- Author:
- Hanne <Hanne@hanne-nielsens-macbook.local>
- Date:
- 2010-07-22 12:32:06+12:00
- Desc:
- Added xul and session file
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/karagiannis_popel_2006/rawfile/523e285aaffb10785700f40009832a0c787ccc6d/karagiannis_popel_2006.cellml
<?xml version="1.0"?>
<!--
This CellML file was generated on 20/06/2007 at 12:39:18 at a.m. using:
COR (0.9.31.649)
Copyright 2002-2007 Dr Alan Garny
http://COR.physiol.ox.ac.uk/ - COR@physiol.ox.ac.uk
CellML 1.0 was used to generate this cellular model
http://www.CellML.org/
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" cmeta:id="bhalla_model_1999" name="karagiannis_model_2006_version01">
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<article>
<articleinfo>
<title>Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
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<title>Model Status</title>
<para>
This version of the model has been checked in COR and PCEnv and it runs - possibly replicating the published results. The units have been checked and they are consistent.
</para>
</section>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
The formation of new biological vessels requires the coordinated assembly of a proliferating syncytium of endothelial cells (EC) at different developmental stages. Angiogenesis may also be an essential mechanism of blood vessel remodelling which occurs during a diverse range of physiological processes; including tissue regeneration following injury and new vessel formation during muscle exercise. It can also occur under pathological conditions such as atherosclerosis and the vascularisation of cancerous tumours.
</para>
<para>
Matrix metalloproteinases (MMPs) are a family of enzymes responsible for the proteolytic processing of extracellular matrix (ECM) structural proteins. During angiogenesis MMPs are expressed by a single endothelial cell at the tip of the new vessel. These enzymes manifest a proteolytic activity that allows the cells of the new vessle to penetrate the ECM. In the mathematical model presented here, Karagiannis and Popel investigate the proteolytic potential of such a tip endothelial cell. The model authors suggest this model provides a foundation for future quantitative studies of angiogenesis in ECMs of different compositions. The model is described in more detail in the figure below:
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model, Emmanouil D. Karagiannis and Aleksander S. Popel, 2006, <emphasis>The Journal of Theoretical Biology</emphasis>, 238, 124-145. <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16005020&dopt=Abstract">PubMed ID: 16005020</ulink>
</para>
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<caption>A schematic diagram of the signalling pathway.</caption>
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</sect1>
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xml:lang="en">The model runs in PCEnv - but I'm not 100% sure whether or not it replicates the published results - these are displayed slightly differently.</rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#a586bdb1-b899-4bd3-b8dd-78b2ca4d888a"><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#da962da4-ac4a-4b92-ac1f-d06ddb7c626d"/></N><ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#ca9d9678-4e5b-4d68-bd15-07752a2ccb96"/></ORG><EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#fe1f1b96-2b82-45e7-88ea-b96c3421133e"/></EMAIL></rdf:Description><rdf:Description rdf:about="rdf:#aef7d271-e105-4eee-9957-52b39414ae08"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-10-04T11:51:16+13:00</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#3f9dc794-6e5b-49b6-84f0-89b05afaf9de"><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine</Given><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Lloyd</Family><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">May</Other></rdf:Description><rdf:Description rdf:about="rdf:#e5ffec31-c21d-4c11-b42c-f35d558d6515"><rdf:type><rdf:Description rdf:about="http://www.cellml.org/bqs/1.0#Person"/></rdf:type><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#8c30ab00-7bcf-4dda-8454-8ecd25b241b1"/></N></rdf:Description><rdf:Description rdf:about="rdf:#fe1f1b96-2b82-45e7-88ea-b96c3421133e"><rdf:type><rdf:Description rdf:about="http://imc.org/vCard/3.0#internet"/></rdf:type><rdf:value xml:lang="en">m.mccormick@auckland.ac.nz</rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#2399e3b7-2089-4469-b7a5-0415743eb85d"><rdf:value xml:lang="en">I ran the model in COR and corrected the units definitions such that the units are now consistent.</rdf:value><modified xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#aef7d271-e105-4eee-9957-52b39414ae08"/></modified><cmeta:modifier><rdf:Description rdf:about="rdf:#5f7da291-d686-4233-9373-9c12e2493c3f"/></cmeta:modifier></rdf:Description><rdf:Description rdf:about="#bhalla_model_1999"><cmeta:comment><rdf:Description rdf:about="rdf:#a68258d6-cd5a-4466-8c53-d6b98b59858b"/></cmeta:comment><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:nodeID="n1"/></reference><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#8611abeb-7251-4c7c-b77b-d53109cb7a7e"/></reference><simulation xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n2"/></simulation></rdf:Description><rdf:Description rdf:about="rdf:#dc3a4c12-5778-4714-ae7a-f166889677f6"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">The Journal of Theoretical Biology</title></rdf:Description><rdf:Description rdf:about="rdf:#9408a46f-72a6-4451-871d-2610c6385d6b"><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#d254b5df-8a75-498b-87f9-af51138e2f2c"/></creator><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Distinct modes of collagen type I proteolysis by matrix metalloproteinase (MMP) 2 and membrane type I MMP during the migration of a tip endothelial cell: insights from a computational model</title><volume xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">238</volume><first_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">124</first_page><Journal xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#dc3a4c12-5778-4714-ae7a-f166889677f6"/></Journal><last_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">145</last_page><issued xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#bbe7a8cd-622f-4fe3-8695-b62ed6f43d36"/></issued></rdf:Description><rdf:Description rdf:about="rdf:#a68258d6-cd5a-4466-8c53-d6b98b59858b"><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#84dc990f-40f3-4dc5-b1ef-663571e7a988"/></creator><rdf:value xml:lang="en"></rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#e0483129-551d-4f00-a107-0e111c7463f0"><rdf:type><rdf:Description rdf:about="http://www.cellml.org/bqs/1.0#Person"/></rdf:type><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#72276d58-1f9a-49f0-86b5-3e249603e27d"/></N></rdf:Description><rdf:Description rdf:nodeID="n3"><rdf:type><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/></rdf:type><rdf:_2 xml:lang="en">cerebral aneurysm</rdf:_2><rdf:_1 xml:lang="en">signal transduction</rdf:_1></rdf:Description><rdf:Description rdf:about="rdf:#8c30ab00-7bcf-4dda-8454-8ecd25b241b1"><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Aleksander</Given><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Popel</Family><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">S</Other></rdf:Description><rdf:Description rdf:about="rdf:#1f556ae5-8d3f-4dd1-baef-886653e71c94"><FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine Lloyd</FN></rdf:Description><rdf:Description rdf:about="rdf:#84dc990f-40f3-4dc5-b1ef-663571e7a988"><FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en"></FN></rdf:Description><rdf:Description rdf:nodeID="n4"><rdf:rest><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/></rdf:rest><rdf:first><rdf:Description rdf:nodeID="n5"/></rdf:first></rdf:Description><rdf:Description rdf:nodeID="n1"><subject xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:nodeID="n6"/></subject></rdf:Description><rdf:Description rdf:about="rdf:#ca9d9678-4e5b-4d68-bd15-07752a2ccb96"><Orgname xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">The University of Auckland</Orgname><Orgunit xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">The Bioengineering Institute</Orgunit></rdf:Description><rdf:Description rdf:nodeID="n2"><boundIntervals xmlns="http://www.cellml.org/metadata/simulation/1.0#"><rdf:Description rdf:nodeID="n4"/></boundIntervals></rdf:Description><rdf:Description rdf:about="rdf:#72276d58-1f9a-49f0-86b5-3e249603e27d"><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Emmanouil</Given><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Karagiannis</Family><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">D</Other></rdf:Description><rdf:Description rdf:nodeID="n5"><maximumStepSize xmlns="http://www.cellml.org/metadata/simulation/1.0#" xml:lang="en">0.1</maximumStepSize></rdf:Description><rdf:Description rdf:about="rdf:#d254b5df-8a75-498b-87f9-af51138e2f2c"><rdf:type><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Seq"/></rdf:type><rdf:_2><rdf:Description rdf:about="rdf:#e5ffec31-c21d-4c11-b42c-f35d558d6515"/></rdf:_2><rdf:_1><rdf:Description rdf:about="rdf:#e0483129-551d-4f00-a107-0e111c7463f0"/></rdf:_1></rdf:Description><rdf:Description rdf:about=""><publisher xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en"></publisher><created xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#b6e82467-8ac7-4dcf-a5e8-9d66ea48278c"/></created><cmeta:comment><rdf:Description rdf:about="rdf:#81ca4b4c-8a9e-490b-ba87-8f3f8978b9ae"/></cmeta:comment><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#a586bdb1-b899-4bd3-b8dd-78b2ca4d888a"/></creator><cmeta:modification><rdf:Description rdf:about="rdf:#2399e3b7-2089-4469-b7a5-0415743eb85d"/></cmeta:modification></rdf:Description><rdf:Description rdf:about="rdf:#8611abeb-7251-4c7c-b77b-d53109cb7a7e"><Pubmed_id xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">16005020</Pubmed_id><JournalArticle xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#9408a46f-72a6-4451-871d-2610c6385d6b"/></JournalArticle></rdf:Description><rdf:Description rdf:about="rdf:#b6e82467-8ac7-4dcf-a5e8-9d66ea48278c"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-08-27T00:00:00+00:00</W3CDTF></rdf:Description><rdf:Description rdf:nodeID="n6"><rdf:value><rdf:Description rdf:nodeID="n3"/></rdf:value><subject_type xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">keyword</subject_type></rdf:Description></rdf:RDF></model>
