updated starter pathway titles, update instructions, update titles fo…

…r stages
wikipathways · Aug 3, 2023 · 37701cd · 37701cd
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diff --git a/data/WP3966.gpml → data/draw-catalysis-start.gpml b/data/WP3966.gpml → data/draw-catalysis-start.gpml
diff --git a/data/WP3910.gpml → data/draw-complex-start.gpml b/data/WP3910.gpml → data/draw-complex-start.gpml
diff --git a/data/WP3905.gpml → data/met-1-first-start.gpml b/data/WP3905.gpml → data/met-1-first-start.gpml
diff --git a/data/WP3909.gpml → data/met-1-indirect-start.gpml b/data/WP3909.gpml → data/met-1-indirect-start.gpml
diff --git a/data/WP3907.gpml → data/met-1-last-start.gpml b/data/WP3907.gpml → data/met-1-last-start.gpml
diff --git a/data/WP3908.gpml → data/met-1-second-start.gpml b/data/WP3908.gpml → data/met-1-second-start.gpml
diff --git a/stages/draw-catalysis/index.html b/stages/draw-catalysis/index.html
@@ -32,7 +32,7 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
           <h1>
             <a id="intro" class="anchor" href="#intro" aria-hidden="true">
               <span aria-hidden="true" class="octicon octicon-link">
-                Draw Catalysis
+                Draw a Catalysis Reaction
               </span>
             </a>
           </h1>
@@ -46,6 +46,7 @@ <h2>Background</h2>
           <h2>Your Mission</h2>
           <p>Draw the <b>catalysis reaction</b> depicted in this figure:</p>
           <img src="draw-catalysis-solution.png" width="350px">
+            <br />
 	  <p>This reaction is described in many publications. For our example, we will use the publication from <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3121847/" target=_blank>Strushkevich et al.</a>
 		which includes the following sentence:</p>
 		  <blockquote>"The first step in steroid hormone biosynthesis is the <b>conversion</b> of <b>cholesterol</b> to <b>pregnenolone</b> and isocaproic aldehyde by mitochondrial <b>CYP11A1</b>."</blockquote>
@@ -60,7 +61,7 @@ <h2>Your Mission</h2>
           <br>
 
           <ul>
-            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/WP3966.gpml">WP3966</a>. This starter pathway already contains the metabolite Data Nodes, and the conversion interaction between them.</li>
+            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/draw-catalysis-start.gpml">draw-catalysis-start.gpml</a>. This starter pathway already contains the metabolite Data Nodes, and the conversion interaction between them.</li>
             <li>Launch PathVisio and open the dowloaded file via <b>File > Open</b>.</li>
 		    <li>Select <b>GeneProduct</b> from the <b>Data Node</b> palette in the <b>Objects</b> tab.</li>
                 <li>Click on the canvas to place the node.</li>
@@ -74,7 +75,7 @@ <h2>Your Mission</h2>
                 <li>(Optional) Align nodes using toolbar actions.</li>
                 <li>Done!</li>
             <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
 
           <div id="upload-target-container"></div>  

diff --git a/stages/draw-complex/index.html b/stages/draw-complex/index.html
@@ -32,7 +32,7 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
           <h1>
             <a id="intro" class="anchor" href="#intro" aria-hidden="true">
               <span aria-hidden="true" class="octicon octicon-link">
-                Draw a Complex
+                Draw a Protein Complex
               </span>
             </a>
           </h1>
@@ -50,14 +50,14 @@ <h2>Your Mission</h2>
             <br>
 
           <ul>
-        <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/WP3910.gpml">WP3910</a>.</li>
+        <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/draw-complex-start.gpml">draw-complex-start.gpml</a>.</li>
             <li>Launch PathVisio and open the dowloaded file via <b>File > Open</b>.</li>		  
                 <li>Select the two data nodes by click-and-drag.</li>
 		<li>Click the <b>Stack vertical centers</b> button <img src="../../images/stack-vertical.png"> from the toolbar.</li>
 		<li>With the two data nodes selected, right-click and select <b>Create complex</b>.</li>
                 <li>Done!</li>
             <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
 
           <div id="upload-target-container"></div>  

diff --git a/stages/draw-conversion/index.html b/stages/draw-conversion/index.html
@@ -32,7 +32,7 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
           <h1>
             <a id="intro" class="anchor" href="#intro" aria-hidden="true">
               <span aria-hidden="true" class="octicon octicon-link">
-                Draw a Conversion
+                Draw a Conversion Reaction
               </span>
             </a>
           </h1>
@@ -41,7 +41,7 @@ <h2>Background</h2>
 
           <p>The conversion of one metabolite into another comprises the fundamental biological process of <a href="https://en.wikipedia.org/wiki/Metabolism" target="_blank">metabolism</a>. 
 		  Often catalyzed by enzymes and chained together in a series, each conversion reaction involves a change in the chemical structure of a metabolite or small molecule. 
-		  Conversion reactions are thus drawn as <b>two metabolites and a mim-conversion interaction</b>, pointing from the subtrate to the product. <a href="https://discover.nci.nih.gov/mim/">MIM</a> 
+		  Conversion reactions are thus drawn as <b>two metabolites and a mim-conversion interaction</b>, pointing from the substrate to the product. <a href="https://discover.nci.nih.gov/mim/">MIM</a> 
 		  is a diagram convention that includes specific notations for interactions, which are included in WikiPathways. Since their meaning is specific, they should be used only in specific circumstances, 
 		  as in this case, for a conversion between two metabolites.</p>
 		<p>Note that for the example below, we are <b>only</b> modeling part of the full reaction; we are excluding the enzyme that catalyses the reaction. The next step will show
@@ -56,22 +56,23 @@ <h2>Your Mission</h2>
 		<li>Launch PathVisio and select <b>File > New</b> to start a new pathway. Close the <b>Pathway attributes</b> dialog.</li>
 		<li>In the upper left of the canvas, the <b>Pathway Information</b> area will be displayed, and will say "Title: New Pathway". Select this by clicking on it, and in the <b>Properties</b> tab select "Homo sapiens" in the <b>Species</b> menu.
 		<li>Select <b>Metabolite</b> from the <b>Data Node</b> palette in the <b>Objects</b> tab.</li>
-                <li>Click on the canvas to place the node.</li>
-                <li>Double-click on the node to open its properties.</li>
+        <li>Click on the canvas to place the node.</li>
+        <li>Double-click on the node to open its properties.</li>
 		<li>Search for “glucose”; Choose any of the entries that just say “glucose”; Click <b>OK</b> to select the identifier, and then click <b>OK</b> again to close the node properties window.</li>
-                <li>Repeat these steps to make the “glucose 6-phosphate” metabolite node. Note that searching for exact matches of metabolite names can be tricky, as some databases
+        <li>Repeat these steps to add the “glucose 6-phosphate” metabolite node. Note that searching for exact matches of metabolite names can be tricky, as some databases
 		      might use the name "glucose 6-phosphate", while others use "glucose-6-phosphate". </li>
 		<li>Select the <b>mim-conversion</b> arrow from the <b>MIM interactions</b> palette in the <b>Objects</b> tab: <img src="../../images/mim-conversion-glyph.png"></li>
-                <li>Click anywhere on the canvas to create the interaction.</li>
-                <li>Drag each end of the interaction over a target area on each node (highlighted in green on hover); Note source vs target. The video below shows how to attach the ends of the interaction to the nodes.<br />
+        <li>Click anywhere on the canvas to create the interaction.</li>
+        <li>Drag each end of the interaction over a target area on each node (highlighted in green on hover) to connect the interaction to the node, noting source vs target. The video below shows how to attach the ends of the interaction to the nodes.<br /><br />
 		      <video controls="controls" name="Connect Interactions" width="250">
   			<source src="ConnectInteractionsPV.mov">
 			</video></li>
-                <li>(Optional) Align nodes using toolbar actions. To align nodes, select them both, then click the <b>Align horizontal centers</b> button
+              <br />
+        <li>(Optional) Align nodes using toolbar actions. To align nodes, select them both, then click the <b>Align horizontal centers</b> button
 		      <img src="align-horizontal.png"> from the toolbar.</li>
                 <li>Done!</li>
-            <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+        <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
+        <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
 
           <div id="upload-target-container"></div>  

diff --git a/stages/draw-geneproduct/index.html b/stages/draw-geneproduct/index.html
@@ -53,12 +53,12 @@ <h2>Your Mission</h2>
 			  by clicking on it, and in the <b>Properties</b> tab select "Homo sapiens" in the <b>Species</b> menu.
 		<li>Select <b>GeneProduct</b> from the <b>Data Node</b> palette in the <b>Objects</b> tab.</li>
                 <li>Click on the canvas to place the node.</li>
-                <li>Double-click on the node to open its properties.</li>
+                <li>Double-click on the node to open the <b>DataNode properties</b> dialog.</li>
                 <li>Search for “ACO2”; Choose any of the entries that just say “ACO2”. In terms of choosing which identifier system to use, we recommend the following priority order: Ensembl, Entrez, other systems.</li> 
 		<li>Click <b>OK</b> to select the identifier, and then click <b>OK</b> again to close the node properties window.</li>
                 <li>Done!</li>
             <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
 
           <div id="upload-target-container"></div>  

diff --git a/stages/draw-metabolite/index.html b/stages/draw-metabolite/index.html
@@ -48,7 +48,7 @@ <h2>Your Mission</h2>
 
 
           <ul>
-		  <li>Launch PathVisio and select <b>File > New</b> to start a new pathway. Close the Pathway attributes dialog.</li>
+		  <li>Launch PathVisio and select <b>File > New</b> to start a new pathway. Close the <b>Pathway attributes</b> dialog.</li>
 		  <li>In the upper left of the canvas, the <b>Pathway Information</b> area will be displayed, and will say "Title: New Pathway". Select this
 			  by clicking on it, and in the <b>Properties</b> tab select "Homo sapiens" in the <b>Species</b> menu.
 		      <li>Select <b>Metabolite</b> from the <b>Data Node</b> palette in the <b>Objects</b> tab.</li>
@@ -58,7 +58,7 @@ <h2>Your Mission</h2>
 			Click <b>OK</b> to select the identifier, and then click <b>OK</b> again to close the node properties window.</li>
                 <li>Done!</li>
             <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
 
           <div id="upload-target-container"></div>  

diff --git a/stages/met-1-first/index.html b/stages/met-1-first/index.html
@@ -32,15 +32,15 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
           <h1>
             <a id="intro" class="anchor" href="#intro" aria-hidden="true">
               <span aria-hidden="true" class="octicon octicon-link">
-                My First Metabolic Pathway - Cholesterol conversion
+                My First Metabolic Pathway - First Catalysis
               </span>
             </a>
           </h1>
 
           <h2>Background</h2>
 
           <p>Because of the importance of cholesterol, all animal cells are able to synthesize it. The cholesterol biosynthesis starts 
-          with Acetyl-CoA.</p>
+          with the cataluzed conversion of Acetyl-CoA into HMG-CoA.</p>
 
           <h2>Your Mission</h2>
           <p>Complete the first step of the cholesterol biosynthesis pathway, the conversion of Acetyl-CoA to HMG-CoA, catalyzed by 
@@ -49,7 +49,7 @@ <h2>Your Mission</h2>
           <br><br>
 
           <ul>
-            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/WP3905.gpml">WP3905</a>.</li>	
+            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/met-1-first-start.gpml">met-1-first-start.gpml</a>.</li>	
 	        <li>Launch PathVisio and open the dowloaded file via <b>File > Open</b>. The two metabolites, Acetyl-CoA and HMG-CoA, and the conversion between them have already been added. You will be adding the enzyme and the catalysis interaction.</li>
           <ul>
 		<h4>Add the enzyme</h4>
@@ -68,42 +68,8 @@ <h4>Add and connect the catalysis arrow</h4>
                 <li>Done!</li>
               </ul>
             <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to to check if it is correct.</li>
           </ul>
-	  <!--
-          <form style="padding:0px; background:none;">
-                  <input type="hidden" name="wpidload" value="WP3905">
-          </form>
-          <button id="download-from-page" type="button" class="btn btn-primary btn-lg" style="display:none;">Launch Editor</button>
-          -->
-          <!-- Button trigger modal -->
-	  <!--	
-          <button id="launch-modal" type="button" class="btn btn-primary btn-lg" data-toggle="modal" data-target="#myModal">
-            Launch Editor
-          </button>
-          -->
-
-          <!-- Modal -->
-	<!--
-          <div class="modal fade" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel">
-            <div class="modal-dialog" role="document">
-              <div class="modal-content">
-                <div class="modal-header">
-                  <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                  <h4 class="modal-title" id="myModalLabel"></h4>
-                </div>
-                <div class="modal-body">
-                  <img src="../../images/jnlp-instructions.png">
-                </div>
-                <div class="modal-footer">
-                  <label><input type="checkbox" id="dont-show-instructions" value="first_checkbox"> Don't show instructions again </label>
-                  <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-                  <button id="download-from-modal" type="button" class="btn btn-primary" data-dismiss="modal">Download</button>
-                </div>
-              </div>
-            </div>
-          </div>  
-	-->
 
           <div id="upload-target-container"></div>  
 	  <div id="next-button">

diff --git a/stages/met-1-indirect/index.html b/stages/met-1-indirect/index.html
@@ -32,7 +32,7 @@ <h2>Organized training challenges for new WikiPathways authors</h2>
           <h1>
             <a id="intro" class="anchor" href="#intro" aria-hidden="true">
               <span aria-hidden="true" class="octicon octicon-link">
-                My First Metabolic Pathway - Indirect steps
+                My First Metabolic Pathway - Indirect Steps
               </span>
             </a>
           </h1>
@@ -51,7 +51,7 @@ <h2>Your Mission</h2>
           <br><br>
 
           <ul>
-            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/WP3909.gpml">WP3909</a>.</li>	
+            <li>Download the starter pathway here: <a href="https://academy.wikipathways.org/data/met-1-indirect-start.gpml">met-1-indirect-start.gpml</a>.</li>	
             <li>Launch PathVisio and open the dowloaded file via <b>File > Open</b>.</li>
             <ul>
 		<h4>Add the metabolite</h4>
@@ -85,42 +85,8 @@ <h4>Add and connect the catalysis arrow</h4>
                 <li>Done!</li>
               </ul>
               <li>Save your work as a GPML file under <b>File > Save As</b>.</li>
-            <li>Drag-and-drop the GPML file below to submit.</li>
+            <li>Drag-and-drop the GPML file below to check if it is correct.</li>
           </ul>
-		<!--
-          <form style="padding:0px; background:none;">
-                  <input type="hidden" name="wpidload" value="WP3909">
-          </form>
-          <button id="download-from-page" type="button" class="btn btn-primary btn-lg" style="display:none;">Launch Editor</button>
--->
-	  <!-- Button trigger modal -->
-		<!--
-          <button id="launch-modal" type="button" class="btn btn-primary btn-lg" data-toggle="modal" data-target="#myModal">
-            Launch Editor
-          </button>
--->
-
-          <!-- Modal -->
-<!--
-          <div class="modal fade" id="myModal" tabindex="-1" role="dialog" aria-labelledby="myModalLabel">
-            <div class="modal-dialog" role="document">
-              <div class="modal-content">
-                <div class="modal-header">
-                  <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
-                  <h4 class="modal-title" id="myModalLabel"></h4>
-                </div>
-                <div class="modal-body">
-                  <img src="../../images/jnlp-instructions.png">
-                </div>
-                <div class="modal-footer">
-                  <label><input type="checkbox" id="dont-show-instructions" value="first_checkbox"> Don't show instructions again </label>
-                  <button type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
-                  <button id="download-from-modal" type="button" class="btn btn-primary" data-dismiss="modal">Download</button>
-                </div>
-              </div>
-            </div>
-          </div>  
--->
 
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 	  <div id="next-button">