Skip to content

GitLab

Commit 29f4e76f authored by cylon-x's avatar cylon-x 🤖
Browse files

Merge branch 'repo_update' of https://git-r3lab.uni.lu/covid/models into repo_update

parents b7663394 48692107
Pipeline #37179 passed with stages
in 3 minutes and 51 seconds
Expand all Hide whitespace changes
Inline Side-by-side
Curation/Apoptosis/Apoptosis_stable.xml
View file @ 29f4e76f
......@@ -1782,7 +1782,6 @@ MESH Id is provided for the phenotype 'Apoptosis'.
<celldesigner:protein id="pr28" name="Orf3a" type="GENERIC"/>
<celldesigner:protein id="pr29" name="MAPK14" type="GENERIC"/>
<celldesigner:protein id="pr32" name="E" type="GENERIC"/>
<celldesigner:protein id="pr33" name="Orf7a" type="GENERIC"/>
<celldesigner:protein id="pr34" name="M" type="GENERIC"/>
<celldesigner:protein id="pr36" name="Orf3b" type="GENERIC"/>
<celldesigner:protein id="pr37" name="Orf8a" type="GENERIC"/>
......@@ -1790,6 +1789,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:protein id="pr39" name="Orf6" type="GENERIC"/>
<celldesigner:protein id="pr40" name="S" type="GENERIC"/>
<celldesigner:protein id="pr41" name="Orf9b" type="GENERIC"/>
<celldesigner:protein id="pr33" name="Orf7a" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes/>
<celldesigner:listOfRNAs/>
......@@ -2056,6 +2056,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:catalyzed reaction="re19"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s45">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59637"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s94" id="s94" name="E" compartment="c5" initialAmount="0">
......@@ -2070,20 +2079,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:catalyzed reaction="re23"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s39" id="s39" name="Orf7a" compartment="c5" initialAmount="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr33</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re23"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s94">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59637"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s38" id="s38" name="M" compartment="c5" initialAmount="0">
......@@ -2214,6 +2218,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr36</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s144">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59633"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s145" id="s145" name="Orf8a" compartment="c5" initialAmount="0">
......@@ -2225,6 +2238,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr37</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s145">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:Q7TFA0"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s146" id="s146" name="N" compartment="c5" initialAmount="0">
......@@ -2236,6 +2258,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr38</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s146">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59595"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s147" id="s147" name="Orf6" compartment="c5" initialAmount="0">
......@@ -2247,6 +2278,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr39</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s147">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59634"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s148" id="s148" name="S" compartment="c5" initialAmount="0">
......@@ -2258,6 +2298,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr40</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s148">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59594"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s149" id="s149" name="Orf9b" compartment="c5" initialAmount="0">
......@@ -2269,6 +2318,15 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
<celldesigner:proteinReference>pr41</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s149">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59636"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s150" id="s150" name="BAD" compartment="c5" initialAmount="0">
......@@ -2361,6 +2419,38 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:extension>
</annotation>
</species>
<species metaid="s39" id="s39" name="Orf7a" compartment="c5" initialAmount="0" charge="0">
<notes>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<title/>
</head>
<body>COVID19 Disease Map
</body>
</html>
</notes>
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
<celldesigner:speciesIdentity>
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr33</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re23"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s39">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:Q19QW4"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re1" id="re1" reversible="false">
......@@ -2738,7 +2828,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:linkTarget>
<celldesigner:line width="3.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="INHIBITION" modifiers="s116" aliases="sa29" targetLineIndex="-1,7" editPoints="0.0025603618302028064,0.020742578188163163 0.9875528009624692,-0.1008400438617616">
<celldesigner:modification type="INHIBITION" modifiers="s116" aliases="sa29" targetLineIndex="-1,7" editPoints="0.0025603618302028064,0.020742578188163385 0.9875528009624693,-0.10084004386176137">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
......@@ -2927,7 +3017,7 @@ MESH Id is provided for the phenotype &apos;Apoptosis&apos;.
</celldesigner:linkTarget>
<celldesigner:line width="3.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="INHIBITION" modifiers="s156" aliases="csa11" targetLineIndex="-1,2" editPoints="0.07210651322633788,0.0028511662646293345 0.0736675660903392,-0.03662814449375329">
<celldesigner:modification type="INHIBITION" modifiers="s156" aliases="csa11" targetLineIndex="-1,2" editPoints="0.07210651322633832,0.0028511662646293345 0.07366756609033964,-0.03662814449375329">
<celldesigner:connectScheme connectPolicy="square">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="vertical"/>
......
Curation/ETC/ETC_stable.xml
View file @ 29f4e76f
This diff is collapsed.
Curation/HMOX1 pathway/HMOX1_Pathway_V4.xml 0 → 100644
View file @ 29f4e76f
This diff is collapsed.
Curation/Inflammasomes/NLRP3_Activation_V4.xml 0 → 100644
View file @ 29f4e76f
This diff is collapsed.
Curation/Inflammasomes/NLRP3_Activation_stable.xml 0 → 100644
View file @ 29f4e76f
This diff is collapsed.
Curation/JNK pathway/JNK_pathway_stable.xml
View file @ 29f4e76f
......@@ -2330,6 +2330,15 @@ Uniprot:P0QGFD
<celldesigner:catalyzed reaction="re4"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s105">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59632"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s104" id="s104" name="7a" compartment="c2" initialAmount="0">
......@@ -2344,6 +2353,15 @@ Uniprot:P0QGFD
<celldesigner:catalyzed reaction="re4"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s104">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59635"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s106" id="s106" name="S" compartment="c2" initialAmount="0">
......@@ -2368,6 +2386,15 @@ Uniprot:P0QGFD
<celldesigner:catalyzed reaction="re42"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s106">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59594"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
<species metaid="s103" id="s103" name="3b" compartment="c2" initialAmount="0">
......@@ -2382,6 +2409,15 @@ Uniprot:P0QGFD
<celldesigner:catalyzed reaction="re36"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#s103">
<bqmodel:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:uniprot:P59633"/>
</rdf:Bag>
</bqmodel:is>
</rdf:Description>
</rdf:RDF>
</annotation>
</species>
</listOfSpecies>
......@@ -2414,7 +2450,7 @@ Uniprot:P0QGFD
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s49" aliases="csa2" targetLineIndex="-1,4" editPoints="0.6490041839468192,-0.29949358690347117">
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s49" aliases="csa2" targetLineIndex="-1,4" editPoints="0.6490041839468192,-0.29949358690347183">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
......@@ -3290,7 +3326,7 @@ Uniprot:P0QGFD
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s6" aliases="sa5" targetLineIndex="-1,4" editPoints="0.3049969275981761,-0.14963021895091022">
<celldesigner:modification type="PHYSICAL_STIMULATION" modifiers="s6" aliases="sa5" targetLineIndex="-1,4" editPoints="0.3049969275981761,-0.14963021895091067">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
......
Curation/Kynurenine Pathway/Kynurenine_pathway_V2.xml 0 → 100644
View file @ 29f4e76f
This diff is collapsed.
Curation/SARS-CoV-2 proteins/Orf3b/Orf3b_0620_2020.xml
View file @ 29f4e76f
......@@ -399,6 +399,14 @@
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
<celldesigner:compartmentAlias id="ca5" compartment="c5">
<celldesigner:class>SQUARE</celldesigner:class>
<celldesigner:bounds x="235.0" y="485.0" w="240.0" h="255.0"/>
<celldesigner:namePoint x="407.5" y="698.5"/>
<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
<celldesigner:paint color="ffcccc00" scheme="Color"/>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:compartmentAlias>
</celldesigner:listOfCompartmentAliases>
<celldesigner:listOfComplexSpeciesAliases>
<celldesigner:complexSpeciesAlias id="csa4" species="s23" compartmentAlias="ca4">
......@@ -451,6 +459,7 @@
<celldesigner:backupSize w="0.0" h="0.0"/>
<celldesigner:backupView state="none"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="126.0" height="120.0"/>
<celldesigner:singleLine width="2.0"/>
<celldesigner:paint color="fff7f7f7" scheme="Color"/>
......@@ -528,13 +537,13 @@
</celldesigner:complexSpeciesAlias>
</celldesigner:listOfComplexSpeciesAliases>
<celldesigner:listOfSpeciesAliases>
<celldesigner:speciesAlias id="sa1" species="s1">
<celldesigner:speciesAlias id="sa1" species="s1" compartmentAlias="ca5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="314.83333333333326" y="510.58333333333326" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:innerPosition x="79.83333333333326" y="25.583333333333258"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffcccc" scheme="Color"/>
......@@ -547,14 +556,14 @@
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa4" species="s7">
<celldesigner:speciesAlias id="sa4" species="s7" compartmentAlias="ca5">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="301.83333333333326" y="687.0833333333333" w="244.0" h="29.0"/>
<celldesigner:bounds x="380.0" y="635.0" w="80.0" h="30.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="244.0" height="29.0"/>
<celldesigner:innerPosition x="145.0" y="150.0"/>
<celldesigner:boxSize width="80.0" height="30.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffffff66" scheme="Color"/>
</celldesigner:usualView>
......@@ -587,11 +596,10 @@
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa7" species="s12">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="116.83333333333331" y="690.0833333333333" w="90.0" h="25.0"/>
<celldesigner:bounds x="115.0" y="637.5" w="90.0" h="25.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="90.0" height="25.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ff66ff66" scheme="Color"/>
......@@ -853,11 +861,11 @@
</celldesigner:speciesAlias>
<celldesigner:speciesAlias id="sa48" species="s43" complexSpeciesAlias="csa8">
<celldesigner:activity>inactive</celldesigner:activity>
<celldesigner:bounds x="1022.3333333333333" y="438.66666666666663" w="80.0" h="40.0"/>
<celldesigner:bounds x="1025.0" y="445.0" w="80.0" h="40.0"/>
<celldesigner:font size="12"/>
<celldesigner:view state="usual"/>
<celldesigner:usualView>
<celldesigner:innerPosition x="9.333333333333258" y="53.66666666666663"/>
<celldesigner:innerPosition x="12.0" y="60.0"/>
<celldesigner:boxSize width="80.0" height="40.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="ffccffcc" scheme="Color"/>
......@@ -1055,7 +1063,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1074,7 +1082,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1093,7 +1101,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1207,7 +1215,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1226,7 +1234,7 @@
<celldesigner:briefView>
<celldesigner:innerPosition x="0.0" y="0.0"/>
<celldesigner:boxSize width="80.0" height="60.0"/>
<celldesigner:singleLine width="0.0"/>
<celldesigner:singleLine width="1.0"/>
<celldesigner:paint color="3fff0000" scheme="Color"/>
</celldesigner:briefView>
<celldesigner:info state="empty" angle="-1.5707963267948966"/>
......@@ -1253,11 +1261,7 @@
<celldesigner:protein id="pr23" name="TCRβ" type="GENERIC"/>
</celldesigner:listOfProteins>
<celldesigner:listOfGenes>
<celldesigner:gene id="gn1" name="IFNB1" type="GENE">
<celldesigner:listOfRegions>
<celldesigner:region id="tr2" name="Promoter" size="0.24" pos="0.15647058823529414" type="RegulatoryRegion" active="false"/>
</celldesigner:listOfRegions>
</celldesigner:gene>
<celldesigner:gene id="gn1" name="IFNB1" type="GENE"/>
</celldesigner:listOfGenes>
<celldesigner:listOfRNAs>
<celldesigner:RNA id="rn1" name="IFNB1" type="RNA"/>
......@@ -1322,9 +1326,16 @@
</celldesigner:extension>
</annotation>
</compartment>
<compartment metaid="c5" id="c5" name="nucleus" size="1" units="volume" outside="default">
<annotation>
<celldesigner:extension>
<celldesigner:name>nucleus</celldesigner:name>
</celldesigner:extension>
</annotation>
</compartment>
</listOfCompartments>
<listOfSpecies>
<species metaid="s1" id="s1" name="Orf3b" compartment="default" initialAmount="0" charge="0">
<species metaid="s1" id="s1" name="Orf3b" compartment="c5" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
......@@ -1332,10 +1343,13 @@
<celldesigner:class>PROTEIN</celldesigner:class>
<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
</celldesigner:speciesIdentity>
<celldesigner:listOfCatalyzedReactions>
<celldesigner:catalyzed reaction="re5"/>
</celldesigner:listOfCatalyzedReactions>
</celldesigner:extension>
</annotation>
</species>
<species metaid="s7" id="s7" name="IFNB1" compartment="default" initialAmount="0" charge="0">
<species metaid="s7" id="s7" name="IFNB1" compartment="c5" initialAmount="0" charge="0">
<annotation>
<celldesigner:extension>
<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
......@@ -1742,54 +1756,6 @@
</species>
</listOfSpecies>
<listOfReactions>
<reaction metaid="re11" id="re4" reversible="false">
<annotation>
<celldesigner:extension>
<celldesigner:reactionType>NEGATIVE_INFLUENCE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s1" alias="sa1"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s7" alias="sa4">
<celldesigner:linkAnchor position="NNW"/>
</celldesigner:baseProduct>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:extension>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
<rdf:Description rdf:about="#re11">
<bqmodel:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:doi:10.1101%2F2020.05.11.088179"/>
</rdf:Bag>
</bqmodel:isDescribedBy>
</rdf:Description>
</rdf:RDF>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00005" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfReactants>
<listOfProducts>
<speciesReference metaid="CDMT00006" species="s7">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa4</celldesigner:alias>
</celldesigner:extension>
</annotation>
</speciesReference>
</listOfProducts>
</reaction>
<reaction metaid="re12" id="re5" reversible="false">
<annotation>
<celldesigner:extension>
......@@ -1806,6 +1772,19 @@
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:line width="1.0" color="ff000000"/>
<celldesigner:listOfModification>
<celldesigner:modification type="INHIBITION" modifiers="s1" aliases="sa1" targetLineIndex="-1,3">
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
<celldesigner:lineDirection index="0" value="unknown"/>
</celldesigner:listOfLineDirection>
</celldesigner:connectScheme>
<celldesigner:linkTarget species="s1" alias="sa1">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:linkTarget>
<celldesigner:line width="1.0" color="ff000000"/>
</celldesigner:modification>
</celldesigner:listOfModification>
</celldesigner:extension>
</annotation>
<listOfReactants>
......@@ -1826,6 +1805,15 @@
</annotation>
</speciesReference>
</listOfProducts>
<listOfModifiers>
<modifierSpeciesReference metaid="CDMT00001" species="s1">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa1</celldesigner:alias>
</celldesigner:extension>
</annotation>
</modifierSpeciesReference>
</listOfModifiers>
</reaction>
<reaction metaid="re13" id="re6" reversible="false">
<annotation>
......@@ -2321,14 +2309,10 @@
<celldesigner:extension>
<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
<celldesigner:baseReactants>
<celldesigner:baseReactant species="s22" alias="sa38">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseReactant>
<celldesigner:baseReactant species="s22" alias="sa38"/>
</celldesigner:baseReactants>
<celldesigner:baseProducts>
<celldesigner:baseProduct species="s73" alias="sa78">
<celldesigner:linkAnchor position="INACTIVE"/>
</celldesigner:baseProduct>
<celldesigner:baseProduct species="s73" alias="sa78"/>
</celldesigner:baseProducts>
<celldesigner:connectScheme connectPolicy="direct">
<celldesigner:listOfLineDirection>
......@@ -2339,7 +2323,7 @@
</celldesigner:extension>
</annotation>
<listOfReactants>
<speciesReference metaid="CDMT00001" species="s22">
<speciesReference metaid="CDMT00002" species="s22">
<annotation>
<celldesigner:extension>
<celldesigner:alias>sa38</celldesigner:alias>
......@@ -2348,7 +2332,7 @@
</speciesReference>