- Author:
- David Nickerson <nickerso@users.sourceforge.net>
- Date:
- 2015-05-25 08:31:46+12:00
- Desc:
- adding a SED-ML document which does nested repeated tasks to iterate over clamp potential and temperature; doesn't work with get-sed-ml-client
- Permanent Source URI:
- https://models.physiomeproject.org/w/andre/HH/rawfile/957c2190e1eed47d7634613250bc274dc836b826/supplement.xml
<?xml version="1.0" encoding="iso-8859-1"?>
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<vCard:Orgname>National University of Singapore</vCard:Orgname>
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<vCard:FN>D P Nickerson</vCard:FN>
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<vCard:Orgname>National University of Singapore</vCard:Orgname>
<vCard:Orgunit>Division of Bioengineering</vCard:Orgunit>
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<rdf:Description>
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<dc:title>
Reference Description of a HH-based Modelling Study
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
This is a complete description of the models and numerical experiments performed in this Hodgkin & Huxley based modelling article. Herein you will find all the information required to completely recreate and validate the work presented in the article.
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</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
This is a demonstration of the complete specification of a reference description of an entire cellular electrophysiology model publication. In this reference description you will find descriptions and results of simulation experiments performed to validate the base model upon which this fictitious modelling article, as well as some fancy extensions and modifications of the base model along with the novel insights obtained thenceforth.
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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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</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-16</dcterms:W3CDTF>
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<dc:publisher>
Division of Bioengineering, National University of Singapore
</dc:publisher>
<csim:citation rdf:parseType="Resource">
<csim:authors>
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<dc:creator rdf:resource="#andre"/>
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<dc:creator rdf:resource="#andre2"/>
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<rdf:li rdf:parseType="Resource">
<dc:creator rdf:resource="#andre3"/>
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<dc:title>
Investigation of membrane conductance and ion concentrations using Hodgkin & Huxley's squid axon model
</dc:title>
<dcterms:issued>2021</dcterms:issued>
<dcterms:bibliographicCitation>
Fan J Eve Cool. 2021 Jun;1(1):12-67
</dcterms:bibliographicCitation>
</csim:citation>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Escaped the HTML code in the description in order to get this RDF code to validate.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-16</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Re-wording some bits and pieces in order to add apostrophes (') to the text in order to test the escaping when generating the JSON reference description.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-23</dcterms:W3CDTF>
</dcterms:modified>
</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Adding in the potassium channel validation study.
</rdf:value>
<cmeta:modifier rdf:resource="#andre"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-31</dcterms:W3CDTF>
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<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Adding in the membrane conductance study.
</rdf:value>
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<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
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</cmeta:modification>
<cmeta:modification rdf:parseType="Resource">
<rdf:value>
Adding in the ion concentration study.
</rdf:value>
<cmeta:modifier rdf:resource="#andre3"/>
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
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(http://www.w3schools.com/rdf/rdf_collections.asp)
As seen in the previous chapter: You cannot close a container. A container says that the containing resources are members - it does not say that other members are not allowed.
RDF collections are used to describe group that contains ONLY the specified members.
-->
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<rdf:Description rdf:about="#model-validation-task"/>
<rdf:Description rdf:about="#membrane-conductance-task"/>
<rdf:Description rdf:about="#ion-concentrations-task"/>
</csim:tasks>
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<csim:task>
<rdf:Description rdf:ID="model-validation-task">
<dc:title>
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 study.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
Do we need any further 'description'?
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre2"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-07-16</dcterms:W3CDTF>
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<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 our 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>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/INa-gating-kinetics-graphs.xml#INa-gating-rates"/>
<rdf:Description rdf:about="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 our 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>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/IK-gating-kinetics-graphs.xml#IK-gating-rates"/>
<rdf:Description rdf:about="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 our 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>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-1"/>
<rdf:Description rdf:about="experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-2"/>
<rdf:Description rdf:about="experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-3"/>
<rdf:Description rdf:about="experiments/voltage-clamp-graphs.xml#voltage-clamp-currents-4"/>
<rdf:Description rdf:about="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 our 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>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#potential"/>
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#currents"/>
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#gates"/>
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#potential-zoom"/>
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#currents-zoom"/>
<rdf:Description rdf:about="experiments/periodic-stimulus-graphs.xml#gates-zoom"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="membrane-conductance-task">
<dc:title>
The effect of membrane conductance
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
In this study we investigate the effect of changing membrane conductances for the three ionic currents in the Hodgkin & Huxley model.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
Given the validation studies have shown our implementation of the Hodgkin & Huxley model produces acceptable results, we now investigate the changes in simulated action potentials due to changes in maximal membrane conductance.
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre2"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
</dcterms:created>
<csim:tasks rdf:parseType="Collection">
<rdf:Description rdf:about="#gNa"/>
<rdf:Description rdf:about="#gK"/>
<rdf:Description rdf:about="#gleak"/>
<rdf:Description rdf:about="#combinedConductances"/>
</csim:tasks>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="gNa">
<dc:title>
Sodium channel conductance
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we investigate the changes in cellular electrophysiology due to altering the maximal sodium channel conductance.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
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<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gNa_potential"/>
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gNa_INa"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="gK">
<dc:title>
Potassium channel conductance
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we investigate the changes in cellular electrophysiology due to altering the maximal potassium channel conductance.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gK_potential"/>
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gK_IK"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="gleak">
<dc:title>
Leakage current conductance
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we investigate the changes in cellular electrophysiology due to altering the maximal leak current conductance.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gleak_potential"/>
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#gleak_Ileak"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="combinedConductances">
<dc:title>
Comparison of changes
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we compare the changes in action potentials due to altering the maximal conductance of each of the ionic currents in the model by the different amounts.
</rdf:value>
</dcterms:abstract>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#combined_potential_050"/>
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#combined_potential_150"/>
<rdf:Description rdf:about="experiments/membrane-conductance-graphs.xml#combined_potential_200"/>
</csim:graphs>
</rdf:Description>
</csim:task>
<csim:task>
<rdf:Description rdf:ID="ion-concentrations-task">
<dc:title>
Varying ion concentrations
</dc:title>
<dcterms:abstract rdf:parseType="Resource">
<rdf:value>
Here we investigate the effect on action potential dynamics due to changing ion concentrations.
</rdf:value>
</dcterms:abstract>
<dcterms:description rdf:parseType="Resource">
<rdf:value>
In their 1952 masterpiece, Hodgkin & Huxley specified the experimentally observed range for each of the ionic current reversal potentials. Given the Nernst equation, the observed variation is most likely due to changing intra- or extracellular ion concentrations. Thus we examine the effect of ion concentration by altering the reversal potential of each current.
</rdf:value>
</dcterms:description>
<dc:creator rdf:resource="#andre"/>
<dcterms:created rdf:parseType="Resource">
<dcterms:W3CDTF>2008-08-14</dcterms:W3CDTF>
</dcterms:created>
<csim:graphs rdf:parseType="Collection">
<rdf:Description rdf:about="experiments/concentration-graphs.xml#sodium"/>
<rdf:Description rdf:about="experiments/concentration-graphs.xml#potassium"/>
<rdf:Description rdf:about="experiments/concentration-graphs.xml#leak"/>
</csim:graphs>
</rdf:Description>
</csim:task>
</rdf:Description>
</rdf:RDF>
