Merge pull request #1 from KlasJoenssson/UppdateCheatSheet

Update cheat sheet
bioclipse · Mar 13, 2012 · c68bb8b · c68bb8b
2 parents 26ee791 + 341466c
commit c68bb8b
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Showing 4 changed files with 16 additions and 17 deletions.
diff --git a/plugins/net.bioclipse.qsar.ui/cheatsheets/getting_started.xml b/plugins/net.bioclipse.qsar.ui/cheatsheets/getting_started.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <cheatsheet
-      title="Calculating CDK Properties">
+      title="Getting started with Bioclipse-QSAR">
    <intro>
       <description>
          This tutorial gives a brief introduction for working with the Bioclipse-QSAR functionality in Bioclipse.
@@ -11,7 +11,7 @@
          title="Step 1: Creating a QSAR Project">
       <description>
 
-			Go to menu <b>File > New... > Other</b> and create a new QSAR Project.
+			Go to menu <b>File > New... > QSAR</b> and create a new QSAR Project.
 
       </description>
       <command
@@ -23,11 +23,11 @@
          title="Step 2: Using the QSAR editor">
       <description>
 
-			Double-clicking on the file qsar.xml in the Navigator opens the QSAR Editor. 
-			This editor allows for the setup of daaset in a novel file format called QSAR-ML.<br/><br/>
+			Double-clicking on the file qsar.xml in your QSAR project-folder in the Navigator opens the QSAR Editor. 
+			This editor allows for the setup of dataset in a novel file format called QSAR-ML.<br/><br/>
 
 			The tabs at the bottom of the editor allows for specifying data and metadata for the 
-			qsar dataset.<br/><br/>
+			QSAR dataset.<br/><br/>
 
 			The tab <b>Information</b> allows for adding metadata about the dataset.<br/><br/>
 
@@ -42,9 +42,8 @@
 
 			The tab <b>Sources</b> displays the QSAR-ML source.<br/><br/>
 
-			Note that the dataset is built in the background when you save, 
-			if you have at least one structure and one descriptor chosen. The results are cached 
-			so it will not be calculated again if already calculated. 
+			Saving the file and then pressing the build-button, the gear with a green triangle in the bottom right corner, will calculate the values.
+			 The results are cached so it will not be calculated again if already calculated. 
 			The calculated values are saved in the QSAR-ML but also in a comma-separated 
 			file called <b>dataset.csv</b>.  <br/><br/>
 

diff --git a/plugins/net.bioclipse.qsar.ui/cheatsheets/qsar-r.xml b/plugins/net.bioclipse.qsar.ui/cheatsheets/qsar-r.xml
@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <cheatsheet
-      title="Accessing QSAR data from R">
-   <intro>
+      title="Using QSAR data in R<intro>
       <description>
          This tutorial demonstrates how to use R to analyze QSAR. Note that R is experimental and must be installed from the experimental update site before following this tutorial.
       </description>
@@ -10,8 +9,8 @@
          <item
          title="Step 1: Open the R Console">
       <description>
-			If you have R installed, you can access it directly from Bioclipse via the R-console. 
-			Reveal the R-console from the menu <b>Window > Show View > Other</b> and select <b>R Console</b> 
+			If you have R installed, then installing the Bioclipse-R Intergration feature let you  access R directly from Bioclipse via the R-console. 
+			Reveal the R-console from the menu <b>Window > Show View > Other</b> and select <b>R Console</b>. 
       </description>
       <command
             required="false"
@@ -25,7 +24,7 @@
 
 		Loading the dataset into R can be achieved by entering, in the R Console:<br/><br/>
 			         
-		<b>dataset=read.delim(file="myQsarProject/dataset.csv", sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>
+		<b>dataset &lt;- read.delim(file="myQsarProject/dataset.csv", sep=",", header=TRUE, row.names=1, na.strings="NaN")</b>
          
       </description>
       
@@ -37,7 +36,7 @@
       
       		Here is a simple example to demonstrate how the read file can be analyzed in R:<br/><br/>
 
-			<b>datasat=as.matrix(dataset)</b><br/><br/>
+			<b>dataset &lt;- as.matrix(dataset)</b><br/><br/>
 			<b>mod &lt;- lm(dataset[,1] ~ dataset[,2:ncol(dataset)], na.action=na.omit)</b><br/><br/>			
 			<b>plot(mod)</b><br/><br/>
          

diff --git a/plugins/net.bioclipse.qsar.ui/cheatsheets/scripting_qsar.xml b/plugins/net.bioclipse.qsar.ui/cheatsheets/scripting_qsar.xml
@@ -56,14 +56,15 @@
 
          <b>qsar.calculate(molecules, descriptors)</b><br/><br/>
 
-		The gist 95189 shows a script to demonstrate this.
+		The gist 95189 shows a script to demonstrate this. To run it; just save it as a JavaScript, 
+		e.g. as &qt;qsar-multi.js&qt;. Then open the file and run it.
 
       </description>
 
        <action
 			pluginId="net.bioclipse.scripting.ui"
 			class="net.bioclipse.scripting.ui.actions.ScriptAction"
-			param1="res=gist.download(95189,&quot;/Virtual/qsar-multi.js&quot;); ui.open(res); js.executeFile(res)"/>
+			param1="ui.open(gist.download(95189))"/>
 
    </item>
 

diff --git a/plugins/net.bioclipse.qsar.ui/plugin.xml b/plugins/net.bioclipse.qsar.ui/plugin.xml
@@ -157,7 +157,7 @@
             composite="false"
             contentFile="cheatsheets/qsar-r.xml"
             id="net.bioclipse.qsar.cheatsheet.qsar_r"
-            name="Accessing QSAR data from R"/>
+            name="Using QSAR data in R"/>
 
    </extension>
    <extension