General Function Checklist

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Default Data Providers

Select File -> Preferences -> Data Sources tab.

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

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• Data Sources table.

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• Observation:  The table lists several Quickload sites. (They may be different from those shown below.) If any are shown with a red background, that means that there is a problem with the site - IGB can't reach it. This is a bug and should be reported.

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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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Confirm that closing


Close this information window and opening another shows correctly updated information

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Confirm that the information window functions for each data source type , 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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Confirm the following species / genome versions are available 

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Open the A_thaliana_Jun_

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2009 genome.

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

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Homo Sapiens/
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Open the H_sapiens_Dec_

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2013 genome.

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

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• Important:

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• The Cytobands track is visible

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1. Navigate to chr1:45,

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1. 691,

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1. 287-45,

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1. 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

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Add a quickload data provider and confirm it is working as expected

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Data Providers

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

Enter a name for this quickload site and click the "Submit" buttonObservations:

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1. Click Submit.
2. 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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Confirm restarting IGB does not cause the newly added site to be forgotten


Click Choose local folder.

• The user's file chooser opens correctly.
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Ensure that the edit button in the Data Sources window opens a new window and allows a user to modify the data source URL or to choose a local folder. Note that default data sources cannot be modified. 


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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 Ensure that data sources can be deleted using the Remove button in the Data Sources window


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

Add a few "Secured" quickload sites and confirm they are working as expected

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

1. Name: secure1
2. Type: Quickload
3. URL: http://igbquickload.org/secureQuickloadTestSites/secureSiteTest

   username/password 

   • • • guest/guest

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   1. 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

       

      username/password

      • • • guest2/guest2
      1. 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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      Navigate to the Arabidopsis thaliana
      

      Close Preferences and open the A_thaliana_Jun_2009 genome version.Confirm the

      • The two

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      • secured Quickloads are listed in the

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      • 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

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      • either of the secured Quickloads.
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      Confirm restarting IGB does not cause the newly added sites to be forgotten
      

      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

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      • for either of the secured Quickloads upon restarting IGB.
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