General Function Checklist

Default Data Providers

In IGB, select Select File -> Preferences -> Data Sources tab .Check that the Default DataProviders

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

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• .

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

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Confirm that clicking on a [i] Click on the icon in the rightmost 'information' column of the Data Sources window above opens a window 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 window and opening another shows correctly updated information

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

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Open the A_thaliana_Jun_2009

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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_

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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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In the human genome




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1. Navigate to chr1:45,691,287-45,691,329

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2. Click

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1. Load Sequence

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1. . 

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

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Adding/Removing/Editing Data Providers

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1. Select File -> Preferences -> Data

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1. Sources tab.
2. Click

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1. Add...

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1.  
   1. Name: myQuickload
   2. Type: Quickload
   3. URL:

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1. 1. http://www.igbquickload.org/quickload/

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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.

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1. Select File -> Preferences -> Data

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1. Sources tab.

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• myQuickload is still

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• present in the Data Sources table.

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Select myQuickload

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and click Edit...Confirm that the Edit... button opens a new window and allows a user to modify the data source URL or to choose a local folder

• 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

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1. myQuickloadv2.
2. Click Remove...

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• 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

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Quickload sites:

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

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1. 1. . A prompt should appear asking for a username and password:
      1. Username: guest
      2. Password: guest

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1. 1. 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

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1. 1. . A prompt should appear asking for a username and password: 
      1. Username:

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1. 1. 1. guest2
      2. Password: guest2

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1. 1. 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

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• or red

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Close Preferences and open the A_thaliana_Jun_2009 genome

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.Confirm the two sites (secure1 and secure2)

• The two secured Quickloads are listed in the

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• Available Data

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• 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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