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<body xmlns="http://www.w3.org/1999/xhtml">Drosophila melanogaster, body segmentation</body>
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<vCard:Given>Tomas</vCard:Given>
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<vCard:EMAIL>thelika@unmc.edu</vCard:EMAIL>
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<vCard:Orgname>University of Nebraska - Lincoln</vCard:Orgname>
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<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">WG_external is an external activator in the Body segmentation in drosophila 2013 model</span></p></body>
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<p>This is an external activator of the Body Segmentation in Drosophila 2013 paper</p></body>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<qual:qualitativeSpecies metaid="d74ee6a4-c9e0-4fc6-b6b9-81d5b8485c7e" qual:compartment="cytosol" qual:constant="false" qual:id="S_1" qual:initialLevel="0" qual:maxLevel="1" qual:name="wg">
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<body xmlns="http://www.w3.org/1999/xhtml">
<p>Wingless<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/P09615" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">P09615</a></div><div>Gene Name: wg</div><div>Gene ID:&nbsp;<span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">34009</span></div></p></body>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hedgehog (HH) segment polarity gene<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q02936" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">Q02936</a></div><div>Gene Name: hh</div><div>Gene ID:&nbsp;<span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">42737</span></div></p></body>
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<rdf:li rdf:resource="urn:miriam:pubmed:1340474"/>
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<rdf:Bag>
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<notes>
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<p>transcription factor Engrailed in drosophila segmentation</p></body>
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<annotation>
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<notes>
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<p>Transcriptional active form of CI in Drosophila Segmentation</p></body>
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<qual:qualitativeSpecies metaid="_6e7a2227-fc73-4e88-a5b9-0a0d03a6a4a7" qual:compartment="cytosol" qual:constant="false" qual:id="S_5" qual:initialLevel="0" qual:maxLevel="1" qual:name="PTC_protein">
<notes>
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<p>Protein for the gene that expresses&nbsp;<font color="#4f4f4f" face="Arial, Verdana" size="2"><span style="line-height: 1.5em; background-color: rgb(255, 255, 255); orphans: 3; widows: 3;">Transmembrane receptor protein</span></font><span style="orphans: 3; widows: 3;">s patched (PTC) in drosophila segmentation</span><div>for more information:&nbsp;http://www.ncbi.nlm.nih.gov/mesh/67099744</div></p></body>
</notes>
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<rdf:Description rdf:about="#_6e7a2227-fc73-4e88-a5b9-0a0d03a6a4a7">
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<rdf:Bag>
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</annotation>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Represents pH<div><br/></div><div>Phagocytosis (mouse) in coninfection for more info:</div><div>http://www.ncbi.nlm.nih.gov/mesh/68010587</div><div><hr/></div><div><br/></div><div>PH protein in the Drosophila segmentation model (2013)</div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:23520449"/>
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<notes>
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<p>Smoothened (SMO)<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/Q29NW6" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(255, 255, 255);">Q29NW6</a></div><div>Gene Name: smo</div><div>Gene ID:&nbsp;<span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">33196</span></div></p></body>
</notes>
<annotation>
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<rdf:Description rdf:about="#_2966c97a-8209-4f44-93a5-203fa83ebf2f">
<dcterms:modified rdf:parseType="Resource">
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<rdf:li rdf:resource="urn:miriam:pubmed:9649421"/>
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<rdf:Bag>
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<rdf:Bag>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Repressor protein gene CI<div>Gene Name: cI</div><div>Gene ID:&nbsp;<span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">1261955</span></div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#ff492a41-11c2-4b29-bb1a-8a9c72aad4b8">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12782112"/>
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:2384212"/>
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<annotation>
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Patched (ptc) membrane protein<div>UniProt ID:&nbsp;<a href="http://www.uniprot.org/uniprot/P18502" style="text-decoration: none; color: rgb(64, 148, 180); border-bottom-width: 0px; cursor: pointer; font-family: Verdana, Arial, sans-serif; font-size: 13.0571994781494px; line-height: 20.081974029541px; background-color: rgb(222, 239, 245);">P18502</a></div><div>Gene Name: ptc</div><div>Gene ID:&nbsp;<span style="color: rgb(87, 87, 87); font-family: arial, helvetica, clean, sans-serif; font-size: 11.6999998092651px; line-height: 16.199821472168px; background-color: rgb(213, 222, 227);">35851</span></div></p></body>
</notes>
<annotation>
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<rdf:Description rdf:about="#_85ddf8e5-4111-408a-815b-b5386ec9a32f">
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<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Transcriptionally repressive form of CI protein in Drosophila segmentation</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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<qual:qualitativeSpecies metaid="dda66db0-1c9a-4b60-923a-25830f387a7d" qual:compartment="cytosol" qual:constant="false" qual:id="S_13" qual:initialLevel="0" qual:maxLevel="1" qual:name="WG_protein">
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#dda66db0-1c9a-4b60-923a-25830f387a7d">
<dcterms:modified rdf:parseType="Resource">
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<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12782112"/>
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</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:23520449"/>
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</bqbiol:isDescribedBy>
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</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="a1c090c8-60c4-4447-a0fe-0f6ec9a86537" qual:compartment="cytosol" qual:constant="false" qual:id="S_14" qual:initialLevel="0" qual:maxLevel="1" qual:name="CI_protein">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="background-color: rgb(255, 255, 255); color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 14.40000057220459px;">Cytosolic protein cubitus&nbsp;interruptus</span><div style="font-size: 12px; color: rgb(79, 79, 79); font-family: Arial, sans-serif; line-height: 14.40000057220459px; background-color: rgb(255, 255, 255);">For more information:&nbsp;http://www.ncbi.nlm.nih.gov/mesh/?term=cubitus+interruptus</div></p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#a1c090c8-60c4-4447-a0fe-0f6ec9a86537">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-11-15T19:54:44Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:23520449"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12782112"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
<qual:qualitativeSpecies metaid="_5926d309-0ac4-43b2-a3af-3f39e9f7b95b" qual:compartment="cytosol" qual:constant="false" qual:id="S_15" qual:initialLevel="0" qual:maxLevel="1" qual:name="HH_protein">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Hedgehog Transcription factor for drosophila segmentation</p></body>
</notes>
<annotation>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
<rdf:Description rdf:about="#_5926d309-0ac4-43b2-a3af-3f39e9f7b95b">
<dcterms:modified rdf:parseType="Resource">
<dcterms:W3CDTF>2015-11-15T19:54:44Z</dcterms:W3CDTF>
</dcterms:modified>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:12782112"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
<bqbiol:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:pubmed:23520449"/>
</rdf:Bag>
</bqbiol:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
</qual:qualitativeSpecies>
</qual:listOfQualitativeSpecies>
<qual:listOfTransitions xmlns:qual="http://www.sbml.org/sbml/level3/version1/qual/version1">
<qual:transition qual:id="tr_S_1">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIA in conjunction with SLP and not CIR regulate Wg [1,2]. wg in conjunction with either CIA and SLP and not CIR regulates wg itself [1,2].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_1_in_S_12" qual:qualitativeSpecies="S_12" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">slp encodes two forkhead domain&nbsp;</span><span style="font-size: 10pt;">transcription factors with similar functions that activate&nbsp;</span><span style="font-size: 10pt;">wg transcription</span>" [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>Wg positively regulates itself [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">CI is cleaved to form CIR, a transcriptional&nbsp;</span><span style="font-size: 10pt;">repressor that represses wg</span>" [1,2,3]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_1_in_S_4" qual:qualitativeSpecies="S_4" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">When&nbsp;</span><span style="font-size: 10pt;">SMO is active, CI is converted to a transcriptional&nbsp;</span><span style="font-size: 10pt;">activator CIA that promotes the transcription of wg</span>" [1,2,3,4,5]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_1" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<or/>
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_2">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>EN_protein positively regulates Hh, while CIR negatively regulates Hh [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_2_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIR a transcriptional repressor that represses Hh transcription [1,2,4,5]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_2_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"EN, the homeodomain-containing product of the en gene, promotes the transcription of the hedgehog gene (hh)" [1,2,3]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_2" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_3">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>WG_external positively regulates En and SLP in conjunction negatively regulates En [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_3_in_S_12" qual:qualitativeSpecies="S_12" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>SLP negatively regulates En [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_3_in_S_16" qual:qualitativeSpecies="S_16" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>WG_external positively regulates En [1,2]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_3" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_16 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_12 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_4">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein in conjunction with either hh_external or PTC_protein positively regulates CIA [1,2,3,4,5,6].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_4_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein in conjunction with either hh_external or PTC_protein positively regulates CIA [1,6].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein in conjunction with either hh_external or PTC_protein positively regulates CIA [1,6].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_4_in_S_14" qual:qualitativeSpecies="S_14" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">When&nbsp;</span><span style="font-size: 10pt;">SMO is active, CI is converted to a transcriptional&nbsp;</span><span style="font-size: 10pt;">activator CIA" [1,2,3,4,5,6]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_4" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_5">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">ptc activates PTC_protein [1,2]. PTC_protein in conjunction with hh_external positively regulates PTC_protein [1,2].</span></p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_5_in_S_10" qual:qualitativeSpecies="S_10" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ptc activates PTC_protein [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_5_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PTC_protein self regulates [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_5_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">The important&nbsp;</span><span style="font-size: 10pt;">role of HH in the networkis re?ected in the fact that it&nbsp;</span><span style="font-size: 10pt;">affects the future expression of four other proteins (CIA,</span><span style="font-size: 10pt;"><br/></span><span style="font-size: 10pt;">CIR, PTC and PH) in the neighboring cells</span>" [1,2]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_5" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_10 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<and/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_6">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PTC_protein in conjunction with hh_external positively regulates PH [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_6_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PTC_protein in conjunction with hh_external positively regulates PH [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_6_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>"The important&nbsp;<span style="font-size: 10pt;">role of HH in the networkis re?ected in the fact that it&nbsp;</span><span style="font-size: 10pt;">affects the future expression of four other proteins (CIA,</span></div><div>CIR, PTC and PH) in the neighboring cells" [1,2]</div></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_6" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_7">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>PTC_protein positively regulates SMO. hh_external positively regulates SMO. [1,2,3]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_7_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">Binding of HH&nbsp;</span><span style="font-size: 10pt;">to PTC removes the inhibition of SMO" [1,2,3]</span></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_7_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"<span style="font-size: 10pt;">Binding of HH&nbsp;</span><span style="font-size: 10pt;">to PTC removes the inhibition of SMO" [1,2,3]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_7" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<or/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_8">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>EN_protein positively regulates Ci [1,2,3].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_8_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">"</span><span style="font-size: 10pt;">EN contains a&nbsp;</span><span style="font-size: 10pt;">separate repression domain&nbsp;</span><span style="font-size: 10pt;">that affects the transcription of ci" [1,2,3]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_8" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<not/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_9">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>en positively regulates EN_protein [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_9_in_S_3" qual:qualitativeSpecies="S_3" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>"WG_external and SLP in conjunction positively regulate En" [1,2]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_9" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_3 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_10">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIA and EN_protein and not CIR positively regulate Ptc [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_10_in_S_11" qual:qualitativeSpecies="S_11" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIA and EN_protein and not CIR positively regulate Ptc [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_10_in_S_9" qual:qualitativeSpecies="S_9" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIA and EN_protein and not CIR positively regulate Ptc [1,2]</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_10_in_S_4" qual:qualitativeSpecies="S_4" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CIA and EN_protein and not CIR positively regulate Ptc [1,2]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_10" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<eq/>
<ci> S_4 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<not/>
<apply>
<or/>
<apply>
<eq/>
<ci> S_9 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_11 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_11">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein and PTC_protein and hh_external work in conjunction to positively regulates CIR [1,2].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_11_in_S_5" qual:qualitativeSpecies="S_5" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><div>"existence of PTC in those cells is very important because&nbsp;<span style="font-size: 10pt;">their signaling maintains the production of CIR" [1]</span></div><div>CI_protein and PTC_protein and hh_external work in conjunction to positively regulates CIR [1,2].</div></p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_11_in_S_17" qual:qualitativeSpecies="S_17" qual:sign="negative" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein and PTC_protein and hh_external work in conjunction to positively regulates CIR [1,2].</p></body>
</notes>
</qual:input>
<qual:input qual:id="tr_S_11_in_S_14" qual:qualitativeSpecies="S_14" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>CI_protein and PTC_protein and hh_external work in conjunction to positively regulates CIR [1,2].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_11" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<and/>
<apply>
<and/>
<apply>
<eq/>
<ci> S_14 </ci>
<cn type="integer"> 1 </cn>
</apply>
<apply>
<eq/>
<ci> S_5 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
<apply>
<not/>
<apply>
<eq/>
<ci> S_17 </ci>
<cn type="integer"> 1 </cn>
</apply>
</apply>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_13">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>wg positively regulates WG_protein [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_13_in_S_1" qual:qualitativeSpecies="S_1" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>The segment polarity gene, wg, encodes for the transcription factor WG_protein [1,2]</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_13" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_1 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_14">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ci positively regulates CI_protein [1,2].</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_14_in_S_8" qual:qualitativeSpecies="S_8" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>ci positively regulates CI_protein [1,2].</p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_14" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_8 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
<qual:transition qual:id="tr_S_15">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p>hh positively regulates HH_protein [1,2]</p></body>
</notes>
<qual:listOfInputs>
<qual:input qual:id="tr_S_15_in_S_2" qual:qualitativeSpecies="S_2" qual:sign="positive" qual:thresholdLevel="1" qual:transitionEffect="none">
<notes>
<body xmlns="http://www.w3.org/1999/xhtml">
<p><span style="color: rgb(79, 79, 79); font-family: Arial, sans-serif; font-size: 12px; line-height: 18px; orphans: 3; widows: 3; background-color: rgb(255, 255, 255);">hh positively regulates HH_protein [1,2]</span></p></body>
</notes>
</qual:input>
</qual:listOfInputs>
<qual:listOfOutputs>
<qual:output qual:qualitativeSpecies="S_15" qual:transitionEffect="assignmentLevel"/>
</qual:listOfOutputs>
<qual:listOfFunctionTerms>
<qual:defaultTerm qual:resultLevel="0">
</qual:defaultTerm>
<qual:functionTerm qual:resultLevel="1">
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<eq/>
<ci> S_2 </ci>
<cn type="integer"> 1 </cn>
</apply>
</math>
</qual:functionTerm>
</qual:listOfFunctionTerms>
</qual:transition>
</qual:listOfTransitions>
<listOfCompartments>
<compartment constant="true" id="extracellular" name="extracellular"/>
<compartment constant="true" id="cytosol" name="cytosol"/>
</listOfCompartments>
</model>
</sbml>