<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : renal_H_K_ATPase_model_version02.xml
CREATED : 25th May 2007
LAST MODIFIED : 25th May 2007
AUTHOR : Catherine Lloyd
The Bioengineering Institute
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.1 Specification.
DESCRIPTION : This file contains a CellML description of Alan Weinstein's 1998 mathematical model of the inner medullary collecting duct of the rat: acid/base transport.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqs="http://www.cellml.org/bqs/1.0#" xmlns:cellml="http://www.cellml.org/cellml/1.0#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:pathway_editor="http://www.physiome.com/pathway_editor/1.0#" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" pathway_editor:rendering_config_file="renal_H_K_ATPase_CellMLrender.xml" cmeta:id="renal_H_K_ATPase_model" name="weinstein_1998_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Acid/base Transport in the Inner Medullary Collecting Duct of the Rat</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<section id="sec_status">
<title>Model Status</title>
<para>
This CellML model variant describes the renal H+/K+ ATPase.</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
ABSTRACT: A mathematical model of the inner medullary collecting duct (IMCD) of the rat has been developed that is suitable for simulating luminal buffer titration and ammonia secretion by this nephron segment. Luminal proton secretion has been assigned to an H-K-ATPase, which has been represented by adapting the kinetic model of the gastric enzyme by Brzezinski et al. (P. Brzezinski, B. G. Malmstrom, P. Lorentzon, and B. Wallmark. Biochim. Biophys. Acta 942: 215-219, 1988). In shifting to a 2 H+:1 ATP stoichiometry, the model enzyme can acidify the tubule lumen approximately 3 pH units below that of the cytosol, when luminal K+ is in abundance. Peritubular base exit is a combination of ammonia recycling and HCO3- flux (either via Cl-/HCO3- exchange or via a Cl- channel). Ammonia recycling involves NH4(+) uptake on the Na-K-ATPase followed by diffusive NH3 exit [S. M. Wall. Am. J. Physiol. 270 (Renal Physiol. 39): F432-F439, 1996]; model calculations suggest that this is the principal mode of base exit. By virtue of this mechanism, the model also suggests that realistic elevations in peritubular K+ concentration will compromise IMCD acid secretion. Although ammonia recycling is insensitive to carbonic anhydrase (CA) inhibition, the base exit linked to HCO3- flux provides a CA-sensitive component to acid secretion. In model simulations, it is observed that increased luminal NaCl entry increases ammonia cycling but decreases peritubular Cl-/HCO3- exchange (due to increased cell Cl-). This parallel system of peritubular base exit stabilizes acid secretion in the face of variable Na+ reabsorption.</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
<ulink url="http://ajprenal.physiology.org/cgi/content/abstract/274/5/F856">A mathematical model of the inner medullary collecting duct of the rat: acid/base transport</ulink>, Alan M. Weinstein, 1998, <ulink url="http://ajpcon.physiology.org/">
<emphasis>American Journal of Physiology</emphasis>
</ulink>, 274(5 Pt 2), F856-67. (<ulink url="http://ajprenal.physiology.org/cgi/reprint/274/5/F856.pdf">PDF</ulink> and <ulink url="http://ajprenal.physiology.org/cgi/content/full/274/5/F856">text</ulink> versions of the article are available to Journal subscribers.) <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=6496750&dopt=Abstract">PubMed ID: 6496750</ulink>
</para>
<informalfigure float="0" id="fig_pathway_rendering">
<mediaobject>
<imageobject>
<objectinfo>
<title>pathway_rendering</title>
</objectinfo>
<imagedata fileref="weinstein_1998b.png"/>
</imageobject>
</mediaobject>
<caption>Conventional rendering of the renal H-K-ATPase adapted from the gastric H-K-ATPase model. This model has a stoichiometry of two H<superscript>+</superscript> and two K<superscript>+</superscript> per ATP. E<subscript>1</subscript> and E<subscript>2</subscript> are the cytosolic- and luminal-facing enzymes, respectively.</caption>
</informalfigure>
</sect1>
</article>
</documentation>
<units name="millimolar">
<unit units="mole" prefix="micro"/>
<unit units="litre" exponent="-1"/>
</units>
<units name="first_order_rate_constant">
<unit units="second" exponent="-1"/>
</units>
<units name="second_order_rate_constant">
<unit units="millimolar" exponent="-1"/>
<unit units="second" exponent="-1"/>
</units>
<component name="environment">
<variable units="second" public_interface="out" name="time"/>
</component>
<component name="K2_E1" cmeta:id="K2_E1">
<variable units="millimolar" public_interface="out" name="K2_E1"/>
<variable units="second_order_rate_constant" public_interface="in" name="k1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k1_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k9"/>
<variable units="first_order_rate_constant" public_interface="in" name="k9_"/>
<variable units="millimolar" public_interface="in" name="K2_E2"/>
<variable units="millimolar" public_interface="in" name="K2_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K2_E1 </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k9 </ci>
<ci> K2_E2 </ci>
</apply>
<apply>
<times/>
<ci> k1_ </ci>
<ci> K2_E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k9_ </ci>
<ci> K2_E1 </ci>
</apply>
<apply>
<times/>
<ci> k1 </ci>
<ci> ATP </ci>
<ci> K2_E1 </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="K2_E1_ATP" cmeta:id="K2_E1_ATP">
<variable units="millimolar" public_interface="out" name="K2_E1_ATP"/>
<variable units="second_order_rate_constant" public_interface="in" name="k1"/>
<variable units="first_order_rate_constant" public_interface="in" name="k1_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2a"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2a_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k11"/>
<variable units="first_order_rate_constant" public_interface="in" name="k11_"/>
<variable units="millimolar" public_interface="in" name="K2_E2_ATP"/>
<variable units="millimolar" public_interface="in" name="K2_E1"/>
<variable units="millimolar" public_interface="in" name="K_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K2_E1_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k1 </ci>
<ci> ATP </ci>
<ci> K2_E1 </ci>
</apply>
<apply>
<times/>
<ci> k11 </ci>
<ci> K2_E2_ATP </ci>
</apply>
<apply>
<times/>
<ci> k2a_ </ci>
<ci> K </ci>
<ci> K_E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k11_ </ci>
<ci> K2_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k1_ </ci>
<ci> K2_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k2a </ci>
<ci> K2_E1_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="K_E1_ATP" cmeta:id="K_E1_ATP">
<variable units="millimolar" public_interface="out" name="K_E1_ATP"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2a"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2a_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2b"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2b_"/>
<variable units="millimolar" public_interface="in" name="K2_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="E1_ATP"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K_E1_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k2a </ci>
<ci> K2_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k2b_ </ci>
<ci> K </ci>
<ci> E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k2a_ </ci>
<ci> K_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k2b </ci>
<ci> K_E1_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="E1_ATP" cmeta:id="E1_ATP">
<variable units="millimolar" public_interface="out" name="E1_ATP"/>
<variable units="first_order_rate_constant" public_interface="in" name="k2b"/>
<variable units="second_order_rate_constant" public_interface="in" name="k2b_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k3a"/>
<variable units="first_order_rate_constant" public_interface="in" name="k3a_"/>
<variable units="millimolar" public_interface="in" name="H_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="K_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> E1_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k2b </ci>
<ci> K_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k3a_ </ci>
<ci> H_E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k2b_ </ci>
<ci> K </ci>
<ci> E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k3a </ci>
<ci> H </ci>
<ci> E1_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="H_E1_ATP" cmeta:id="H_E1_ATP">
<variable units="millimolar" public_interface="out" name="H_E1_ATP"/>
<variable units="second_order_rate_constant" public_interface="in" name="k3a"/>
<variable units="first_order_rate_constant" public_interface="in" name="k3a_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k3b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k3b_"/>
<variable units="millimolar" public_interface="in" name="H2_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="E1_ATP"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> H_E1_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k3a </ci>
<ci> H </ci>
<ci> E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k3b_ </ci>
<ci> H2_E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k3a_ </ci>
<ci> H_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k3b </ci>
<ci> H </ci>
<ci> H_E1_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="H2_E1_ATP" cmeta:id="H2_E1_ATP">
<variable units="millimolar" public_interface="out" name="H2_E1_ATP"/>
<variable units="first_order_rate_constant" public_interface="in" name="k4"/>
<variable units="second_order_rate_constant" public_interface="in" name="k4_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k3b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k3b_"/>
<variable units="millimolar" public_interface="in" name="H_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="H2_E1_P"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> H2_E1_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k3b </ci>
<ci> H </ci>
<ci> H_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k4_ </ci>
<ci> ADP </ci>
<ci> H2_E1_P </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k3b_ </ci>
<ci> H2_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k4 </ci>
<ci> H2_E1_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="H2_E1_P" cmeta:id="H2_E1_P">
<variable units="millimolar" public_interface="out" name="H2_E1_P"/>
<variable units="first_order_rate_constant" public_interface="in" name="k4"/>
<variable units="second_order_rate_constant" public_interface="in" name="k4_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k5"/>
<variable units="first_order_rate_constant" public_interface="in" name="k5_"/>
<variable units="millimolar" public_interface="in" name="H2_E2_P"/>
<variable units="millimolar" public_interface="in" name="H2_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="ADP"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
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<diff/>
<bvar>
<ci>time</ci>
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<ci> H2_E1_P </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k4 </ci>
<ci> H2_E1_ATP </ci>
</apply>
<apply>
<times/>
<ci> k5_ </ci>
<ci> H2_E2_P </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k4_ </ci>
<ci> ADP </ci>
<ci> H2_E1_P </ci>
</apply>
<apply>
<times/>
<ci> k5 </ci>
<ci> H2_E1_P </ci>
</apply>
</apply>
</apply>
</apply>
</math>
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<component name="H2_E2_P" cmeta:id="H2_E2_P">
<variable units="millimolar" public_interface="out" name="H2_E2_P"/>
<variable units="first_order_rate_constant" public_interface="in" name="k6a"/>
<variable units="second_order_rate_constant" public_interface="in" name="k6a_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k5"/>
<variable units="first_order_rate_constant" public_interface="in" name="k5_"/>
<variable units="millimolar" public_interface="in" name="H2_E1_P"/>
<variable units="millimolar" public_interface="in" name="H_E2_P"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci>time</ci>
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<ci> H2_E2_P </ci>
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<ci> k6a_ </ci>
<ci> H </ci>
<ci> H_E2_P </ci>
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<times/>
<ci> k5 </ci>
<ci> H2_E1_P </ci>
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<ci> k6a </ci>
<ci> H2_E2_P </ci>
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<ci> k5_ </ci>
<ci> H2_E2_P </ci>
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<component name="H_E2_P" cmeta:id="H_E2_P">
<variable units="millimolar" public_interface="out" name="H_E2_P"/>
<variable units="first_order_rate_constant" public_interface="in" name="k6a"/>
<variable units="second_order_rate_constant" public_interface="in" name="k6a_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k6b"/>
<variable units="second_order_rate_constant" public_interface="in" name="k6b_"/>
<variable units="millimolar" public_interface="in" name="H2_E2_P"/>
<variable units="millimolar" public_interface="in" name="E2_P"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
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<bvar>
<ci>time</ci>
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<ci> H_E2_P </ci>
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<ci> k6a </ci>
<ci> H2_E2_P </ci>
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<ci> k6b_ </ci>
<ci> H </ci>
<ci> E2_P </ci>
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<apply>
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<times/>
<ci> k6a_ </ci>
<ci> H </ci>
<ci> H_E2_P </ci>
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<apply>
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<ci> k6b </ci>
<ci> H_E2_P </ci>
</apply>
</apply>
</apply>
</apply>
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</component>
<component name="E2_P" cmeta:id="E2_P">
<variable units="millimolar" public_interface="out" name="E2_P"/>
<variable units="first_order_rate_constant" public_interface="in" name="k6b"/>
<variable units="second_order_rate_constant" public_interface="in" name="k6b_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k7a"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7a_"/>
<variable units="millimolar" public_interface="in" name="H_E2_P"/>
<variable units="millimolar" public_interface="in" name="K_E2_P"/>
<variable units="millimolar" public_interface="in" name="H"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="second" public_interface="in" name="time"/>
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<ci>time</ci>
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<ci> E2_P </ci>
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<ci> k7a_ </ci>
<ci> K_E2_P </ci>
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<ci> H_E2_P </ci>
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<ci> k6b_ </ci>
<ci> H </ci>
<ci> E2_P </ci>
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<ci> k7a </ci>
<ci> K </ci>
<ci> E2_P </ci>
</apply>
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</math>
</component>
<component name="K_E2_P" cmeta:id="K_E2_P">
<variable units="millimolar" public_interface="out" name="K_E2_P"/>
<variable units="second_order_rate_constant" public_interface="in" name="k7a"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7a_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k7b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7b_"/>
<variable units="millimolar" public_interface="in" name="E2_P"/>
<variable units="millimolar" public_interface="in" name="K2_E2_P"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
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<ci> k7b </ci>
<ci> K </ci>
<ci> K_E2_P </ci>
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</component>
<component name="K2_E2_P" cmeta:id="K2_E2_P">
<variable units="millimolar" public_interface="out" name="K2_E2_P"/>
<variable units="first_order_rate_constant" public_interface="in" name="k8"/>
<variable units="second_order_rate_constant" public_interface="in" name="k8_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k7b"/>
<variable units="first_order_rate_constant" public_interface="in" name="k7b_"/>
<variable units="millimolar" public_interface="in" name="K_E2_P"/>
<variable units="millimolar" public_interface="in" name="K2_E2"/>
<variable units="millimolar" public_interface="in" name="P"/>
<variable units="millimolar" public_interface="in" name="K"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K2_E2_P </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k7b </ci>
<ci> K </ci>
<ci> K_E2_P </ci>
</apply>
<apply>
<times/>
<ci> k8_ </ci>
<ci> P </ci>
<ci> K2_E2 </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k8 </ci>
<ci> K2_E2_P </ci>
</apply>
<apply>
<times/>
<ci> k7b_ </ci>
<ci> K2_E2_P </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="K2_E2" cmeta:id="K2_E2">
<variable units="millimolar" public_interface="out" name="K2_E2"/>
<variable units="first_order_rate_constant" public_interface="in" name="k8"/>
<variable units="second_order_rate_constant" public_interface="in" name="k8_"/>
<variable units="first_order_rate_constant" public_interface="in" name="k9"/>
<variable units="first_order_rate_constant" public_interface="in" name="k9_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k10"/>
<variable units="first_order_rate_constant" public_interface="in" name="k10_"/>
<variable units="millimolar" public_interface="in" name="K2_E2_ATP"/>
<variable units="millimolar" public_interface="in" name="K2_E1"/>
<variable units="millimolar" public_interface="in" name="K2_E2_P"/>
<variable units="millimolar" public_interface="in" name="P"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K2_E2 </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k8 </ci>
<ci> K2_E2_P </ci>
</apply>
<apply>
<times/>
<ci> k10_ </ci>
<ci> K2_E2_ATP </ci>
</apply>
<apply>
<times/>
<ci> k9_ </ci>
<ci> K2_E1 </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k8_ </ci>
<ci> P </ci>
<ci> K2_E2 </ci>
</apply>
<apply>
<times/>
<ci> k10 </ci>
<ci> ATP </ci>
<ci> K2_E2 </ci>
</apply>
<apply>
<times/>
<ci> k9 </ci>
<ci> K2_E2 </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component name="K2_E2_ATP" cmeta:id="K2_E2_ATP">
<variable units="millimolar" public_interface="out" name="K2_E2_ATP"/>
<variable units="first_order_rate_constant" public_interface="in" name="k11"/>
<variable units="first_order_rate_constant" public_interface="in" name="k11_"/>
<variable units="second_order_rate_constant" public_interface="in" name="k10"/>
<variable units="first_order_rate_constant" public_interface="in" name="k10_"/>
<variable units="millimolar" public_interface="in" name="K2_E1_ATP"/>
<variable units="millimolar" public_interface="in" name="K2_E2"/>
<variable units="millimolar" public_interface="in" name="ATP"/>
<variable units="second" public_interface="in" name="time"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> K2_E2_ATP </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> k10 </ci>
<ci> ATP </ci>
<ci> K2_E2 </ci>
</apply>
<apply>
<times/>
<ci> k11_ </ci>
<ci> K2_E1_ATP </ci>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> k10_ </ci>
<ci> K2_E2_ATP </ci>
</apply>
<apply>
<times/>
<ci> k11 </ci>
<ci> K2_E2_ATP </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
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<variable units="millimolar" public_interface="out" name="K" initial_value="20.0"/>
<variable units="millimolar" public_interface="out" name="H" initial_value="4.0"/>
<variable units="millimolar" public_interface="out" name="P" initial_value="5.0"/>
<variable units="millimolar" public_interface="out" name="ATP" initial_value="2.0"/>
<variable units="millimolar" public_interface="out" name="ADP" initial_value="0.04"/>
<variable units="second_order_rate_constant" public_interface="out" name="k1" initial_value="1.3E7"/>
<variable units="first_order_rate_constant" public_interface="out" name="k1_" initial_value="6.5"/>
<variable units="first_order_rate_constant" public_interface="out" name="k2a" initial_value="8.9E3"/>
<variable units="second_order_rate_constant" public_interface="out" name="k2a_" initial_value="7.3E4"/>
<variable units="first_order_rate_constant" public_interface="out" name="k2b" initial_value="8.9E3"/>
<variable units="second_order_rate_constant" public_interface="out" name="k2b_" initial_value="7.3E4"/>
<variable units="second_order_rate_constant" public_interface="out" name="k3a" initial_value="5.3E9"/>
<variable units="first_order_rate_constant" public_interface="out" name="k3a_" initial_value="6.6E2"/>
<variable units="second_order_rate_constant" public_interface="out" name="k3b" initial_value="5.3E9"/>
<variable units="first_order_rate_constant" public_interface="out" name="k3b_" initial_value="6.6E2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k4" initial_value="5E1"/>
<variable units="second_order_rate_constant" public_interface="out" name="k4_" initial_value="2.5E6"/>
<variable units="first_order_rate_constant" public_interface="out" name="k5" initial_value="4E1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k5_" initial_value="2E2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k6a" initial_value="5E7"/>
<variable units="second_order_rate_constant" public_interface="out" name="k6a_" initial_value="8E12"/>
<variable units="first_order_rate_constant" public_interface="out" name="k6b" initial_value="5E7"/>
<variable units="second_order_rate_constant" public_interface="out" name="k6b_" initial_value="8E12"/>
<variable units="second_order_rate_constant" public_interface="out" name="k7a" initial_value="2.6E10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k7a_" initial_value="1.5E8"/>
<variable units="second_order_rate_constant" public_interface="out" name="k7b" initial_value="2.6E10"/>
<variable units="first_order_rate_constant" public_interface="out" name="k7b_" initial_value="1.5E8"/>
<variable units="first_order_rate_constant" public_interface="out" name="k8" initial_value="5.4E1"/>
<variable units="second_order_rate_constant" public_interface="out" name="k8_" initial_value="3.2E1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k9" initial_value="1.75E0"/>
<variable units="first_order_rate_constant" public_interface="out" name="k9_" initial_value="3.5E1"/>
<variable units="second_order_rate_constant" public_interface="out" name="k10" initial_value="5E4"/>
<variable units="first_order_rate_constant" public_interface="out" name="k10_" initial_value="5E1"/>
<variable units="first_order_rate_constant" public_interface="out" name="k11" initial_value="5E2"/>
<variable units="first_order_rate_constant" public_interface="out" name="k11_" initial_value="5E0"/>
</component>
<connection>
<map_components component_2="environment" component_1="K2_E1"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="K2_E1_ATP"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="E1_ATP"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="K_E1_ATP"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="H_E1_ATP"/>
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<connection>
<map_components component_2="environment" component_1="H2_E1_ATP"/>
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<connection>
<map_components component_2="environment" component_1="H2_E1_P"/>
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<connection>
<map_components component_2="environment" component_1="H_E2_P"/>
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<connection>
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<connection>
<map_components component_2="environment" component_1="E2_P"/>
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</connection>
<connection>
<map_components component_2="environment" component_1="K_E2_P"/>
<map_variables variable_2="time" variable_1="time"/>
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<connection>
<map_components component_2="environment" component_1="K2_E2_P"/>
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<connection>
<map_components component_2="environment" component_1="K2_E2"/>
<map_variables variable_2="time" variable_1="time"/>
</connection>
<connection>
<map_components component_2="environment" component_1="K2_E2_ATP"/>
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</connection>
<connection>
<map_components component_2="K2_E1_ATP" component_1="K2_E1"/>
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<map_variables variable_2="K2_E1_ATP" variable_1="K2_E1_ATP"/>
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<connection>
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<connection>
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<map_variables variable_2="K2_E1_ATP" variable_1="K2_E1_ATP"/>
</connection>
<connection>
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<map_variables variable_2="K_E1_ATP" variable_1="K_E1_ATP"/>
<map_variables variable_2="E1_ATP" variable_1="E1_ATP"/>
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<connection>
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<map_variables variable_2="K2_E1_ATP" variable_1="K2_E1_ATP"/>
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<connection>
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<map_variables variable_2="E1_ATP" variable_1="E1_ATP"/>
<map_variables variable_2="H_E1_ATP" variable_1="H_E1_ATP"/>
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<connection>
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<map_variables variable_2="H2_E1_ATP" variable_1="H2_E1_ATP"/>
<map_variables variable_2="H_E1_ATP" variable_1="H_E1_ATP"/>
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<connection>
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<map_variables variable_2="H2_E1_P" variable_1="H2_E1_P"/>
<map_variables variable_2="H2_E1_ATP" variable_1="H2_E1_ATP"/>
</connection>
<connection>
<map_components component_2="H2_E2_P" component_1="H2_E1_P"/>
<map_variables variable_2="H2_E1_P" variable_1="H2_E1_P"/>
<map_variables variable_2="H2_E2_P" variable_1="H2_E2_P"/>
</connection>
<connection>
<map_components component_2="H2_E2_P" component_1="H_E2_P"/>
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<map_variables variable_2="H2_E2_P" variable_1="H2_E2_P"/>
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<connection>
<map_components component_2="E2_P" component_1="H_E2_P"/>
<map_variables variable_2="H_E2_P" variable_1="H_E2_P"/>
<map_variables variable_2="E2_P" variable_1="E2_P"/>
</connection>
<connection>
<map_components component_2="K_E2_P" component_1="E2_P"/>
<map_variables variable_2="E2_P" variable_1="E2_P"/>
<map_variables variable_2="K_E2_P" variable_1="K_E2_P"/>
</connection>
<connection>
<map_components component_2="K2_E2_P" component_1="K_E2_P"/>
<map_variables variable_2="K_E2_P" variable_1="K_E2_P"/>
<map_variables variable_2="K2_E2_P" variable_1="K2_E2_P"/>
</connection>
<connection>
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<map_variables variable_2="K2_E2" variable_1="K2_E2"/>
<map_variables variable_2="K2_E2_P" variable_1="K2_E2_P"/>
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<connection>
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<map_variables variable_2="K2_E2_ATP" variable_1="K2_E2_ATP"/>
</connection>
<connection>
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<map_variables variable_2="k9" variable_1="k9"/>
<map_variables variable_2="k9_" variable_1="k9_"/>
<map_variables variable_2="k1" variable_1="k1"/>
<map_variables variable_2="k1_" variable_1="k1_"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="K2_E1_ATP"/>
<map_variables variable_2="k2a" variable_1="k2a"/>
<map_variables variable_2="k2a_" variable_1="k2a_"/>
<map_variables variable_2="k1" variable_1="k1"/>
<map_variables variable_2="k1_" variable_1="k1_"/>
<map_variables variable_2="k11" variable_1="k11"/>
<map_variables variable_2="k11_" variable_1="k11_"/>
<map_variables variable_2="K" variable_1="K"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="K_E1_ATP"/>
<map_variables variable_2="k2a" variable_1="k2a"/>
<map_variables variable_2="k2a_" variable_1="k2a_"/>
<map_variables variable_2="k2b" variable_1="k2b"/>
<map_variables variable_2="k2b_" variable_1="k2b_"/>
<map_variables variable_2="K" variable_1="K"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="E1_ATP"/>
<map_variables variable_2="k2b" variable_1="k2b"/>
<map_variables variable_2="k2b_" variable_1="k2b_"/>
<map_variables variable_2="k3a" variable_1="k3a"/>
<map_variables variable_2="k3a_" variable_1="k3a_"/>
<map_variables variable_2="K" variable_1="K"/>
<map_variables variable_2="H" variable_1="H"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="H_E1_ATP"/>
<map_variables variable_2="k3a" variable_1="k3a"/>
<map_variables variable_2="k3a_" variable_1="k3a_"/>
<map_variables variable_2="k3b" variable_1="k3b"/>
<map_variables variable_2="k3b_" variable_1="k3b_"/>
<map_variables variable_2="H" variable_1="H"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="H2_E1_ATP"/>
<map_variables variable_2="k3b" variable_1="k3b"/>
<map_variables variable_2="k3b_" variable_1="k3b_"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k4_" variable_1="k4_"/>
<map_variables variable_2="H" variable_1="H"/>
<map_variables variable_2="ADP" variable_1="ADP"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="H_E2_P"/>
<map_variables variable_2="k6b" variable_1="k6b"/>
<map_variables variable_2="k6b_" variable_1="k6b_"/>
<map_variables variable_2="k6a" variable_1="k6a"/>
<map_variables variable_2="k6a_" variable_1="k6a_"/>
<map_variables variable_2="H" variable_1="H"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="H2_E2_P"/>
<map_variables variable_2="k5" variable_1="k5"/>
<map_variables variable_2="k5_" variable_1="k5_"/>
<map_variables variable_2="k6a" variable_1="k6a"/>
<map_variables variable_2="k6a_" variable_1="k6a_"/>
<map_variables variable_2="H" variable_1="H"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="H2_E1_P"/>
<map_variables variable_2="k5" variable_1="k5"/>
<map_variables variable_2="k5_" variable_1="k5_"/>
<map_variables variable_2="k4" variable_1="k4"/>
<map_variables variable_2="k4_" variable_1="k4_"/>
<map_variables variable_2="ADP" variable_1="ADP"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="E2_P"/>
<map_variables variable_2="k7a" variable_1="k7a"/>
<map_variables variable_2="k7a_" variable_1="k7a_"/>
<map_variables variable_2="k6b" variable_1="k6b"/>
<map_variables variable_2="k6b_" variable_1="k6b_"/>
<map_variables variable_2="K" variable_1="K"/>
<map_variables variable_2="H" variable_1="H"/>
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<connection>
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<map_variables variable_2="k7b_" variable_1="k7b_"/>
<map_variables variable_2="K" variable_1="K"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="K2_E2_P"/>
<map_variables variable_2="k7b" variable_1="k7b"/>
<map_variables variable_2="k7b_" variable_1="k7b_"/>
<map_variables variable_2="k8" variable_1="k8"/>
<map_variables variable_2="k8_" variable_1="k8_"/>
<map_variables variable_2="P" variable_1="P"/>
<map_variables variable_2="K" variable_1="K"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="K2_E2"/>
<map_variables variable_2="k8" variable_1="k8"/>
<map_variables variable_2="k8_" variable_1="k8_"/>
<map_variables variable_2="k9" variable_1="k9"/>
<map_variables variable_2="k9_" variable_1="k9_"/>
<map_variables variable_2="k10" variable_1="k10"/>
<map_variables variable_2="k10_" variable_1="k10_"/>
<map_variables variable_2="P" variable_1="P"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
</connection>
<connection>
<map_components component_2="reaction_constants" component_1="K2_E2_ATP"/>
<map_variables variable_2="k10" variable_1="k10"/>
<map_variables variable_2="k10_" variable_1="k10_"/>
<map_variables variable_2="k11" variable_1="k11"/>
<map_variables variable_2="k11_" variable_1="k11_"/>
<map_variables variable_2="ATP" variable_1="ATP"/>
</connection>
<rdf:RDF>
<rdf:Bag rdf:about="rdf:#9936f30b-e0e9-4d99-94fa-5bb550cd222e">
<rdf:li>acid/base transport</rdf:li>
<rdf:li>renal</rdf:li>
<rdf:li>electrophysiology</rdf:li>
<rdf:li>collecting duct</rdf:li>
<rdf:li>rat</rdf:li>
<rdf:li>kidney</rdf:li>
</rdf:Bag>
<rdf:Seq rdf:about="rdf:#d9f541c8-a0de-4e25-89d9-de145f08381e">
<rdf:li rdf:resource="rdf:#b66ec299-f2d2-412a-b1f3-e23bc958de00"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#2147935c-c415-4142-89bf-649c06b8e5f4">
<vCard:N rdf:resource="rdf:#afd461a5-9ba1-4992-852a-840cb57ecb39"/>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:publisher>The University of Auckland, Bioengineering Institute</dc:publisher>
<cmeta:comment rdf:resource="rdf:#c5701989-734c-44fb-9a9a-a9329c43cd09"/>
<dcterms:created rdf:resource="rdf:#1500fab7-6fd2-46fb-943d-ba6d6d60abbb"/>
<dc:creator rdf:resource="rdf:#3e7283b5-f1bc-4a08-bdff-e3debd03664d"/>
<cmeta:modification rdf:resource="rdf:#1020e132-994d-4578-b383-b24972a75e48"/>
<cmeta:modification rdf:resource="rdf:#686412fb-dbb7-43fb-a215-85af16e52550"/>
<cmeta:modification rdf:resource="rdf:#7322e08b-7903-45a2-aefe-0697d4d8d3ea"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#3ffd19e0-9bfa-4694-a8e4-190e410a02a1">
<dc:creator rdf:resource="rdf:#d9f541c8-a0de-4e25-89d9-de145f08381e"/>
<dc:title>A mathematical model of the inner medullary collecting duct of the
rat: acid/base transport</dc:title>
<bqs:volume>274</bqs:volume>
<bqs:first_page>F856</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#c1d48d2b-7297-4bed-a707-cd74355881f4"/>
<dcterms:issued rdf:resource="rdf:#802f90fc-9d11-4d28-83dc-4801497a04ae"/>
<bqs:last_page>F867</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c1d48d2b-7297-4bed-a707-cd74355881f4">
<dc:title>Journal of Physiology</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1500fab7-6fd2-46fb-943d-ba6d6d60abbb">
<dcterms:W3CDTF>2007-05-25T00:00:00+00:00</dcterms:W3CDTF>
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<dcterms:W3CDTF>2007-06-05T09:30:31+12:00</dcterms:W3CDTF>
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<vCard:Given>James</vCard:Given>
<vCard:Family>Lawson</vCard:Family>
<vCard:Other>Richard</vCard:Other>
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<rdf:Description rdf:about="#renal_H_K_ATPase_model">
<dc:title>
The 1998 Weinstein mathematical model of the renal H-K-ATPase.
</dc:title>
<cmeta:bio_entity>Renal Medullary Cell</cmeta:bio_entity>
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<bqs:reference rdf:resource="rdf:#c4c40ace-ab16-432d-9526-f1b1cab77aa0"/>
<cmeta:species>Rat</cmeta:species>
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<rdf:Description rdf:about="rdf:#3facc7aa-1a7c-4fb9-938f-4362f8e49103">
<dcterms:W3CDTF>2008-05-09T14:28:04+12:00</dcterms:W3CDTF>
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<rdf:Description rdf:about="rdf:#a865ad48-59c3-49f5-800c-7e11b4508f95">
<bqs:Pubmed_id>9612322</bqs:Pubmed_id>
<bqs:JournalArticle rdf:resource="rdf:#3ffd19e0-9bfa-4694-a8e4-190e410a02a1"/>
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<rdf:Description rdf:about="rdf:#921d66c7-7386-41cf-acb2-23a5ff979903">
<vCard:FN>Catherine Lloyd</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#c5701989-734c-44fb-9a9a-a9329c43cd09">
<dc:creator rdf:resource="rdf:#311e4d45-57db-4383-9c4f-72750a39cbdd"/>
<rdf:value>This CellML model represents only a small part of the model described in Weinstein et al.'s paper - namely, the H+ K+ ATPase pump</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1020e132-994d-4578-b383-b24972a75e48">
<dcterms:modified rdf:resource="rdf:#f9932100-ae1e-4368-b98b-b4e62eec97da"/>
<rdf:value>Fixed documentation to show proper diagram.</rdf:value>
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<rdf:Description rdf:about="rdf:#7322e08b-7903-45a2-aefe-0697d4d8d3ea">
<dcterms:modified rdf:resource="rdf:#89a52636-941a-4ef6-80b9-d7f859cd105f"/>
<rdf:value>The new version of this model has been re-coded to remove the reaction element and replace it with a simple MathML description of the model reaction kinetics. This is thought to be truer to the original publication, and information regarding the enzyme kinetics etc will later be added to the metadata through use of an ontology.
For some reason I can't open this file in PCEnv - I'm not sure why. It may be something to do with the name of the file? This particular Weinstein publication has two models in it - a gastric and a renal one.</rdf:value>
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<dc:creator rdf:resource="rdf:#921d66c7-7386-41cf-acb2-23a5ff979903"/>
<rdf:value>This is the CellML description of Weinstein's 1998 mathematical model of the renal H-K-ATPase in rats.</rdf:value>
</rdf:Description>
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<vCard:Given>Alan</vCard:Given>
<vCard:Family>Weinstein</vCard:Family>
<vCard:Other>M</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#fe8d3f00-454d-47cb-94aa-e3f30fb5c8e8">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Institute</vCard:Orgunit>
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<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
<rdf:value>c.lloyd@auckland.ac.nz</rdf:value>
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<rdf:Description rdf:about="rdf:#802f90fc-9d11-4d28-83dc-4801497a04ae">
<dcterms:W3CDTF>1998-05</dcterms:W3CDTF>
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<vCard:N rdf:resource="rdf:#8be48139-6a99-4bca-9666-333ea3474262"/>
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<rdf:Description rdf:about="rdf:#f9932100-ae1e-4368-b98b-b4e62eec97da">
<dcterms:W3CDTF>2008-05-13T15:43:04+12:00</dcterms:W3CDTF>
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<rdf:Description rdf:about="rdf:#5d7bd9ab-b5b7-4882-aa64-6380dd9be145">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#55f3e14f-2c34-4820-a65a-dabcf14028a8">
<vCard:Given>Catherine</vCard:Given>
<vCard:Family>Lloyd</vCard:Family>
<vCard:Other>May</vCard:Other>
</rdf:Description>
<rdf:Description rdf:about="rdf:#8be48139-6a99-4bca-9666-333ea3474262">
<vCard:Given>James</vCard:Given>
<vCard:Family>Lawson</vCard:Family>
<vCard:Other>Richard</vCard:Other>
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<dcterms:modified rdf:resource="rdf:#3facc7aa-1a7c-4fb9-938f-4362f8e49103"/>
<rdf:value>Fixed a minor connection error - units defined for connected variables made consistent.</rdf:value>
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<bqs:subject_type>keyword</bqs:subject_type>
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<rdf:Description rdf:about="rdf:#311e4d45-57db-4383-9c4f-72750a39cbdd">
<vCard:FN>James Lawson</vCard:FN>
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</model>
