From 46863b421d7cfdd140b33e24f43a8500cd7e86ff Mon Sep 17 00:00:00 2001
From: hasanbalci <balcihasan99@gmail.com>
Date: Wed, 21 Aug 2024 11:31:50 -0400
Subject: [PATCH] Update SBML samples #692

---
 app/js/app-menu.js                            |    9 +-
 app/samples/PTK6_Activates_STAT3.nwt          |  547 +++++
 ...ion_of_genes_involved_in_WNT_signaling.nwt |  415 ++++
 app/samples/apoptotic_reaction_model.nwt      | 1799 -----------------
 app/samples/insulin_induced_signalling.nwt    |  841 --------
 ...inetics_of_PFOA_and_PFOS_in_the_monkey.nwt |  342 ++--
 index.html                                    |    9 +-
 7 files changed, 1145 insertions(+), 2817 deletions(-)
 create mode 100644 app/samples/PTK6_Activates_STAT3.nwt
 create mode 100644 app/samples/RUNX1_regulates_transcription_of_genes_involved_in_WNT_signaling.nwt
 delete mode 100644 app/samples/apoptotic_reaction_model.nwt
 delete mode 100644 app/samples/insulin_induced_signalling.nwt

diff --git a/app/js/app-menu.js b/app/js/app-menu.js
index 08937d9a..eac9c628 100644
--- a/app/js/app-menu.js
+++ b/app/js/app-menu.js
@@ -973,11 +973,10 @@ module.exports = function() {
       "#load-sample18" : 'signaling-downstream-of-AKT2-3.nwt',
       "#load-sample19" : 'pd_learners_card.nwt',
       "#load-sample20" : 'af_learners_card.nwt',
-      "#load-sample21" : 'interaction_topologies_of_MAPK_cascade.nwt',
-      "#load-sample22" : 'pharmacokinetics_of_PFOA_and_PFOS_in_the_monkey.nwt',
-      "#load-sample23" : 'apoptotic_reaction_model.nwt',
-      "#load-sample24" : 'insulin_induced_signalling.nwt',
-
+      "#load-sample21" : 'RUNX1_regulates_transcription_of_genes_involved_in_WNT_signaling.nwt',
+      "#load-sample22" : 'PTK6_Activates_STAT3.nwt',
+      "#load-sample23" : 'pharmacokinetics_of_PFOA_and_PFOS_in_the_monkey.nwt',
+      "#load-sample24" : 'interaction_topologies_of_MAPK_cascade.nwt'
     };
 
     for ( var selector in selectorToSampleFileName ) {
diff --git a/app/samples/PTK6_Activates_STAT3.nwt b/app/samples/PTK6_Activates_STAT3.nwt
new file mode 100644
index 00000000..58f4f4ad
--- /dev/null
+++ b/app/samples/PTK6_Activates_STAT3.nwt
@@ -0,0 +1,547 @@
+<?xml version='1.0' encoding='UTF-8' standalone='yes'?>
+<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
+  <map language="sbml">
+    <extension>
+      <renderInformation 
+        xmlns="http://www.sbml.org/sbml/level3/version1/render/version1" id="renderInformation" program-name="sbgnviz" program-version="6.0.1" background-color="#00000000">
+        <listOfColorDefinitions>
+          <colorDefinition id="color_1" value="#f7f7f77f"/>
+          <colorDefinition id="color_2" value="#555555"/>
+          <colorDefinition id="color_3" value="#d1e5f0ff"/>
+          <colorDefinition id="color_4" value="#92c5deff"/>
+          <colorDefinition id="color_5" value="#f4a582ff"/>
+          <colorDefinition id="color_6" value="#ffffffff"/>
+          <colorDefinition id="color_7" value="#fddbc7ff"/>
+        </listOfColorDefinitions>
+        <listOfBackgroundImages/>
+        <listOfStyles>
+          <style id="nodef7f7f75555553.2514normalnormalHelvetica00010.5" idList="comp_0 comp_1">
+            <g font-size="14" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="3.25" fill="color_1" background-image-opacity="1" background-opacity="0.5"/>
+          </style>
+          <style id="noded1e5f05555551.2511normalnormalHelvetica00011" idList="species_5 species_9 species_6 species_8 species_13 species_26 species_27">
+            <g font-size="11" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="1.25" fill="color_3" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="node92c5de5555551.2511normalnormalHelvetica00011" idList="species_2 species_11 species_3 species_10 species_20 species_22 species_0 species_12 species_1 species_15 species_14 species_17 species_25 species_16 species_21 species_7 species_24">
+            <g font-size="11" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="1.25" fill="color_4" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="nodef4a5825555551.2511normalnormalHelvetica00011" idList="species_19 species_23">
+            <g font-size="11" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="1.25" fill="color_5" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="nodeffffff5555551.2511" idList="SbmlReactionExporter_3 SbmlReactionExporter_5 SbmlReactionExporter_8 SbmlReactionExporter_0 SbmlReactionExporter_1 SbmlReactionExporter_2 SbmlReactionExporter_4 SbmlReactionExporter_6 SbmlReactionExporter_7">
+            <g stroke="color_2" stroke-width="1.25" fill="color_6" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="nodefddbc75555551.2511normalnormalHelvetica00011" idList="species_4 species_18">
+            <g font-size="11" font-family="Helvetica" font-weight="normal" font-style="normal" font-color="#000" stroke="color_2" stroke-width="1.25" fill="color_7" background-image-opacity="1" background-opacity="1"/>
+          </style>
+          <style id="edge5555551.25" idList="species_6_SbmlReactionExporter_0 species_4_SbmlReactionExporter_0 species_18_SbmlReactionExporter_0 species_3_SbmlReactionExporter_0 SbmlReactionExporter_0_species_13 species_14_SbmlReactionExporter_1 species_25_SbmlReactionExporter_1 SbmlReactionExporter_1_species_27 species_27_SbmlReactionExporter_2 species_4_SbmlReactionExporter_2 species_18_SbmlReactionExporter_2 SbmlReactionExporter_2_species_13 species_5_SbmlReactionExporter_3 species_23_SbmlReactionExporter_3 SbmlReactionExporter_3_species_9 species_3_SbmlReactionExporter_4 SbmlReactionExporter_4_species_8 species_23_SbmlReactionExporter_5 SbmlReactionExporter_5_species_17 species_9_SbmlReactionExporter_5 species_12_SbmlReactionExporter_6 species_13_SbmlReactionExporter_6 SbmlReactionExporter_6_species_6 species_25_SbmlReactionExporter_7 species_17_SbmlReactionExporter_7 SbmlReactionExporter_7_species_26 species_8_SbmlReactionExporter_8 SbmlReactionExporter_8_species_5">
+            <g stroke="color_2" stroke-width="1.25"/>
+          </style>
+        </listOfStyles>
+      </renderInformation>
+      <nwt:mapProperties 
+        xmlns:nwt="https://newteditor.org/">
+        <compoundPadding>0</compoundPadding>
+        <extraCompartmentPadding>14</extraCompartmentPadding>
+        <extraComplexPadding>10</extraComplexPadding>
+        <arrowScale>1.25</arrowScale>
+        <showComplexName>true</showComplexName>
+        <dynamicLabelSize>regular</dynamicLabelSize>
+        <inferNestingOnLoad>false</inferNestingOnLoad>
+        <fitLabelsToNodes>false</fitLabelsToNodes>
+        <fitLabelsToInfoboxes>false</fitLabelsToInfoboxes>
+        <recalculateLayoutOnComplexityManagement>true</recalculateLayoutOnComplexityManagement>
+        <rearrangeOnComplexityManagement>true</rearrangeOnComplexityManagement>
+        <animateOnDrawingChanges>true</animateOnDrawingChanges>
+        <adjustNodeLabelFontSizeAutomatically>false</adjustNodeLabelFontSizeAutomatically>
+        <enablePorts>true</enablePorts>
+        <enableSIFTopologyGrouping>false</enableSIFTopologyGrouping>
+        <allowCompoundNodeResize>true</allowCompoundNodeResize>
+        <mapColorScheme>opposed_red_blue</mapColorScheme>
+        <mapColorSchemeStyle>solid</mapColorSchemeStyle>
+        <mapName>PTK6 Activates STAT3</mapName>
+        <mapDescription/>
+        <highlightColor>#0B9BCD</highlightColor>
+        <extraHighlightThickness>2</extraHighlightThickness>
+        <mapPD2AFConverted>false</mapPD2AFConverted>
+      </nwt:mapProperties>
+    </extension>
+    <glyph id="comp_0" class="compartment">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
+          <w>340.90775759776295</w>
+          <h>181.31795863479397</h>
+          <minW>0</minW>
+          <minH>0</minH>
+          <WLBias>0</WLBias>
+          <WRBias>0</WRBias>
+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
+        </nwt:extraInfo>
+      </extension>
+      <label text="nucleoplasm"/>
+      <bbox x="393.4693689635838" y="313.7086568786726" w="368.90775759776295" h="209.31795863479397"/>
+    </glyph>
+    <glyph id="species_5" class="complex sbml" compartmentRef="comp_0">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
+          <w>73.25</w>
+          <h>43.25</h>
+          <minW>0</minW>
+          <minH>0</minH>
+          <WLBias>0</WLBias>
+          <WRBias>0</WRBias>
+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
+        </nwt:extraInfo>
+      </extension>
+      <label text="2x(p-Y705-STAT3)"/>
+      <bbox x="470.77766839463106" y="329.3336568786726" w="93.25" h="63.25"/>
+    </glyph>
+    <glyph id="species_2" class="protein" compartmentRef="species_5">
+      <label text="STAT3"/>
+      <bbox x="482.40266839463106" y="340.9586568786726" w="70" h="40"/>
+    </glyph>
+    <glyph id="species_9" class="complex sbml" compartmentRef="comp_0">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
+          <w>73.25</w>
+          <h>96.5</h>
+          <minW>0</minW>
+          <minH>0</minH>
+          <WLBias>0</WLBias>
+          <WRBias>0</WRBias>
+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
+        </nwt:extraInfo>
+      </extension>
+      <label text="p-Y705-STAT3 dimer:SOCS3 Gene"/>
+      <bbox x="653.5021265613468" y="356.68458029630256" w="93.25" h="116.5"/>
+    </glyph>
+    <glyph id="species_11" class="protein" compartmentRef="species_9">
+      <label text="STAT3"/>
+      <bbox x="665.1271265613468" y="368.30958029630256" w="70" h="40"/>
+    </glyph>
+    <glyph id="species_19" class="gene" compartmentRef="species_9">
+      <label text="SOCS3"/>
+      <bbox x="665.1271265613468" y="421.55958029630256" w="70" h="40"/>
+    </glyph>
+    <glyph id="species_23" class="gene" compartmentRef="comp_0">
+      <label text="SOCS3"/>
+      <bbox x="559.738601776424" y="413.1439052985688" w="70" h="40"/>
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+    <glyph id="SbmlReactionExporter_3" class="process" compartmentRef="comp_0">
+      <bbox x="604.943166799554" y="364.1978084656806" w="14.285714285714286" h="14.285714285714286"/>
+      <port id="SbmlReactionExporter_3.1" x="622.0860239424111" y="371.3406656085378"/>
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+    <glyph id="comp_1" class="compartment">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
+          <w>758.2389330850008</w>
+          <h>383.95044206415537</h>
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+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
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+      <label text="cytosol"/>
+      <bbox x="-98.60482278220866" y="559.6056279798092" w="786.2389330850008" h="411.95044206415537"/>
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+      <label text="STAT3"/>
+      <bbox x="165.80062768286336" y="685.4993460084221" w="70" h="40"/>
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+    <glyph id="species_4" class="simple molecule" compartmentRef="comp_1">
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+    <glyph id="species_6" class="complex sbml" compartmentRef="comp_1">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
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+          <h>96.5</h>
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+    <glyph id="species_8" class="complex sbml" compartmentRef="comp_1">
+      <extension>
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+          xmlns:nwt="https://newteditor.org/">
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+          <h>43.25</h>
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+          <WRBias>0</WRBias>
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+          <HBBias>0</HBBias>
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+      </extension>
+      <label text="2x(p-Y705-STAT3)"/>
+      <bbox x="330.8885275419173" y="575.2306279798092" w="93.25" h="63.25"/>
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+    <glyph id="species_0" class="protein" compartmentRef="species_8">
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+    <glyph id="species_13" class="complex sbml" compartmentRef="comp_1">
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+          <HTBias>0</HTBias>
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+      <label text="p-Y342-BRK:p-Y250-STAP2"/>
+      <bbox x="63.32736771142572" y="839.4310700439646" w="93.25" h="116.5"/>
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+    <glyph id="species_26" class="complex sbml" compartmentRef="comp_1">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
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+          <h>96.5</h>
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+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
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+      <label text="p-Y342-BRK:SOCS3"/>
+      <bbox x="476.3396591018161" y="590.5877504654816" w="93.25" h="116.5"/>
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+      <label text="PTK6"/>
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+      <label text="SOCS3"/>
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+    <glyph id="species_27" class="complex sbml" compartmentRef="comp_1">
+      <extension>
+        <nwt:extraInfo 
+          xmlns:nwt="https://newteditor.org/">
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+          <h>96.5</h>
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+          <HTBias>0</HTBias>
+          <HBBias>0</HBBias>
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+      <label text="p-Y342-PTK6:STAP2"/>
+      <bbox x="261.6224811690078" y="823.2657960969696" w="93.25" h="116.5"/>
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diff --git a/app/samples/pharmacokinetics_of_PFOA_and_PFOS_in_the_monkey.nwt b/app/samples/pharmacokinetics_of_PFOA_and_PFOS_in_the_monkey.nwt
index 61abfa1c..3480b6db 100644
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diff --git a/index.html b/index.html
index 0e7099ea..7c1e9824 100644
--- a/index.html
+++ b/index.html
@@ -127,20 +127,19 @@
                       </li>
                       <li class="divider" style="margin-top: 0"></li>
                       <li>
-                        <a href="#" id="load-sample21">Interaction topologies of MAPK cascade
-                          (M1_K2_PSEQ)</a>
+                        <a href="#" id="load-sample21">RUNX1 regulates transcription of genes in WNT signaling</a>
                       </li>
                       <li>
-                        <a href="#" id="load-sample22">Pharmacokinetics of PFOA and PFOS in the monkey
+                        <a href="#" id="load-sample22">PTK6 activates STAT3
                         </a>
                       </li>
                       <li>
-                        <a href="#" id="load-sample23">Apoptotic Reaction Model
+                        <a href="#" id="load-sample23">Pharmacokinetics of PFOA and PFOS in the monkey
                         </a>
                       </li>
                       <li>
                         <a href="#" id="load-sample24">
-                          Insulin induced signalling (PFKL phosphorylation)</a>
+                          Interaction topologies of MAPK cascade (M1_K2_PSEQ)</a>
                       </li>
                     </ul>
                   </li>