Location: Leloup, Goldbeter, 2004 @ d4b0eb6fd446 / mRNAs.cellml

Author:
Mona Zhu <devnull@localhost>
Date:
2011-01-19 09:13:28+13:00
Desc:
Fixed small error
Permanent Source URI:
http://models.cellml.org/workspace/leloup_goldbeter_2004/rawfile/d4b0eb6fd4468971504a57ac37cb8819b07b40a9/mRNAs.cellml

<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="mRNAs" name="mRNAs">
	<!-- documentation -->
	<documentation xmlns="http://cellml.org/tmp-documentation">
		<article>
		  <articleinfo>
			  <title>Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</title>
				  <author>
						<firstname>Mona</firstname>
							<surname>Zhu</surname>
						<affiliation>
							<shortaffil>Auckland Bioengineering Institute, The University of Auckland</shortaffil>
						</affiliation>
				  </author>
		</articleinfo>
			<section id="sec_status">
				<title>Model Status</title>
					<para>This is an import for the model "leloup_2004_1.1model.cellml". It is used to define a reoccuring structure within the model and may be used for multiple equations in the model. This file is known to run only in OpenCell in conjunction with the base file.
					</para>
			</section>
			<sect1 id="sec_structure">
				<title>Model Structure</title>
				<para>Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms, Jean-Christophe Leloup and Albert Goldbeter, 2004, 
				<emphasis>Journal of Theoretical Biology</emphasis>, 230, 541-562. <ulink url="http://www.ncbi.nlm.nih.gov/pubmed/15363675">PubMed ID: 15363675</ulink>
				</para>
			</sect1>
		</article>
	</documentation>
	
	<!-- units -->
	<units name="hour">
		<unit multiplier="3600.0" units="second"/>
	</units>
	<units name="nanomolar">
		<unit prefix="nano" units="mole"/>
		<unit exponent="-1" units="litre"/>
	</units>
	<units name="flux">
		<unit units="nanomolar"/>
		<unit exponent="-1" units="hour"/>
	</units>
	<units name="first_order_rate_constant">
		<unit exponent="-1" units="hour"/>
	</units>
	<units name="second_order_rate_constant">
		<unit exponent="-1" units="nanomolar"/>
		<unit exponent="-1" units="hour"/>
	</units>

	<!-- components -->
	<component xmlns:cmeta="http://www.cellml.org/metadata/1.1#" cmeta:id="MP" name="interface">
		<variable cmeta:id="MP_MP" initial_value="M_init" name="M" public_interface="out" units="nanomolar"/>
		<variable name="vs" public_interface="in" units="flux"/>
		<variable name="vm" public_interface="in" units="flux"/>
		<variable name="kdm" public_interface="in" units="first_order_rate_constant"/>
		<variable name="B" public_interface="in" units="nanomolar"/>
		<variable name="Km" public_interface="in" units="nanomolar"/>
		<variable name="c" public_interface="in" units="dimensionless"/>
		<variable name="A" public_interface="in" units="nanomolar"/>
		<variable name="time" public_interface="in" units="hour"/>
		<variable name="M_init" public_interface="in" units="nanomolar"/>
		<math xmlns="http://www.w3.org/1998/Math/MathML">
			<apply>
				<eq/>
				<apply>
					<diff/>
					<bvar>
					<ci>time</ci>
					</bvar>
					<ci>M</ci>
				</apply>
				<apply>
					<minus/>
					<apply>
						<times/>
						<ci>vs</ci>
						<apply>
							<divide/>
							<apply>
								<power/>
								<ci>A</ci>
								<ci>c</ci>
							</apply>
							<apply>
								<plus/>
								<apply>
									<power/>
									<ci>B</ci>
									<ci>c</ci>
								</apply>
								<apply>
									<power/>
									<ci>A</ci>
									<ci>c</ci>
								</apply>
							</apply>
						</apply>
					</apply>
					<apply>
						<plus/>
						<apply>
							<times/>
							<ci>vm</ci>
							<apply>
								<divide/>
								<ci>M</ci>
								<apply>
									<plus/>
									<ci>Km</ci>
									<ci>M</ci>
								</apply>
							</apply>
						</apply>
						<apply>
							<times/>
							<ci>kdm</ci>
							<ci>M</ci>
						</apply>
					</apply>
				</apply>
			</apply>
		</math>
	</component>
   
   	<!-- metadata -->
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		<rdf:Description rdf:about="">
			<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
				<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
					<vCard:Family>Zhu</vCard:Family>
					<vCard:Given>Xin Yue</vCard:Given>
					<vCard:Other>Mona</vCard:Other>
				</vCard:N>
				<vCard:EMAIL xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
					<rdf:value>xzhu055@aucklanduni.ac.nz</rdf:value>
					<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
				</vCard:EMAIL>
				<vCard:ORG xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
					<vCard:Orgname>The University of Auckland</vCard:Orgname>
					<vCard:Orgunit>Auckland Bioengineering Institute</vCard:Orgunit>
				</vCard:ORG>
			</dc:creator>
			<dcterms:created xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
				<dcterms:W3CDTF>29-12-2010</dcterms:W3CDTF>
			</dcterms:created>
		</rdf:Description>
		<rdf:Description rdf:about="#leloup_2004_1.1model">
			<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</dc:title>
			<cmeta:comment rdf:parseType="Resource">
				<rdf:value>This is a CellML description of Leloup and Goldbeter's 2004 mathematical model of the mammalian circadian clock.
				</rdf:value>
				<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/" rdf:parseType="Resource">
					<vCard:FN xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#">Mona Zhu</vCard:FN>
				</dc:creator>
			</cmeta:comment>
			<bqs:reference xmlns:bqs="http://www.cellml.org/bqs/1.1#" rdf:parseType="Resource">
				<bqs:Pubmed_id>15363675</bqs:Pubmed_id>
				<bqs:JournalArticle rdf:parseType="Resource">
					<dc:creator xmlns:dc="http://purl.org/dc/elements/1.1/">
						<rdf:Seq>
							<rdf:li rdf:parseType="Resource">
								<bqs:Person rdf:parseType="Resource">
									<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
										<vCard:Family>Leloup</vCard:Family>
										<vCard:Given>Jean-Christophe</vCard:Given>
									</vCard:N>
								</bqs:Person>
							</rdf:li>
							<rdf:li rdf:parseType="Resource">
								<bqs:Person rdf:parseType="Resource">
									<vCard:N xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" rdf:parseType="Resource">
										<vCard:Family>Goldbeter</vCard:Family>
										<vCard:Given>Albert</vCard:Given>
									</vCard:N>
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							</rdf:li>
						</rdf:Seq>
					</dc:creator>
					<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms</dc:title>
					<dcterms:issued xmlns:dcterms="http://purl.org/dc/terms/" rdf:parseType="Resource">
						<dcterms:W3CDTF>1999-05</dcterms:W3CDTF>
					</dcterms:issued>
					<bqs:Journal rdf:parseType="Resource">
						<dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Journal of Theoretical Biology</dc:title>
					</bqs:Journal>
					<bqs:volume>230</bqs:volume>
					<bqs:first_page>541</bqs:first_page>
					<bqs:last_page>562</bqs:last_page>
				</bqs:JournalArticle>
			</bqs:reference>
		</rdf:Description>
	</rdf:RDF>
</model>