- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2009-07-07 22:22:32+12:00
- Desc:
- renaming files in order to move to a single reference description for the entire tutorial
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/a1/rawfile/0c824288680f5949ea1972a76176826599ef6d26/tutorial/IUPS-2009-tutorial.xml
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<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
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<csim:referenceDescription>
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<dc:title>
Modification of the Hodgkin-Huxley equations applicable to Purkinje fibre action and pacemaker potentials in CellML
</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 basic premise based on 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 gradually modify it to reproduce some of the key features of the Noble 1962 model.
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<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 :)
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<dc:creator rdf:resource="#andre"/>
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<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<dc:publisher>
Auckland Bioengingeering Institute, The University of Auckland.
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<bqs:Pubmed_id>19380314</bqs:Pubmed_id>
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<bqs:Pubmed_id>19163192</bqs:Pubmed_id>
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<bqs:Pubmed_id>18606438</bqs:Pubmed_id>
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<bqs:Pubmed_id>18310619</bqs:Pubmed_id>
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Escaped the HTML code in the description in order to get this RDF code to validate.
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<dc:title>
HH Model Validation
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<dcterms:abstract rdf:parseType="Resource">
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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.
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<dcterms:description rdf:parseType="Resource">
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The original source of these models is http://www.bioeng.nus.edu.sg/compbiolab/p3/.
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<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Taking the original task description and modifying for this tutorial.
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<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<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"/>
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<csim:task>
<rdf:Description rdf:ID="INa-gating-kinetics">
<dc:title>
HH Sodium Channel Kinetics Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
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Validation study investigating the kinetics of the sodium channel of the base implementation of the Hodgkin & Huxley model.
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<dcterms:W3CDTF>2008-07-16</dcterms:W3CDTF>
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<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.
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<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<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"/>
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<csim:task>
<rdf:Description rdf:ID="IK-gating-kinetics">
<dc:title>
HH Potassium Channel Kinetics Validation
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
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Validation study investigating the kinetics of the potassium channel of the base implementation of the Hodgkin & Huxley model.
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<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-31</dcterms:W3CDTF>
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<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>
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<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"/>
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<csim:task>
<rdf:Description rdf:ID="voltage-clamp">
<dc:title>
HH Voltage Clamp Validation
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<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.
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<dc:creator rdf:resource="#andre"/>
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<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>
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<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>
HH 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.
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<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) ...
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<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2009-07-06</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"/>
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