- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2011-06-21 15:56:12+12:00
- Desc:
- adding a standalone version of the SED-ML document for this example, updating to pass validation using Frank's new web tools
- Permanent Source URI:
- https://models.cellml.org/workspace/a1/rawfile/1e62f9a11a1b467aff7bc1ddd0b4fc8ac3f052c0/tutorial/IUPS-2009-tutorial.xml
<?xml version="1.0" encoding="iso-8859-1"?>
<rdf:RDF
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:cmeta="http://www.cellml.org/metadata/1.0#"
xmlns:bqs="http://www.cellml.org/bqs/1.0#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
xmlns:cs="http://www.cellml.org/metadata/simulation/1.0#"
xmlns:cg="http://www.cellml.org/metadata/graphs/1.0#"
xmlns:csim="http://cellml.sourceforge.net/CellMLSimulator/#">
<rdf:Description rdf:ID="andre">
<vCard:N rdf:parseType="Resource">
<vCard:Family>Nickerson</vCard:Family>
<vCard:Given>David</vCard:Given>
</vCard:N>
<vCard:EMAIL rdf:parseType="Resource">
<rdf:value>d.nickerson@auckland.ac.nz</rdf:value>
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
</vCard:EMAIL>
<vCard:ORG rdf:parseType="Resource">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
</vCard:ORG>
</rdf:Description>
<rdf:Description>
<csim:referenceDescription>
<rdf:Description rdf:ID="reference-description">
<dc:title>
A series of cardiac cellular electrophysiological modelling case studies in the use of CellML and associated metadata.
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
This reference description is attempting to document a introductory tutorial for CellML emphasising the modularity, reuse, and exchange features that are available when developing models in a CellML 1.1 framework. The focus of this tutorial is the application of a CellML based modelling framework in the area of cardiac cellular electrophysiology.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
The reference description can be browsed via the tree hierarchy over on the left hand side of the page or by navigating from the list of tasks given below. All you need to do is assume that there is an associated, peer-reviewed article which summarises this reference description and perhaps provides some further analysis of the novel insights mentioned above :)
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:created>
<dc:publisher>
Auckland Bioengingeering Institute, The University of Auckland.
</dc:publisher>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>19380314</bqs:Pubmed_id>
</bqs:reference>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>19163192</bqs:Pubmed_id>
</bqs:reference>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>18606438</bqs:Pubmed_id>
</bqs:reference>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>18310619</bqs:Pubmed_id>
</bqs:reference>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Restructure the reference description to be suitable for the complete IUPS 2009 tutorial.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:tasks rdf:parseType="Collection">
<rdf:Description rdf:about="#hh-to-n62"/>
<rdf:Description rdf:about="#tnnp-stimulus-protocol"/>
</csim:tasks>
</rdf:Description>
</csim:referenceDescription>
<csim:task>
<rdf:Description rdf:ID="hh-to-n62">
<dc:title>
Modifying Hodgkin & Huxley toward Noble 1962
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
This section of the tutorial illustrates the modularity and resuse aspects of CellML. An accurate representation of the original Hodgkin & Huxley 1952 squid axon model has previously been published and made available on a web server at NUS in Singapore. In this task we first validate this implementation of the model and then modify it through the replacement of the potassium current for a model available in the CellML model repository and the slight modification of some parameters. These modifications are sufficient to turn the short duration nerve action potential into a long lasting action potential similar to the Noble 1962 cardiac Purkinje fibre action potential.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
The basic premise of this example is based on the first biophysical cardiac cellular electrophysiology model, published by Denis Noble in 1962, which defines a modification of the Hodgkin-Huxley 1952 squid axon model capable of reproducing the action and pacemaker potentials observed in Purkinje fibres. In this tutorial we start with a CellML description of the Hodgkin-Huxley model and modify it to reproduce some of the key features of the Noble 1962 model.
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<csim:tasks rdf:parseType="Collection">
<rdf:Description rdf:about="#hh-model-validation-task"/>
<rdf:Description rdf:about="#modification-to-n62-task"/>
</csim:tasks>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="hh-model-validation-task">
<dc:title>
HH Model Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
This is the parent task for the simulation experiments used to validate the base Hodgkin & Huxley model implemented for this tutorial. The model has been previously implemented and is available online from the Computational Bioengineering Laboratory at the National University of Singapore.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
The original source of these models is http://www.bioeng.nus.edu.sg/compbiolab/p3/. All the graphs illustrated here are simulated directly from the data described on the NUS server.
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:created>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:tasks rdf:parseType="Collection">
<rdf:Description rdf:about="#INa-gating-kinetics"/>
<rdf:Description rdf:about="#IK-gating-kinetics"/>
<rdf:Description rdf:about="#voltage-clamp"/>
<rdf:Description rdf:about="#applied-stimulus"/>
</csim:tasks>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="INa-gating-kinetics">
<dc:title>
Sodium Channel Kinetics Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Validation study investigating the kinetics of the sodium channel of the base implementation of the Hodgkin & Huxley model.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-16</dcterms:W3CDTF>
</dcterms:created>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial - namely redirecting graph URIs to the NUS server.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/INa-gating-kinetics-graphs.xml#INa-gating-rates"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/INa-gating-kinetics-graphs.xml#INa-gating-SS"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="IK-gating-kinetics">
<dc:title>
Potassium Channel Kinetics Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Validation study investigating the kinetics of the potassium channel of the base implementation of the Hodgkin & Huxley model.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-31</dcterms:W3CDTF>
</dcterms:created>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial - namely redirecting graph URIs to the NUS server.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/IK-gating-kinetics-graphs.xml#IK-gating-rates"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/IK-gating-kinetics-graphs.xml#IK-gating-SS"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="voltage-clamp">
<dc:title>
Voltage Clamp Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Validation study investigating the total membrane current dynamics following the application of voltage clamp protocols using the base implementation of the Hodgkin & Huxley model.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-31</dcterms:W3CDTF>
</dcterms:created>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial - namely redirecting graph URIs to the NUS server.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-1"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-2"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-3"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-4"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-5"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="applied-stimulus">
<dc:title>
Action Potential Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Validation study investigating the dynamic response of the base implementation of the Hodgkin & Huxley model to an applied electrical stimulus current.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-31</dcterms:W3CDTF>
</dcterms:created>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial - namely redirecting graph URIs to the NUS server.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#potential"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#currents"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#gates"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#potential-zoom"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#currents-zoom"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/periodic-stimulus-graphs.xml#gates-zoom"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="modification-to-n62-task">
<dc:title>
Modification toward Noble 1962 model
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
This task defines the modifications made to the base HH implementation in order to approximate the action potential shape of the Noble 1962 model.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
This modified model is defined by: 1) importing the sodium and leakage currents from the base HH model (http://www.bioeng.nus.edu.sg/compbiolab/p3/); 2) importing the stimulus protocol from the base HH model; 3) importing the required units from the base HH model; 4) defining the time component which defines our time variable; 5) ...
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>14480151</bqs:Pubmed_id>
</bqs:reference>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="HH-to-N62-graphs.xml#modified-HH-AP"/>
<rdf:Description rdf:about="HH-to-N62-graphs.xml#modified-HH-currents"/>
<rdf:Description rdf:about="HH-to-N62-graphs.xml#modified-HH-gates"/>
<rdf:Description rdf:about="HH-to-N62-graphs.xml#modified-HH-IK"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="tnnp-stimulus-protocol">
<dc:title>
TNNP stimuli
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we make use of an exisiting encoding of the ten Tusscher et al (2004) human ventricular myocyte model which has a periodic stimulus current applied. We replace this stimulus protocol with one more suited for restitution analysis.
</rdf:value>
</dcterms:abstract>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>18606438</bqs:Pubmed_id>
</bqs:reference>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
Nickerson & Buist (2008) published a study investigating the practical application of CellML 1.1 based on the ten Tusscher et al (2004) human ventricular myocyte electrophysiology model. The online supplement for this study is available at: http://www.bioeng.nus.edu.sg/compbiolab/papers/nickerson-PBMB-2008/, which inlcudes all the simulation experiment descriptions presented in that study.
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<csim:tasks rdf:parseType="Collection">
<rdf:Description rdf:about="#tnnp-periodic-stimulus"/>
<rdf:Description rdf:about="#tnnp-S1S2-stimulus"/>
</csim:tasks>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="tnnp-periodic-stimulus">
<dc:title>
Periodic
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Presentation of the results obtained from the default periodic stimulus simulation experiment from the experiment description provided on the NUS server (http://www.bioeng.nus.edu.sg/compbiolab/papers/nickerson-PBMB-2008/).
</rdf:value>
</dcterms:abstract>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>18606438</bqs:Pubmed_id>
</bqs:reference>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/papers/nickerson-PBMB-2008/experiments/TNNP-periodic-graphs.xml#ActionPotential"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/papers/nickerson-PBMB-2008/experiments/TNNP-periodic-graphs.xml#CalciumTransient"/>
<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/papers/nickerson-PBMB-2008/experiments/TNNP-periodic-graphs.xml#IK"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="tnnp-S1S2-stimulus">
<dc:title>
S1-S2 restitution
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Apply a S1-S2 restitution stimulus protocol to the base TNNP model. Here we present results for a couple of different values for the S2 interval to illustrate how the complete sequence could be performed in order to obtain the restitution curve.
</rdf:value>
</dcterms:abstract>
<bqs:reference rdf:parseType="Resource">
<bqs:Pubmed_id>18606438</bqs:Pubmed_id>
</bqs:reference>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="TNNP-S1S2-graphs.xml#S1S2-ActionPotential"/>
</csim:graphs>
</rdf:Description>
</csim:task>
</rdf:Description>
</rdf:RDF>
