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Added a step about downloading DS models in the cheat sheet
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KlasJoensson committed Nov 9, 2012
1 parent 0b2a618 commit 0534b20
Showing 1 changed file with 18 additions and 7 deletions.
25 changes: 18 additions & 7 deletions plugins/net.bioclipse.ds.ui/cheatsheets/gettingstarted.xml
Expand Up @@ -21,7 +21,18 @@ In the top menu, select option <b>Window &gt; Open Perspective &gt; Other...</b>
serialization="org.eclipse.ui.perspectives.showPerspective(org.eclipse.ui.perspectives.showPerspective.perspectiveId=net.bioclipse.ds.ui.perspective)"/>
</item>
<item
title="Step 2: Open a chemical structure">
title="Step 2: Download DS models">
<description>
Before running any tests, one or several models needs to be downloaded. To do this choose <b>Install > DS Models...</b>, then select the wanted model(s) and
click <b>Finish</b>.<br/><br/>
To install the downloaded model(s) Bioclipse needs to be restarted.
</description>
<command
required="false"
serialization="net.bioclipse.ui.install.ShowRepositoryCatalog(org.eclipse.equinox.p2.ui.discovery.commands.RepositoryParameter=http://pele.farmbio.uu.se/bioclipse/dsmodels,net.bioclipse.ui.install.commands.RepositoryStrategyParameter=net.bioclipse.ui.install.discovery.DSModelsDiscoveryStrategy)"/>
</item>
<item
title="Step 3: Open a chemical structure">
<description>
In the Bioclipse Navigator, double-click a chemical structure to open it in the chemical editor. It is also possible to edit molecules.
</description>
Expand All @@ -35,7 +46,7 @@ In the top menu, select option <b>Window &gt; Open Perspective &gt; Other...</b>
/>
</item>
<item
title="Step 3: Run the Tests">
title="Step 4: Run the Tests">
<description>
The Tests can be run by right clicking in the Decision Support tab or by clicking the "Run all tests" button (with a 'play' icon) in the Decision Support View.
</description>
Expand All @@ -45,13 +56,13 @@ In the top menu, select option <b>Window &gt; Open Perspective &gt; Other...</b>
required="false"/>
</item>
<item
title="Step 4: Examine the Test results.">
title="Step 5: Examine the Test results.">
<description>
Each individual test can be examined by expanding it and selecting the results. If the test displays substructures, as for the Signature Significance, then the atoms that belongs to the substructure will be displayed in the chemical editor. Entire molecules will be displayed in the 2D viewer.
</description>
</item>
<item
title="Step 5: Generate a report">
title="Step 6: Generate a report">
<description>
By right clicking in the Decision Support tab it is possible to generate a Report. Note that it takes over 20 seconds to open the first report, while after this generating reports is much faster.
</description>
Expand All @@ -62,7 +73,7 @@ In the top menu, select option <b>Window &gt; Open Perspective &gt; Other...</b>
</item>

<item
title="Step 6: Open an SDFile">
title="Step 7: Open an SDFile">
<description>
In the Bioclipse Navigator, double-click an SDFile to open it in the MoleculesTable.
</description>
Expand All @@ -77,13 +88,13 @@ In the top menu, select option <b>Window &gt; Open Perspective &gt; Other...</b>
/-->
</item>
<item
title="Step 7: Calculate all tests and consensus">
title="Step 8: Calculate all tests and consensus">
<description>
Right-click in the MoleculesTable and select Decision Support > Consensus Classification
</description>
</item>
<item
title="Step 8: Switch between tabs in the Molecules Table">
title="Step 9: Switch between tabs in the Molecules Table">
<description>
Select one of the structures in the MoleculesTable and then click the tab <b>Single molecule</b> at the bottom of the editor. Here you can run individual tests, make changes to the molecule, and when you switch back to the tab <b>Molecules</b> the updated values are calculated in the background and the visualization is updated (just wait a few seconds for it to complete).
</description>
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