- Author:
- Hanne <Hanne@hanne-nielsens-macbook.local>
- Date:
- 2010-01-18 13:26:49+13:00
- Desc:
- Added cmeta:ids to cellml file and added session file
- Permanent Source URI:
- https://models.cellml.org/workspace/wodarz_hamer_2007/rawfile/f2febc8866e0ffb7cfb0395f7ed7746727d8c90c/wodarz_hamer_2007_b.cellml
<?xml version="1.0"?>
<!-- FILE : wodarz_model_2007.xml
CREATED : 16th July 2007
LAST MODIFIED : 16th July 2007
AUTHOR : Catherine Lloyd
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 Wodarz and Hamer's 2007 mathematical model of infection dynamics in HIV-specific CD4+ T cells.
CHANGES:
--><model xmlns="http://www.cellml.org/cellml/1.0#" xmlns:cmeta="http://www.cellml.org/metadata/1.0#" xml:base="file:///Users/Hanne/Desktop/repository%20models/wodarz_hamer_2007/wodarz_hamer_2007_b.cellml" cmeta:id="wodarz_model_2007" name="wodarz_hamer_model_2007_version01">
<documentation xmlns="http://cellml.org/tmp-documentation">
<article>
<articleinfo>
<title>Infection dynamics in HIV-specific CD4 T cells: Does a CD4 T cell boost benefit the host or the virus?</title>
<author>
<firstname>Catherine</firstname>
<surname>Lloyd</surname>
<affiliation>
<shortaffil>Bioengineering Institute, University of Auckland</shortaffil>
</affiliation>
</author>
</articleinfo>
<sect1 id="sec_structure">
<title>Model Structure</title>
<para>
CD4+ T helper cells represent a major target for the replication of human immunodeficiency virus (HIV). Conversely, CD4+ T cells are also an essential component of the immune response to HIV. A considerable proportion of the HIV-specific CD4+ T cells become infected with the virus which, in turn, has important implications for understanding the dynamics between HIV and the immune response. Infection of HIV-specific CD4+ T cells can have several outcomes for the dynamics between the virus and the immune system, including:
</para>
<itemizedlist>
<listitem>
<para>enhanced viral spread through the division of infected CD4+ T cells; and also</para>
</listitem>
<listitem>
<para>impaired effector responses, such as CD8+ cytotoxic T lymphocytes (CTL), through the compromised ability of the CD4+ T cells to deliver help.</para>
</listitem>
</itemizedlist>
<para>
Mathematical models of the kinetics of HIV infection and replication have improved our understanding of the relationship between HIV and immune responses. In their mathematical model(s), described here in CellML, Wodarz and Hamer (2007) characterise the infection dynamics in HIV-specific CD4+ T cells. Their aim was to demonstrate the the potential consequences of autocatalytic virus spread and describe the different roles of CD4+ T cells during HIV infection.
</para>
<para>
The original publication contains four different mathematical models:
</para>
<itemizedlist>
<listitem>
<para>The first is a simple model of autocatalytic virus spread via the division of infected CD4+ T cells. This simple model forms the core of the subsequent, more complex models, and allows some basic analytical insights into the properties of autocatalytic virus spread.</para>
</listitem>
<listitem>
<para>The second model builds on this core model by including a description of the infectious spread of the virus amongst CD4+ T cells.</para>
</listitem>
<listitem>
<para>The third model adds further complexity by incorporating alternative target cells which are do not react against HIV, such as T cells with other specificities and antigen presenting cells.</para>
</listitem>
<listitem>
<para>Finally, the forth model describes CD8+ CTL dynamics during HIV infection, and considers the effects of both cell proliferation and death.</para>
</listitem>
</itemizedlist>
<para>
The CellML model presented here represents the second model. The other three models have also been coded in CellML and can be downloaded as version 1 and version 1 variants 2 and 3 of the model.
</para>
<para>
The complete original paper reference is cited below:
</para>
<para>
Infection dynamics in HIV-specific CD4 T cells: Does a CD4 T cell boost benefit the host or the virus?, Dominik Wodarz and Dean H. Hamer, 2007, <emphasis>Mathematical Biosciences</emphasis> <ulink url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17379260&query_hl=1&itool=pubmed_docsum">PubMed ID: 17379260</ulink>
</para>
</sect1>
</article>
</documentation>
<units name="first_order_rate_constant">
<unit exponent="-1" units="second"/>
</units>
<component name="environment">
<variable cmeta:id="environment_time" name="time" public_interface="out" units="second"/>
</component>
<component cmeta:id="x" name="x">
<variable cmeta:id="x_x" initial_value="0.1" name="x" public_interface="out" units="dimensionless"/>
<variable name="r" public_interface="in" units="first_order_rate_constant"/>
<variable name="v" public_interface="in" units="dimensionless"/>
<variable name="y" public_interface="in" units="dimensionless"/>
<variable name="k" public_interface="in" units="dimensionless"/>
<variable name="d" public_interface="in" units="first_order_rate_constant"/>
<variable name="beta" public_interface="in" units="first_order_rate_constant"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> x </ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> r </ci>
<ci> x </ci>
<ci> v </ci>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<apply>
<plus/>
<ci> x </ci>
<ci> y </ci>
</apply>
<ci> k </ci>
</apply>
</apply>
</apply>
<apply>
<plus/>
<apply>
<times/>
<ci> d </ci>
<ci> x </ci>
</apply>
<apply>
<times/>
<ci> beta </ci>
<ci> x </ci>
<ci> v </ci>
</apply>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="y" name="y">
<variable cmeta:id="y_y" initial_value="0.0" name="y" public_interface="out" units="dimensionless"/>
<variable name="r" public_interface="in" units="first_order_rate_constant"/>
<variable name="v" public_interface="in" units="dimensionless"/>
<variable name="x" public_interface="in" units="dimensionless"/>
<variable name="k" public_interface="in" units="dimensionless"/>
<variable name="a" public_interface="in" units="first_order_rate_constant"/>
<variable name="beta" public_interface="in" units="first_order_rate_constant"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> y </ci>
</apply>
<apply>
<minus/>
<apply>
<plus/>
<apply>
<times/>
<ci> beta </ci>
<ci> x </ci>
<ci> v </ci>
</apply>
<apply>
<times/>
<ci> r </ci>
<ci> y </ci>
<ci> v </ci>
<apply>
<minus/>
<cn xmlns:cellml="http://www.cellml.org/cellml/1.0#" cellml:units="dimensionless"> 1.0 </cn>
<apply>
<divide/>
<apply>
<plus/>
<ci> x </ci>
<ci> y </ci>
</apply>
<ci> k </ci>
</apply>
</apply>
</apply>
</apply>
<apply>
<times/>
<ci> a </ci>
<ci> y </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component cmeta:id="v" name="v">
<variable cmeta:id="v_v" initial_value="1.0" name="v" public_interface="out" units="dimensionless"/>
<variable name="u" public_interface="in" units="first_order_rate_constant"/>
<variable name="eta" public_interface="in" units="first_order_rate_constant"/>
<variable name="y" public_interface="in" units="dimensionless"/>
<variable name="time" public_interface="in" units="second"/>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<apply>
<diff/>
<bvar>
<ci>time</ci>
</bvar>
<ci> v </ci>
</apply>
<apply>
<minus/>
<apply>
<times/>
<ci> eta </ci>
<ci> y </ci>
</apply>
<apply>
<times/>
<ci> u </ci>
<ci> v </ci>
</apply>
</apply>
</apply>
</math>
</component>
<component name="model_parameters">
<variable initial_value="1.0" name="r" public_interface="out" units="first_order_rate_constant"/>
<variable initial_value="10.0" name="k" public_interface="out" units="dimensionless"/>
<variable initial_value="0.1" name="d" public_interface="out" units="first_order_rate_constant"/>
<variable initial_value="0.2" name="beta" public_interface="out" units="first_order_rate_constant"/>
<variable initial_value="0.2" name="a" public_interface="out" units="first_order_rate_constant"/>
<variable initial_value="1.0" name="eta" public_interface="out" units="first_order_rate_constant"/>
<variable initial_value="0.5" name="u" public_interface="out" units="first_order_rate_constant"/>
</component>
<connection>
<map_components component_1="x" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="v" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="y" component_2="environment"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="y" component_2="x"/>
<map_variables variable_1="x" variable_2="x"/>
<map_variables variable_1="y" variable_2="y"/>
</connection>
<connection>
<map_components component_1="x" component_2="v"/>
<map_variables variable_1="v" variable_2="v"/>
</connection>
<connection>
<map_components component_1="x" component_2="model_parameters"/>
<map_variables variable_1="r" variable_2="r"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="d" variable_2="d"/>
<map_variables variable_1="beta" variable_2="beta"/>
</connection>
<connection>
<map_components component_1="y" component_2="v"/>
<map_variables variable_1="v" variable_2="v"/>
<map_variables variable_1="y" variable_2="y"/>
</connection>
<connection>
<map_components component_1="y" component_2="model_parameters"/>
<map_variables variable_1="r" variable_2="r"/>
<map_variables variable_1="k" variable_2="k"/>
<map_variables variable_1="a" variable_2="a"/>
<map_variables variable_1="beta" variable_2="beta"/>
</connection>
<connection>
<map_components component_1="v" component_2="model_parameters"/>
<map_variables variable_1="eta" variable_2="eta"/>
<map_variables variable_1="u" variable_2="u"/>
</connection>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"><rdf:Description rdf:about="rdf:#39074383-8c28-403d-bb59-dac4c5fd9380"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Mathematical Biosciences</title></rdf:Description><rdf:Description rdf:about="rdf:#1a767be3-643c-486c-811f-4dcb1e8723c9"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-02</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#160a60fc-7260-4c13-a11c-7f055d412a6e"><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:#4b4520ce-8e7d-4729-83ab-fbc1da78dcdc"/></N></rdf:Description><rdf:Description rdf:about="rdf:#26118a9d-6018-4598-855d-10953ac95edd"><JournalArticle xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#29f4a722-a049-48b6-a29a-b607763b02b7"/></JournalArticle><Pubmed_id xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">17379260</Pubmed_id></rdf:Description><rdf:Description rdf:about="rdf:#29f4a722-a049-48b6-a29a-b607763b02b7"><Journal xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#39074383-8c28-403d-bb59-dac4c5fd9380"/></Journal><issued xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#1a767be3-643c-486c-811f-4dcb1e8723c9"/></issued><last_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en"></last_page><first_page xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en"></first_page><volume xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en"></volume><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#633015ce-17da-408e-9d22-4040b92dc853"/></creator><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">Infection dynamics in HIV-specific CD4 T cells: Does a CD4 T cell boost benefit the host or the virus?</title></rdf:Description><rdf:Description rdf:about="rdf:#665b4094-dc8e-4545-babd-39d7d81cf26b"><rdf:value xml:lang="en">c.lloyd@auckland.ac.nz</rdf:value><rdf:type><rdf:Description rdf:about="http://imc.org/vCard/3.0#internet"/></rdf:type></rdf:Description><rdf:Description rdf:about="rdf:#8c73d2c9-42f5-4bdc-af90-748f573ae418"><modified xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#e76d4e28-fe06-4e5c-8ab5-eed6f0940699"/></modified><cmeta:modifier><rdf:Description rdf:about="rdf:#8e025f2d-dfe3-4690-9747-764897912e28"/></cmeta:modifier><rdf:value xml:lang="en">added units</rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#4b7658cc-4144-479a-aaf7-cf86bdb397a2"><FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine Lloyd</FN></rdf:Description><rdf:Description rdf:about="rdf:#f9d7d9cb-3df8-452c-bb87-759019c5fa20"><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">May</Other><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></rdf:Description><rdf:Description rdf:about="rdf:#880edbc7-d252-4c09-a3a8-c1512690adf9"><FN xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Catherine Lloyd</FN></rdf:Description><rdf:Description rdf:about="rdf:#21c41487-8a28-4beb-b96d-729d974a2d0e"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-07-16T00:00:00+00:00</W3CDTF></rdf:Description><rdf:Description rdf:about=""><cmeta:comment><rdf:Description rdf:about="rdf:#796d810e-2fcc-42ca-a4c3-f175f07fca75"/></cmeta:comment><publisher xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">The University of Auckland, Bioengineering Institute</publisher><created xmlns="http://purl.org/dc/terms/"><rdf:Description rdf:about="rdf:#21c41487-8a28-4beb-b96d-729d974a2d0e"/></created><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#2f0302e6-a1ba-4289-ae0e-3e683702cd00"/></creator><cmeta:modification><rdf:Description rdf:about="rdf:#8c73d2c9-42f5-4bdc-af90-748f573ae418"/></cmeta:modification></rdf:Description><rdf:Description rdf:about="rdf:#2be71aa3-67df-4bf5-ba2a-edaae86a999a"><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">H</Other><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Dean</Given><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Hamer</Family></rdf:Description><rdf:Description rdf:about="rdf:#633015ce-17da-408e-9d22-4040b92dc853"><rdf:_1><rdf:Description rdf:about="rdf:#160a60fc-7260-4c13-a11c-7f055d412a6e"/></rdf:_1><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:#b119fd3e-05bf-4a7f-9655-cb6731fa5953"/></rdf:_2></rdf:Description><rdf:Description rdf:about="rdf:#ccd516c1-6db0-4187-91f8-84a358b4f7d5"><Other xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">May</Other><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></rdf:Description><rdf:Description rdf:about="x"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">x</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">uninfected HIV-specific CD4+ T cells</alternative></rdf:Description><rdf:Description rdf:about="rdf:#8e025f2d-dfe3-4690-9747-764897912e28"><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#ccd516c1-6db0-4187-91f8-84a358b4f7d5"/></N></rdf:Description><rdf:Description rdf:about="v"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">v</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">free virus particles</alternative></rdf:Description><rdf:Description rdf:about="y"><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">y</title><alternative xmlns="http://purl.org/dc/terms/" xml:lang="en">infected HIV-specific CD4+ T cells</alternative></rdf:Description><rdf:Description rdf:about="rdf:#4b4520ce-8e7d-4729-83ab-fbc1da78dcdc"><Given xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Dominik</Given><Family xmlns="http://www.w3.org/2001/vcard-rdf/3.0#" xml:lang="en">Wodarz</Family></rdf:Description><rdf:Description rdf:about="rdf:#dede96b7-e6bf-4054-a3bb-bf911b231eab"><subject xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#2ccba2c3-dc0f-4c94-b10d-fee8c2157e89"/></subject></rdf:Description><rdf:Description rdf:about="rdf:#b119fd3e-05bf-4a7f-9655-cb6731fa5953"><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:#2be71aa3-67df-4bf5-ba2a-edaae86a999a"/></N></rdf:Description><rdf:Description rdf:about="rdf:#e76d4e28-fe06-4e5c-8ab5-eed6f0940699"><W3CDTF xmlns="http://purl.org/dc/terms/" xml:lang="en">2007-09-06T13:39:32+12:00</W3CDTF></rdf:Description><rdf:Description rdf:about="rdf:#4cce23c8-f8dc-4586-acfb-aed50d513e53"><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:about="#wodarz_model_2007"><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#dede96b7-e6bf-4054-a3bb-bf911b231eab"/></reference><reference xmlns="http://www.cellml.org/bqs/1.0#"><rdf:Description rdf:about="rdf:#26118a9d-6018-4598-855d-10953ac95edd"/></reference><cmeta:comment><rdf:Description rdf:about="rdf:#ddf33ce8-3208-4551-be81-406b9fe2fe76"/></cmeta:comment><title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">
Wodarz and Hamer's 2007 mathematical model of infection dynamics in HIV-specific CD4+ T cells.
</title></rdf:Description><rdf:Description rdf:about="rdf:#2f0302e6-a1ba-4289-ae0e-3e683702cd00"><EMAIL xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#665b4094-dc8e-4545-babd-39d7d81cf26b"/></EMAIL><ORG xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#4cce23c8-f8dc-4586-acfb-aed50d513e53"/></ORG><N xmlns="http://www.w3.org/2001/vcard-rdf/3.0#"><rdf:Description rdf:about="rdf:#f9d7d9cb-3df8-452c-bb87-759019c5fa20"/></N></rdf:Description><rdf:Description rdf:about="rdf:#796d810e-2fcc-42ca-a4c3-f175f07fca75"><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#880edbc7-d252-4c09-a3a8-c1512690adf9"/></creator><rdf:value xml:lang="en">The model runs in PCEnv to replicate the published results.</rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#2ccba2c3-dc0f-4c94-b10d-fee8c2157e89"><subject_type xmlns="http://www.cellml.org/bqs/1.0#" xml:lang="en">keyword</subject_type><rdf:value><rdf:Description rdf:about="rdf:#983a601a-7eb7-40cc-9d48-b5b90f165a94"/></rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#ddf33ce8-3208-4551-be81-406b9fe2fe76"><creator xmlns="http://purl.org/dc/elements/1.1/"><rdf:Description rdf:about="rdf:#4b7658cc-4144-479a-aaf7-cf86bdb397a2"/></creator><rdf:value xml:lang="en">This is a CellML description of Wodarz and Hamer's 2007 mathematical model of infection dynamics in HIV-specific CD4+ T cells.</rdf:value></rdf:Description><rdf:Description rdf:about="rdf:#983a601a-7eb7-40cc-9d48-b5b90f165a94"><rdf:_1 xml:lang="en">immunology</rdf:_1><rdf:type><rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag"/></rdf:type><rdf:_3 xml:lang="en">HIV</rdf:_3><rdf:_2 xml:lang="en">viral dynamics</rdf:_2><rdf:_4 xml:lang="en">CD4+ T cell</rdf:_4></rdf:Description></rdf:RDF></model>
