- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2009-07-07 17:07:09+12:00
- Desc:
- removing comparison traces from HH model as they are no longer relevant
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/a1/rawfile/ee5043691b3de28d909fbbf16c9429416937ef40/tutorial/HH-to-N62-tutorial.xml
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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">
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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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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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<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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Auckland Bioengingeering Institute, The University of Auckland.
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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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HH Model Validation
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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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The original source of these models is http://www.bioeng.nus.edu.sg/compbiolab/p3/.
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<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<rdf:value>
Taking the original task description and modifying for this tutorial.
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<rdf:Description rdf:ID="INa-gating-kinetics">
<dc:title>
HH Sodium Channel Kinetics Validation
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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: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"/>
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HH Potassium Channel Kinetics Validation
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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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<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.
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<cmeta:modifier rdf:resource="#andre"/>
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<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/IK-gating-kinetics-graphs.xml#IK-gating-rates"/>
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HH Voltage Clamp Validation
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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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<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>
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<rdf:Description rdf:about="http://www.bioeng.nus.edu.sg/compbiolab/p3/cellml/experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-1"/>
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<csim:task>
<rdf:Description rdf:ID="applied-stimulus">
<dc:title>
HH Action Potential Validation
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<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.
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<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>
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<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"/>
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<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 groups the series of modifications that we will make to the HH model in order to move toward the Noble 1962 Purkinje fibre model.
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<dcterms:description rdf:parseType="Resource">
<rdf:value>
The tasks grouped here use the base HH model implementation provided on http://www.bioeng.nus.edu.sg/compbiolab/p3/ - as is - and layer on the required modifications using the features defined by CellML 1.1. The goal of the Noble 1962 model was to test whether, with modificaitons, the HH model could be used to describe the long-lasting action and pace-maker potentials of the Purkinjes fibres of the heart. Here we try to achieve something close to this with minimal modification of the base HH model.
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<dc:creator rdf:resource="#andre"/>
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<dcterms:W3CDTF>2009-07-06</dcterms:W3CDTF>
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<bqs:Pubmed_id>14480151</bqs:Pubmed_id>
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<rdf:Description rdf:about="#increase-Cm"/>
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<csim:task>
<rdf:Description rdf:ID="increase-Cm">
<dc:title>
Increasing Cm parameter.
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Noble 1962 scales the HH Cm parameter by a factor of 12. Given the modular nature of the base HH model implementation we are using here, we simply reproduce the experiment from the validation studies but now override the value of Cm with the scaled value.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
As shown in the graphs below, the scaling of Cm on its own completely destroys the generation of the action potentials. Thus indicating further modifications need to be made to achieve the goal of a Purkinje-like action potential.
</rdf:value>
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<dcterms:W3CDTF>2009-07-07</dcterms:W3CDTF>
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<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="increase-Cm-graphs.xml#potential"/>
<rdf:Description rdf:about="increase-Cm-graphs.xml#currents"/>
<rdf:Description rdf:about="increase-Cm-graphs.xml#gates"/>
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</csim:task>
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