptor density
Phosphorylated receptor density
Ratio of plasma membrane surface area to cytosolic volume
Cytosolic volume
Reaction R1 forward rate constant
Reaction R10 forward rate constant
Reaction R11 forward rate constant
Reaction R12 forward rate constant
Reaction R13 forward rate constant
Rate constant for the nonstimulated IP3 production reaction
Reaction R15 forward rate constant
Rate constant for the degradation of IP3
Reaction R2 forward rate constant
Reaction R3 forward rate constant
Forward rate for the binding of ligand to precoupled receptor
Rate constant for the phosphorylation of active receptor
G-protein dissociation rate from the activated receptor
Reaction R7 forward rate constant
Forward rate constant for the binding of calcium to PLC-beta
Reaction R9 forward rate constant
Reaction R1 reverse rate constant
Reaction R10 reverse rate constant
Reaction R11 reverse rate constant
Reaction R2 reverse rate constant
Reaction R3 reverse rate constant
Reverse rate constant for the binding of calcium to PLC-beta
Time
Time domain
Time of ligand stimulation
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