Policy Document
 
DATABASES
SUBMISSIONS
NEWS

 

Site requirements

 
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Manipulating and editing the display

Moving the eBURST diagram:

Left clicking on a blank area of the java applet window and moving the mouse allows the diagram to be dragged around the screen. Where there are multiple unlinked clusters, clicking within an individual cluster produces a green rectangle around it and the mouse can be used to drag that individual cluster around the screen. If you have difficulty selecting a clonal complex, you can click on any line between two of the STs in the complex (the line goes green), and then left clicking allows the whole complex to be moved. Clicking on a line also allows pairs or triplets (etc) of STs to be moved together Clicking in an area outside (or between) the clusters allows you to return to the default where the mouse drags the whole diagram around the screen.

Horizontal and vertical expansion:

Holding down the ‘Alt’ key, left clicking and moving the mouse allows the diagram to be expanded or contracted in the up-down and left-right dimensions. This can also be used to change the shape of individual selected clonal complexes in diagrams that contain multiple complexes. This is useful as sometimes autoediting produced elliptical diagrams which can be made circular using this editing feature.

Rotating and zooming:

Holding down the shift key, left clicking and moving the mouse allows the diagram to be re-sized and rotated. Individual clonal complexes can be selected and individually resized and rotated. Selecting a subgroup founder by clicking on it (making it green), and then shift-left clicking, allows the whole subgroup to be moved and zoomed. You can always return to the original diagram by clicking on ‘draw’.

You need to play with this for a while, and being under 30, with experience of PS2 games, or a flight simulator probably helps.

Manual editing the eBURST diagram:

eBURST v2 automatically optimises the arrangement of STs (auto-editing) and produces eBURST diagrams that need minimal editing. However, the manual editing features of eBURST v1 are retained and, where necessary, can convert the initial auto-edited eBURST diagram into an optimal eBURST diagram for use in a publication or a Powerpoint presentation.

Moving STs:

To move an ST, first click on the circle representing the ST, and a green square appears around the circle to show it has been selected (you may have to move the mouse around slightly to find exacting the right place to click). The selected ST can then be dragged to the required position by moving the mouse. Where there are linked STs that need to be re-positioned, dragging an external ST will move only that ST, whereas dragging an internal ST will move the whole group of linked STs. This prevents the linkages between STs being inadvertently altered while editing the diagram. All of the STs in a subgroup can now be moved together (see also Rotating and Zooming above).

Highlighting connections between STs:

Clicking on a line between STs highlights the connecting line in green.

Options:

The ‘Options’ button opens a new panel which allows changes of the line thickness, font and font sizes, colours of lines or of group and subgroup founders etc.

Removing ST labels:

In the ‘Options’ panel, the ST labels can be removed by setting the text font size to zero.

Saving text output and eBURST diagrams:

The edited eBURST diagram, or the text output of eBURST groups and bootstraps, can be saved to a file and then printed. Diagrams are saved as .png graphics files and should open in a simple photo editor (e.g. Windows Photo Editor). Text is saved as a .txt file and will open in a text editor (e.g. notepad). If you add no extension they will automatically be saved as .png or .txt.

Obtaining more information about groups or STs:

Further information can be obtained about the STs from within an eBURST diagram. The ST of interest should be selected by clicking on it until it becomes green. Then clicking the ‘database’ button in the ‘Diagram Panel’ will open a new panel with the selected ST number already entered. Isolates of the selected ST within the MLST database are returned as the default. Ticking the ‘+ SLVs’ box returns details of the selected ST and all of its SLVs. Obviously linking from the eBURST diagram to a MLST database only works for data submitted to the applet from an MLST database.

Highlighting all SLVs and DLVs of a ST:

Shift and clicking on a ST shows lines from the selected ST to all of its SLVs (pink lines) and DLVs (blue lines). Repeating this process removed these lines. Several STs can be selected in turn to show the SLVs and DLVs of multiple STs. Shift and clicking on a link (line) between two STs shows the SLVs and DLVs of both of the linked STs. Shift and clicking within a clonal complex shows all of the SLVs and DLVs of all of the STs within the clonal complexes. Shift and clicking on an empty area of the diagram shows all of the SLV and DLV links of all of the STs. If you are having difficulties selecting what you want, you can first click on the ST, line, clonal complex, to activate it (make it green), and then press shift and click on it again. These are all toggles and so repeating the process removes the lines. Hint – you can always remove all the lines if you press ‘draw’ to refresh the diagram.

Re-assigning the primary founder:

Click/highlight the ST you wish to assign as the primary founder and then click ‘Founder’ in the ‘Diagram Panel’. The new auto-edited eBURST diagram is drawn, with the user-defined primary founder’ in red, to show that you, rather than eBURST, have made this assignment of the primary founder. Note that the number of SLVs linked to the selected primary founder may well increase considerably (compared to the original eBURST diagram) as all its SLVs will now be preferentially assigned to the new ‘founder’.