General Function Checklist

Default Data Providers

Select File -> Preferences -> Data Sources tab.

• Default data providers (e.g., RNA-Seq, ChIP-Seq, DNA-Seq, etc.) appear in the Data Sources table.

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• None of the rows have a red or yellow background.

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Click on the icon in the Information column for RNA-Seq.

• A window opened with fields and values similar to the example below:

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• The data listed in the Value column are specific to the RNA-Seq data source.

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Close this information window, then click on the icon for UCSC.

• The data listed in the Value column updated appropriately and are specific to the UCSC data source.

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Open the A_thaliana_Jun_2009 genome.

• Several Quickloads are present in the Available Data section (they may be different from those shown below).

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Open the H_sapiens_Dec_2013 genome.

• Several Quickloads are present in the Available Data section (they may be different from those shown below).

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• Important: The Cytobands track is visible

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1. Navigate to chr1:45,691,287-45,691,329
2. Click Load Sequence. 

• Individual base pairs (ACGT) are visible and colored consistently along the coordinates track.

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Adding/Removing/Editing Data Providers

1. Select File -> Preferences -> Data Sources tab.
2. Click Add... 
   1. Name: myQuickload
   2. Type: Quickload
   3. URL: http://www.igbquickload.org/quickload/
3. Click Submit.
4. Close Preferences.

• myQuickload is present in the Available Data section

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1. Close and re-open IGB.
2. Select File -> Preferences -> Data Sources tab.

• myQuickload is still present in the Data Sources table.

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Select myQuickload and click Edit...

• The Edit Data Source window opened.

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Click Choose local folder.

• The user's file chooser opens correctly.

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Change the Name of myQuickload to myQuickloadv2, then click Save Changes.

• The name of myQuickload correctly updated to myQuickloadv2 in both the Data Sources table and the Available Data section.

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1. Select myQuickloadv2.
2. Click Remove...

• The myQuickloadv2 data source was removed from both the Data Sources table and the Available Data section.

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Secured Data Providers

Click Add... and add the following two Quickload sites:

1. Name: secure1
2. Type: Quickload
3. URL: http://igbquickload.org/secureQuickloadTestSites/secureSiteTest
   1. Click Submit. A prompt should appear asking for a username and password:
      1. Username: guest
      2. Password: guest
   2. Make sure Save Password is checked, then click OK.

1. Name: secure2
2. Type: Quickload
3. URL: http://igbquickload.org/secureQuickloadTestSites/secureSiteTest2
   1. Click Submit. A prompt should appear asking for a username and password: 
      1. Username: guest2
      2. Password: guest2
   2. Make sure Save Password is checked, then click OK.

• The two secured Quickloads are added to the Data Sources table and are not highlighted yellow or red.

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Close Preferences and open the A_thaliana_Jun_2009 genome.

• The two secured Quickloads are listed in the Available Data section. 

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1. Add the TAIR10 mRNA data from the secure1 Quickload.
2. Add the TDNA insertion lines data from the secure2 Quickload.
3. Go to Chr1:7,404,452-7,520,146
4. Click Load Data.

• Data loaded from both of the secured Quickloads.

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• You were not prompted for a password for either of the secured Quickloads.

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Restart IGB and open the A_thaliana_Jun_2009 genome.

• The two secured Quickloads are still listed in the Available Data section.

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• You were not prompted for your password again for either of the secured Quickloads upon restarting IGB.

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