- Author:
- pmr2.import <nobody@models.cellml.org>
- Date:
- 2008-01-17 21:14:55+13:00
- Desc:
- committing version01 of tomida_hirose_takizawa_shibasaki_iino_2003
- Permanent Source URI:
- https://models.cellml.org/workspace/tomida_hirose_takizawa_shibasaki_iino_2003/rawfile/25d03fe2e4c076a5b84afec5b17431c342ab8631/tomida_hirose_takizawa_shibasaki_iino_2003.cellml
<?xml version='1.0' encoding='utf-8'?>
<!-- FILE : Tomida2003_v1.xml
CREATED : February 2006
LAST MODIFIED :
AUTHOR : Mike Cooling
Department of Engineering Science
The University of Auckland
MODEL STATUS : This model conforms to the CellML 1.0 Specification released on
10th August 2001, and the CellML Metadata 1.0 Specification released on 16th
January, 2002.
DESCRIPTION : Model of NFAT cycling as per Figure 3A of Tomida et al. 2003 EMBO Journal Vol 22(15) p3825-3832.
CHANGES:
19/10/2006 -
--><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:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" name="Tomida2003" cmeta:id="Tomida2003">
<!--
*******************************************************************************************
*** U N I T S ***
*******************************************************************************************
-->
<units base_unit="yes" name="molecule"/>
<units base_unit="yes" name="minute"/>
<units name="per_minute">
<unit units="minute" exponent="-1"/>
</units>
<units name="molecules_per_minute">
<unit units="minute" exponent="-1"/>
<unit units="molecule"/>
</units>
<!--
*******************************************************************************************
*** C O M P O N E N T S ***
*******************************************************************************************
-->
<component name="model">
<variable units="minute" name="time"/>
<variable units="molecule" name="NFATP_cyt" initial_value="5000"/>
<variable units="molecule" name="NFAT_cyt" initial_value="0"/>
<variable units="molecule" name="NFAT_nuc" initial_value="0"/>
<variable units="molecule" name="NFAT_tot"/>
<variable units="per_minute" name="k1_unstim" initial_value="0"/>
<variable units="per_minute" name="k1_stim" initial_value="0.359"/>
<variable units="per_minute" name="k1"/>
<variable units="per_minute" name="k2" initial_value="0.147"/>
<variable units="per_minute" name="k3" initial_value="0.06"/>
<variable units="per_minute" name="k4" initial_value="0.035"/>
<variable units="minute" name="stim_wavelength" initial_value="3"/>
<variable units="minute" name="stim_duration" initial_value="0.5"/>
<variable units="dimensionless" name="stim_on"/>
<!-- in case want to reach steady state with other models -->
<variable units="minute" name="time_before_stim" initial_value="1"/>
<variable units="molecules_per_minute" name="Jdephosphorylation"/>
<variable units="molecules_per_minute" name="Jtranslocate"/>
<variable units="molecules_per_minute" name="Jexport"/>
<variable units="dimensionless" name="percentage_NFAT_cyt"/>
<variable units="dimensionless" name="percentage_NFATP_cyt"/>
<variable units="dimensionless" name="percentage_NFAT_nuc"/>
<!-- anticipating model extension -->
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="stim_on_eq">
<apply id="stim_on_eq">
<eq/> />
<ci>stim_on</ci>
<piecewise>
<piece>
<cn cellml:units="dimensionless">1</cn>
<apply>
<and/>
<apply>
<geq/>
<ci>time</ci>
<ci>time_before_stim</ci>
</apply>
<apply>
<leq/>
<apply>
<rem/>
<apply>
<minus/>
<ci> time </ci>
<ci> time_before_stim </ci>
</apply>
<ci> stim_wavelength </ci>
</apply>
<ci> stim_duration </ci>
</apply>
</apply>
</piece>
<otherwise>
<cn cellml:units="dimensionless">0</cn>
</otherwise>
</piecewise>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="k1_eq">
<apply id="k1_eq">
<eq/> />
<ci>k1</ci>
<piecewise>
<piece>
<ci>k1_stim</ci>
<apply>
<eq/>
<ci>stim_on</ci>
<cn cellml:units="dimensionless">1</cn>
</apply>
</piece>
<otherwise>
<ci>k1_unstim</ci>
</otherwise>
</piecewise>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Jdephosphorylation_eq">
<apply id="Jdephosphorylation_eq">
<eq/> />
<ci>Jdephosphorylation</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>k1</ci>
<ci>NFATP_cyt</ci>
</apply>
<apply>
<times/>
<ci>k2</ci>
<ci>NFAT_cyt</ci>
</apply>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Jtranslocate_eq">
<apply id="Jtranslocate_eq">
<eq/> />
<ci>Jtranslocate</ci>
<apply>
<times/>
<ci>k3</ci>
<ci>NFAT_cyt</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="Jexport_eq">
<apply id="Jexport_eq">
<eq/> />
<ci>Jexport</ci>
<apply>
<times/>
<ci>k4</ci>
<ci>NFAT_nuc</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="NFATP_cyt_eq">
<apply id="NFATP_cyt_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> NFATP_cyt </ci>
</apply>
<apply>
<minus/>
<ci> Jexport </ci>
<ci> Jdephosphorylation </ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="NFAT_cyt_eq">
<apply id="NFAT_cyt_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> NFAT_cyt </ci>
</apply>
<apply>
<minus/>
<ci> Jdephosphorylation </ci>
<ci> Jtranslocate </ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="NFAT_nuc_eq">
<apply id="NFAT_nuc_eq">
<eq/>
<apply>
<diff/>
<bvar>
<ci> time </ci>
</bvar>
<ci> NFAT_nuc </ci>
</apply>
<apply>
<minus/>
<ci> Jtranslocate </ci>
<ci> Jexport </ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="NFAT_toteq">
<apply id="NFAT_totcyteq">
<eq/>
<ci>NFAT_tot</ci>
<apply>
<plus/>
<ci>NFATP_cyt</ci>
<ci>NFAT_cyt</ci>
<ci>NFAT_nuc</ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="percentage_NFAT_cyteq">
<apply id="percentage_NFAT_cyteq">
<eq/> />
<ci>percentage_NFAT_cyt</ci>
<apply>
<divide/>
<apply>
<times/>
<ci> NFAT_cyt </ci>
<cn cellml:units="dimensionless"> 100 </cn>
</apply>
<ci> NFAT_tot </ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="percentage_NFATP_cyteq">
<apply id="percentage_NFATP_cyteq">
<eq/> />
<ci>percentage_NFATP_cyt</ci>
<apply>
<divide/>
<apply>
<times/>
<ci> NFATP_cyt </ci>
<cn cellml:units="dimensionless"> 100 </cn>
</apply>
<ci> NFAT_tot </ci>
</apply>
</apply>
</math>
<math xmlns="http://www.w3.org/1998/Math/MathML" cmeta:id="percentage_NFAT_nuceq">
<apply id="percentage_NFAT_nuceq">
<eq/> />
<ci>percentage_NFAT_nuc</ci>
<apply>
<divide/>
<apply>
<times/>
<ci> NFAT_nuc </ci>
<cn cellml:units="dimensionless"> 100 </cn>
</apply>
<ci> NFAT_tot </ci>
</apply>
</apply>
</math>
</component>
<rdf:RDF>
<rdf:Seq rdf:about="rdf:#ca92531e-152d-40ed-b3ad-bbd9958d5114">
<rdf:li rdf:resource="rdf:#8d96fcb0-cea4-43e4-a084-da31ec74f35d"/>
<rdf:li rdf:resource="rdf:#bb866231-375e-4873-b09a-ff1ed36030ee"/>
<rdf:li rdf:resource="rdf:#1c92b738-2a9b-4631-bc68-dd63307a56d1"/>
<rdf:li rdf:resource="rdf:#0567acb1-86f9-4b81-b8c4-093fee73bc1f"/>
<rdf:li rdf:resource="rdf:#7ab1c2ee-9080-4f84-92f2-f7a5ba9c4412"/>
</rdf:Seq>
<rdf:Seq rdf:about="rdf:#07e79013-6376-42f0-b131-9795368e2a90">
<rdf:li rdf:resource="rdf:#ec5adb9f-9f7f-4544-aace-b78da7a03803"/>
<rdf:li rdf:resource="rdf:#677c949b-bc18-422b-9ebc-1d39376a14d2"/>
<rdf:li rdf:resource="rdf:#3367689e-e9a4-415c-a2d6-1c0af6d757fd"/>
<rdf:li rdf:resource="rdf:#4a94ebd3-60db-472c-a558-beaba6f892b9"/>
<rdf:li rdf:resource="rdf:#6f1f6aa9-27f2-4c5f-a03a-c74a5d49d454"/>
</rdf:Seq>
<rdf:Description rdf:about="rdf:#443009c4-7d64-4c21-a471-eed7d2db0e4a">
<vCard:Given>M</vCard:Given>
<vCard:Family>Iino</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1ea4ec4e-6318-4536-b885-3fc03152d373">
<vCard:Given>T</vCard:Given>
<vCard:Family>Tomida</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#bb866231-375e-4873-b09a-ff1ed36030ee">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#57c6dd3b-2a0b-4ce7-850e-da46a0081f45"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#0567acb1-86f9-4b81-b8c4-093fee73bc1f">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#f869f3a2-cab9-4e18-bc7a-0a858741d005"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#6f1f6aa9-27f2-4c5f-a03a-c74a5d49d454">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#443009c4-7d64-4c21-a471-eed7d2db0e4a"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1c92b738-2a9b-4631-bc68-dd63307a56d1">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#5816f170-f3da-4b80-8699-034d199523db"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#677c949b-bc18-422b-9ebc-1d39376a14d2">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#46cc5003-ac8e-484e-b1b1-93d8e377f7c7"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#8d96fcb0-cea4-43e4-a084-da31ec74f35d">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#1eabbd4d-d073-49f5-978d-aeeb55c3cb37"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#4a94ebd3-60db-472c-a558-beaba6f892b9">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#ccd188c2-fb2a-47a9-816b-753d5dcacdb0"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#72b9152c-d257-4961-9963-ba6b1d0e125a">
<vCard:Given>A</vCard:Given>
<vCard:Family>Takizawa</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#72fd00d7-ffd1-4504-8028-a61869182560">
<vCard:Orgname>The University of Auckland</vCard:Orgname>
<vCard:Orgunit>The Bioengineering Research Group</vCard:Orgunit>
</rdf:Description>
<rdf:Description rdf:about="rdf:#2ea73608-0617-44b6-a9d7-24a0df481b84">
<vCard:Given>Michael</vCard:Given>
<vCard:Family>Cooling</vCard:Family>
<vCard:Other/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#5816f170-f3da-4b80-8699-034d199523db">
<vCard:Given>A</vCard:Given>
<vCard:Family>Takizawa</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#3367689e-e9a4-415c-a2d6-1c0af6d757fd">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#72b9152c-d257-4961-9963-ba6b1d0e125a"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#8277a7dc-593b-4398-b824-6866d87a31b9">
<rdf:type rdf:resource="http://imc.org/vCard/3.0#internet"/>
<rdf:value>m.cooling@auckland.ac.nz</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#46cc5003-ac8e-484e-b1b1-93d8e377f7c7">
<vCard:Given>K</vCard:Given>
<vCard:Family>Hirose</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="">
<dc:publisher>The University of Auckland, Bioengineering Research Group</dc:publisher>
<dc:creator rdf:resource="rdf:#eca59e0b-4898-4c95-886b-abaf87e71d80"/>
<bqs:JournalArticle rdf:resource="rdf:#abb03b85-bf44-44d2-bc8d-f5a1c704e81f"/>
<bqs:reference rdf:resource="rdf:#b9f1db2c-6aa7-4913-9960-2a0fbe86933d"/>
<cmeta:comment rdf:resource="rdf:#6837803d-d4c9-4820-8159-d60f1cb69b44"/>
<dcterms:created rdf:resource="rdf:#d20d085c-9af9-4b6c-a01f-d6264a50985f"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#39442e55-8c27-4273-9e3a-dbab81f89a5b">
<dc:title>European Molecular Biology Organisation Journal</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#ccd188c2-fb2a-47a9-816b-753d5dcacdb0">
<vCard:Given>F</vCard:Given>
<vCard:Family>Shibasaki</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#d20d085c-9af9-4b6c-a01f-d6264a50985f">
<dcterms:W3CDTF>2005-04-24T00:00:00+00:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#e1a04ea6-b7f0-473e-a840-94a90a1d6ed4">
<dc:creator rdf:resource="rdf:#07e79013-6376-42f0-b131-9795368e2a90"/>
<dc:title>NFAT function as a working memory of Ca2+ signals in decoding Ca2+ oscillation</dc:title>
<bqs:volume>22</bqs:volume>
<bqs:first_page>3825</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#39442e55-8c27-4273-9e3a-dbab81f89a5b"/>
<dcterms:issued rdf:resource="rdf:#02dfa474-3fcf-4d36-a31e-d4382e3c17b8"/>
<bqs:last_page>3832</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="rdf:#ec5adb9f-9f7f-4544-aace-b78da7a03803">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#1ea4ec4e-6318-4536-b885-3fc03152d373"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#eca59e0b-4898-4c95-886b-abaf87e71d80">
<vCard:ORG rdf:resource="rdf:#72fd00d7-ffd1-4504-8028-a61869182560"/>
<vCard:EMAIL rdf:resource="rdf:#8277a7dc-593b-4398-b824-6866d87a31b9"/>
<vCard:N rdf:resource="rdf:#2ea73608-0617-44b6-a9d7-24a0df481b84"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#1eabbd4d-d073-49f5-978d-aeeb55c3cb37">
<vCard:Given>T</vCard:Given>
<vCard:Family>Tomida</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9a31ece6-7bbf-411c-9da7-f18fe3f201b8">
<dc:title>European Molecular Biology Organisation Journal</dc:title>
</rdf:Description>
<rdf:Description rdf:about="rdf:#abb03b85-bf44-44d2-bc8d-f5a1c704e81f">
<dc:creator rdf:resource="rdf:#ca92531e-152d-40ed-b3ad-bbd9958d5114"/>
<dc:title>
NFAT function as a working memory of Ca2+ signals in
decoding Ca2+ oscillation.
</dc:title>
<bqs:volume>22</bqs:volume>
<bqs:first_page>3825</bqs:first_page>
<bqs:Journal rdf:resource="rdf:#9a31ece6-7bbf-411c-9da7-f18fe3f201b8"/>
<dcterms:issued rdf:resource="rdf:#63f7ccb1-91e4-4a46-8503-dba655a8ed0b"/>
<bqs:last_page>3832</bqs:last_page>
</rdf:Description>
<rdf:Description rdf:about="rdf:#63f7ccb1-91e4-4a46-8503-dba655a8ed0b">
<dcterms:W3CDTF>2003</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#9d92607d-6681-45e9-94d2-bcdc5e80c8bc">
<vCard:Given>M</vCard:Given>
<vCard:Family>Iino</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#7ab1c2ee-9080-4f84-92f2-f7a5ba9c4412">
<rdf:type rdf:resource="http://www.cellml.org/bqs/1.0#Person"/>
<vCard:N rdf:resource="rdf:#9d92607d-6681-45e9-94d2-bcdc5e80c8bc"/>
</rdf:Description>
<rdf:Description rdf:about="rdf:#02dfa474-3fcf-4d36-a31e-d4382e3c17b8">
<dcterms:W3CDTF>2003-00-00 00:00</dcterms:W3CDTF>
</rdf:Description>
<rdf:Description rdf:about="rdf:#6837803d-d4c9-4820-8159-d60f1cb69b44">
<dc:creator rdf:resource="rdf:#cbc0d292-6357-44f9-8989-c80e9d588080"/>
<rdf:value>Tomida, T. and Hirose, K. and Takizawa, A. and Shibasaki, F. and Iino, M. NFAT function as a working memory of Ca2+ signals in decoding Ca2+ oscillation. European Molecular Biology Organisation Journal 22,15, 3825-3832 (2003).</rdf:value>
</rdf:Description>
<rdf:Description rdf:about="rdf:#57c6dd3b-2a0b-4ce7-850e-da46a0081f45">
<vCard:Given>K</vCard:Given>
<vCard:Family>Hirose</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#cbc0d292-6357-44f9-8989-c80e9d588080">
<vCard:FN>Michael Cooling</vCard:FN>
</rdf:Description>
<rdf:Description rdf:about="rdf:#f869f3a2-cab9-4e18-bc7a-0a858741d005">
<vCard:Given>F</vCard:Given>
<vCard:Family>Shibasaki</vCard:Family>
</rdf:Description>
<rdf:Description rdf:about="rdf:#b9f1db2c-6aa7-4913-9960-2a0fbe86933d">
<bqs:Pubmed_id/>
<bqs:JournalArticle rdf:resource="rdf:#e1a04ea6-b7f0-473e-a840-94a90a1d6ed4"/>
</rdf:Description>
</rdf:RDF>
</model>
