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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- Navigate to chr1:45,
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- 691,
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- 287-45,
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- 691,329
- 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
- Select File -> Preferences -> Data Sources tab.
- Click Add...
- Name: myQuickload
- Type: Quickload
- URL: http://www.igbquickload.org/
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Enter a name for this quickload site and click the "Submit" buttonObservations:
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- Click Submit.
- Close Preferences.
- myQuickload is present in the Available Data section
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- Close and re-open IGB.
- 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
- Select myQuickloadv2.
- 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:
- Name: secure1
- Type: Quickload
- URL: http://igbquickload.org/secureQuickloadTestSites/secureSiteTest
username/password
- guest/guest
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- Click Submit. A prompt should appear asking for a username and password:
- Username: guest
- Password: guest
- Make sure Save Password is checked, then click OK.
- Click Submit. A prompt should appear asking for a username and password:
- Name: secure2
- Type: Quickload
- URL: http://igbquickload.org/secureQuickloadTestSites/secureSiteTest2
username/password
- guest2/guest2
- Click Submit. A prompt should appear asking for a username and password:
- Username: guest2
- Password: guest2
- Make sure Save Password is checked, then click OK.
- Click Submit. A prompt should appear asking for a username and password:
- 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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- Add the TAIR10 mRNA data from the secure1 Quickload.
- Add the TDNA insertion lines data from the secure2 Quickload.
- Go to Chr1:7,404,452-7,520,146
- 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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