{"identifier":"id","label":"title","items":[{"id":"named_0","type":"root","generated":{"id":"anon_0","tool":"CellMLSimulator","uri":"http://cellml.sourceforge.net/CellMLSimulator","version":"CellMLSimulator 0.3.0-devel-json - revision 211:217 - Thu Jun 11 11:43:39 NZST 2009","date":1246943671000},"uri":"http://models.cellml.org/workspace/a1/@@rawfile/500db4fce527a0e9af04e756ce219f68bd44006a/tutorial/HH-to-N62-tutorial.xml#reference-description","title":"Modification of the Hodgkin-Huxley equations applicable to Purkinje fibre action and pacemaker potentials in CellML","created":{"id":"anon_1","creator":{"id":"anon_2","type":"person","name":"David Nickerson","email":"d.nickerson@auckland.ac.nz","organisation":"Auckland Bioengineering Institute, The University of Auckland"},"created":1246795200000},"publisher":"Auckland Bioengingeering Institute, The University of Auckland.","citations":[{"id":"anon_3","subType":"journal-article","pmid":"19380314","doi":"10.1098/rsta.2008.0296","title":"A physiome standards-based model publication paradigm.","journal":"Philos Transact A Math Phys Eng Sci","volume":"367","number":"1895","year":"2009","month":"4","day":"22","startPage":"1823","endPage":"1867","authors":["David P Nickerson","Martin L Buist"]},{"id":"anon_4","subType":"journal-article","pmid":"19163192","doi":"10.1109/IEMBS.2008.4649689","title":"Interactive reference descriptions of cellular electrophysiology models.","journal":"Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference","volume":"2008","year":"2009","month":"1","day":"24","startPage":"2427","endPage":"2457","authors":["David Nickerson","Martin Buist"]},{"id":"anon_5","subType":"journal-article","pmid":"18606438","doi":"10.1016/j.pbiomolbio.2008.05.006","title":"Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model.","journal":"Prog. Biophys. Mol. Biol.","volume":"98","number":"1","year":"2008","month":"7","day":"9","startPage":"38","endPage":"51","authors":["David Nickerson","Martin Buist"]},{"id":"anon_6","subType":"journal-article","pmid":"18310619","doi":"10.1093/bioinformatics/btn080","title":"Reference descriptions of cellular electrophysiology models.","journal":"Bioinformatics","volume":"24","number":"8","year":"2008","month":"3","day":"4","startPage":"1112","endPage":"1116","authors":["David P Nickerson","Alberto Corrias","Martin L Buist"]}],"abstract":"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.","description":"

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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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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Applies the default set of parameters to the modified HH model and leaves some parameters free for customisation. Applies the periodic stimulus protocol from the original HH implementation from http://www.bioeng.nus.edu.sg/compbiolab/p3/. [David Nickerson]

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The actual definition of the time variable.

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The model parameters.

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The initial conditions - using all default values in this case.

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The Hodgkin & Huxley (1952) model assembled such that given an electrical stimulus current it will simulate action potential transients.

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Here we define the periodic stimulus protocol.

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Here we define the complete set of default parameter values.

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Here we define the complete set set of default initial conditions for the model's differental variables.

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A description of the membrane sodium current of the Hodgkin & Huxley (1952) model.

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A description of the membrane potassium current of the Hodgkin & Huxley (1952) model with some modifications following Noble 1962. The HH n-gate rate constants are slowed by a factor of 100; a base empirical conductance is introduced as an instanteous function of membrane potential;

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A description of the membrane leakage current of the Hodgkin & Huxley (1952) model.

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A description of the voltage-dependent activation rate constant for the m gate of the Hodgkin & Huxley (1952) sodium current.

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A description of the voltage-dependent activation rate constant for the h gate of the Hodgkin & Huxley (1952) sodium current.

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