Using Active Objects Inspector

Step 1: Introduction

This tutorial describes the abilities of Active Objects Inspector and demonstrates several typical scenarios of its usage.

It is recommended that you complete Basic Operation tutorial first.

Step 2: Getting Started

Open Genome Workbench, open the Active Object Inspector (View=>Active Objects Inspector), and land it in the right lower corner.

Step 3: Load a molecule

Click Open command from the File drop-down menu (File=>Open) and select Data from GenBank in the dialog. Type in the "NC_000001" accession.

Click Next and Finish in the next screens. The molecule will be shown in the Project tree.

Step 3: Open the molecule in Graphical Sequence View

Right-click the molecule and select Open New View in the pop-up menu. Select the Graphical Sequence View option in the next screen. The system will open the molecule in Graphical Sequence View. Note: depending on your track configuration, you might see different set/order of tracks.

Step 4: Zoom in to any area

Right-click in a desired area and select the Zoom in command in the context menu or use Zoom in icon on the upper panel or press and hold mouse wheel and drag vertically. Zoom to a desired level where you can clearly see objects of different types.

Step 5: Select various features

Select various features (genes, mRNAs, CDSs, tiling path components) by using control + click.

Step 6: Select a range

Use mouse (ruler area) to select a range.

Step 7: Selections shown

Selections for the current (active) view are now shown in the Active Objects Inspector window.

Step 8: Explore different modes

Active Objects Inspector has different view modes. Currently selections are shown in the Table mode where you can see the Type/Subtype of the selections and description. Please note, that additionally to the selected objects Active Objects Inspector shows main molecule too.

Now select the Brief mode. This mode shows short description for all selections.

Select the Full mode. This mode shows full description in a form of GenBank records for every selected object (might be a bit slow if many objects selected). For the selected range it shows coordinates not only on the main molecule but also on Scaffold and component of the tiling path if available.

Active Object Inspector has option to show active/selected objects in the any opened view available. Use dropdown list to control what views are opened. If you have objects selected in different views and want to see them all as one list, you can choose All Views and will see all selected objects in all available views.

Step 9: Use context menu to Open New View

The Active Object Inspector can be used to specify targets for opening new views, running tools and data export. Let’s select new target NM_000699.4 in GSV, then highlight it in the Active Object Inspector view and perform right click to open context menu.

In the context menu, select the Open New View command to open the Open View dialog. Select the Graphical Sequence View option and click the Next button. Observe that the Open View - Graphical Sequence View dialog is showing all related selections, - two in this case: one is NM_000699.4 and another one is location of this feature on chromosome (location of NM_000699.4 on NC_000001). Note: Genome Workbench will always attempt to extract all appropriate context from any selection and offer them as an argument candidate for a view or a tool.

Let’s us select NM_00699.4 and click the Finish button. Picked up object is opened in the Graphical Sequence View:

Note: in case if we select chromosome location of this feature, GSV will open chromosome NC_000001 zoomed to the NM_00699.4 feature location.

Step 10: Use context menu to Run Tool

Now, let’s go back to our first Graphical View, and additionally to the previously selected feature (NM_00699.4), we select range (NC_000001:103,549,900-103,721,958), then use Control+click to select both active objects in Active Object Inspector view.

Note: it is also possible to select objects in the different views and use All Views option in the Active Object Inspector to open context menu for selected objects form different views.

Perform right-click in any of the selections to display context menu. Select the Run Tool option. The Run Tool menu will open. Select the SPLIGN tool and click the Next button.

Observe that the selected objects became available in the Run Tool Dialog. Select longest range for the genomic sequence and NM feature for cDMA/transcript sequence.

Accept default setting and click Finish. Observe that SPLIGN result is added to the Project view. To see them in the Graphical Sequence View you need to have Alignments tracks available in the view.

Step 11: Conclusion

Active Objects Inspector is a powerful mechanism to quickly make sets of objects and locations and run operations on it like open other views, run tools, export to files.