Location: Sneyd_2016 @ da1f78260d85 / Experiment / Sneyd_2016.cellml

Author:

Leyla <noroozbabaee@gmail.com>

Date:

2021-11-11 23:09:06+13:00

Desc:

All the files are updated!

Permanent Source URI:

https://staging.physiomeproject.org/workspace/7b3/rawfile/da1f78260d851b46a4490c0cde5b78233b64a835/Experiment/Sneyd_2016.cellml

<?xml version='1.0' encoding='UTF-8'?>
<!-- Auther: Leyla Noroozbabee
 Date: 10/10/2021 -->
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                <title xmlns="http://cellml.org/tmp-documentation">A Single Cell Mathematical Model of the Ion Currents Underlying Sinoatrial Node Pacemaker Activity</title>
                <author xmlns="http://cellml.org/tmp-documentation">
                    <firstname xmlns="http://cellml.org/tmp-documentation">Catherine</firstname>
                    <surname xmlns="http://cellml.org/tmp-documentation">Lloyd</surname>
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                        <shortaffil xmlns="http://cellml.org/tmp-documentation">Auckland Bioengineering Institute, The University of Auckland</shortaffil>
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                <title xmlns="http://cellml.org/tmp-documentation">Model Status</title>
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        This CellML model runs in COR and OpenCell to recreate the published results. The units have been checked and they are consistent.&#xd;
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                <title xmlns="http://cellml.org/tmp-documentation">Model Structure</title>
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ABSTRACT: The ionic currents underlying autorhythmicity of the mammalian sinoatrial node and their wider contribution to each phase of the action potential have been investigated in this study using a new single cell mathematical model. The new model provides a review and update of existing formulations of sinoatrial node membrane currents, derived from a wide range of electrophysiological data available in the literature. Simulations of spontaneous activity suggest that the dominant mechanism underlying pacemaker depolarisation is the inward background Na+ current, ib,Na. In contrast to previous models, the decay of the delayed rectifying K+ current, iK, was insignificant during this phase. Despite the presence of a pseudo-outward background current throughout the pacemaker range of potentials (Na-K pump+leak currents), the hyperpolarisation-activated current i(f) was not essential to pacemaker activity. A closer inspection of the current-voltage characteristics of the model revealed that the "instantaneous" time-independent current was inward for holding potentials in the pacemaker range, which rapidly became outward within 2 ms due to the inactivation of the L-type Ca2+ current, iCa,L. This suggests that reports in the literature in which the net background current is outward throughout the pacemaker range of potentials may be exaggerated. The magnitudes of the action potential overshoot and the maximum diastolic potential were determined largely by the reversal potentials of iCa,L and iK respectively. The action potential was sustained by the incomplete deactivation of iCa,L and the Na-Ca exchanger, iNaCa. Despite the incorporation of "square-root" activation by [K]o of all K+ currents, the model was unable to correctly simulate the response to elevated [K]o.</para>
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The original paper reference is cited below:&#xd;
</para>
                <para xmlns="http://cellml.org/tmp-documentation">&#xd;
Ion Currents Underlying Sinoatrial Node Pacemaker Activity: A New Single Cell Mathematical Model, Socrates Dokos, Branko Celler, and Nigel Lovell, 1996, &#xd;
            <emphasis xmlns="http://cellml.org/tmp-documentation">Theoretical Journal of Biology</emphasis>&#xd;
          , 181, 245-272.  <ulink xmlns="http://cellml.org/tmp-documentation" url="http://www.ncbi.nlm.nih.gov/pubmed/8869126">PubMed ID: 8869126</ulink>
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                                <title xmlns="http://cellml.org/tmp-documentation">cell diagram</title>
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                            <imagedata xmlns="http://cellml.org/tmp-documentation" fileref="dokos_1996.png"/>
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                    <caption xmlns="http://cellml.org/tmp-documentation">A schematic diagram of the Dokos <emphasis xmlns="http://cellml.org/tmp-documentation">et al.</emphasis> 1996 mathematical model of the SA node cell.  Sodium, calcium and potassium ions are exchanged between the intracellular and extracellular environments through channels, the sodium-potassium pump and the sodium-calcium exchanger.  Calcium is transferred between the cytosol and the sarcoplasmic reticulum (SR), and between the local regions of the SR.</caption>
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            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">cmeta:id's have been added to several variables to allow creation of a PCEnv session file.</rdf:value>
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            <title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Ion currents underlying sinoatrial node pacemaker activity: a new single cell mathematical model</title>
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            <title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Journal of Theroretical Biology</title>
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            <Orgname xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">The University of Auckland</Orgname>
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        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#75aa486a-f48b-4405-b5e2-dc3a2e627175">
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">This model has been validated by Penny Noble of Oxford University and is known to run in COR and PCEnv. A PCEnv session file is also associated with this version.</rdf:value>
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            <FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">James Lawson</FN>
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            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">added cmeta:id's for some variables to allow referencing by PCEnv</rdf:value>
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            <Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">James</Given>
            <Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Lawson</Family>
            <Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Richard</Other>
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        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#a574a2ba-22e8-4c75-a2ec-c37859024a4b">
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">This is the CellML description of Dokos et al's 1996 mathematical &#xd;
model of the ion currents underlying sinoatrial node pacemaker &#xd;
activity. Please note that equations for reversal potentials were not           included in the original published model and have had to be added.  &#xd;
Also, a current called i_KACh was included in the equations for &#xd;
external and internal potassium ion concentration calculation.  This &#xd;
current had not been previously mentioned in the paper, and as i_KACh &#xd;
is usually referred to in ischemic tissue, and also the background &#xd;
potassium current i_bK had not been included in the equation, I am &#xd;
assuming that this was a typo.  The model authors have been contacted &#xd;
and we are awaiting their reply.</rdf:value>
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            <FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Catherine Lloyd</FN>
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            <publisher xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">The University of Auckland, Bioengineering Institute</publisher>
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            <N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
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            </N>
            <ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#34d6402c-debe-4537-9e31-731d53191d6d"/>
            </ORG>
            <EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#5f4f4c45-bf1b-405d-a10b-abdc66064fe6"/>
            </EMAIL>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#d54dfe01-5253-4e09-ba29-2c899b8f43c3">
            <W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">2003-04-10T00:00:00+00:00</W3CDTF>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#4c91e375-d489-498d-91a9-6ad412eb2cb4">
            <W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">2006-01-01</W3CDTF>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#5c2070b9-7348-4845-990d-be21a6a4dd27">
            <modified xmlns="http://purl.org/dc/terms/">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#16a51c5e-1c96-4dfc-8c81-48e872f171c6"/>
            </modified>
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">This model has been validated by Penny Noble</rdf:value>
            <modifier xmlns="http://www.cellml.org/metadata/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#c0f222ac-f1c1-4aaa-821b-43f5dd20ae0d"/>
            </modifier>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#6ed5da74-dec8-406f-ba93-911f93fd6f69">
            <modified xmlns="http://purl.org/dc/terms/">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#50bd5b2a-64b6-4aaf-beeb-4ec42c7b5865"/>
            </modified>
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Units checked, curated.</rdf:value>
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                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#5abcd52a-3b14-407a-9b90-d2d5a0f21f1a"/>
            </modifier>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#fd71e851-3895-44f3-8e03-176c535ca656">
            <Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Catherine</Given>
            <Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Lloyd</Family>
            <Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">May</Other>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#5f4f4c45-bf1b-405d-a10b-abdc66064fe6">
            <rdf:type xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://imc.org/vCard/3.0#internet"/>
            </rdf:type>
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">c.lloyd@auckland.ac.nz</rdf:value>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#16a51c5e-1c96-4dfc-8c81-48e872f171c6">
            <W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">2007-06-19T15:55:00+12:00</W3CDTF>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#c0f222ac-f1c1-4aaa-821b-43f5dd20ae0d">
            <N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#24727d09-7250-4a4d-bbf0-addb6c67ec23"/>
            </N>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#50bd5b2a-64b6-4aaf-beeb-4ec42c7b5865">
            <W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">2007-12-19T14:19:12+13:00</W3CDTF>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#5abcd52a-3b14-407a-9b90-d2d5a0f21f1a">
            <N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#7f774b4b-e9f8-40f9-b84a-9e59c5d426b1"/>
            </N>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#24727d09-7250-4a4d-bbf0-addb6c67ec23">
            <Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Penny</Given>
            <Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Noble</Family>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#7f774b4b-e9f8-40f9-b84a-9e59c5d426b1">
            <Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Penny</Given>
            <Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Noble</Family>
            <Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">J</Other>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="#dokos_1996">
            <title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">unknown</title>
            <comment xmlns="http://www.cellml.org/metadata/1.0#">
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            <simulation xmlns="http://www.cellml.org/metadata/simulation/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$pk2nE"/>
            </simulation>
            <reference xmlns="http://www.cellml.org/bqs/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#29b2e279-f828-4d28-869a-4bb483ec2507"/>
            </reference>
            <reference xmlns="http://www.cellml.org/bqs/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n1"/>
            </reference>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$pk2nE">
            <boundIntervals xmlns="http://www.cellml.org/metadata/simulation/1.0#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$qk2nE"/>
            </boundIntervals>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n1">
            <subject xmlns="http://purl.org/dc/elements/1.1/">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n2"/>
            </subject>
        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$qk2nE">
            <rdf:first xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$rk2nE"/>
            </rdf:first>
            <rdf:rest xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
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        </rdf:Description>
        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n2">
            <rdf:value xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n3"/>
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            <subject_type xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">keyword</subject_type>
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        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="rdf:#$rk2nE">
            <endingValue xmlns="http://www.cellml.org/metadata/simulation/1.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">2</endingValue>
            <pointDensity xmlns="http://www.cellml.org/metadata/simulation/1.0#nonstandard-" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">100000</pointDensity>
            <maximumStepSize xmlns="http://www.cellml.org/metadata/simulation/1.0#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">0.1</maximumStepSize>
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        <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:nodeID="n3">
            <rdf:type xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
                <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/>
            </rdf:type>
            <rdf:_1 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">cardiac</rdf:_1>
            <rdf:_2 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">electrophysiology</rdf:_2>
            <rdf:_3 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">Sinoatrial Node</rdf:_3>
            <rdf:_4 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">pacemaker</rdf:_4>
            <rdf:_5 xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xml:lang="en" xmlns:xml="http://www.w3.org/XML/1998/namespace">sinoatrial node</rdf:_5>
        </rdf:Description>
    </rdf:RDF>
</model>