Genome Browser Use Case: Access genome browser session via hyperlinks in an excel file

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Genome Browser Use Case: Access genome browser session via hyperlinks in an excel file

Users may would like to link chromosome coordinates in an excel spread sheet to omicsoft genome browser of particular project. This can be achived by 1) create a shared genome browser session; 2) create a http address and 3) incorporate the links to an excel spread sheet.

1. Create a shared genome browser session

1. Open a project that contains NGS data

2. Right click the NGS data and select New Genome Browser

CreateNewBrowser.jpg


3. Click Browser -> Share Browser

ShareBrowser0.jpg


4. Set browser session information.

Please note that the owner of the browser session may control the accessibility of the browser to different user(s) or user group(s) in Viewer(s) section.
For example, uncheck administrators box would remove the administrators from Viewers' list. 

ShareBrowser.jpg


5. Share the browser, and record the browser session ID

BrowserID.jpg


6. Owners of the browser may change the permission of the browser session by re-share the browser (i.e.: repeat step 3 and 4 above)

2. Create a http address for a particular location in the genome browser session

The owner of the browser may create a link of the genome browser and send the link to user(s) and user group(s) to view.

The link can be opened by the viewers via either Array Viewer or Array Studio. Here is an example of the links for Array Viewer and Array Studio respectively:

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.3.226:8065/RemoteServer&browserid=gb000006&Region=21:39880739-39882831
http://omicsoft.com/software/ArrayStudioLauncher/ArrayStudioLauncher.application?server=tcp://192.168.3.226:8065/RemoteServer&browserid=gb000006&Region=21:39880739-39882831

where the owner needs to provide server, browser and coordinate information in the link:

Server information: 	server=tcp://192.168.3.226:8065
Browser session ID:	browserid=gb000006
Genomic coordinates:	Region=21:39880739-39882831

The links may be directly sent to viewers, and viewers may copy and paste the links to IE. IE will then launch Array Studio or Array Viewer in the viewer's desktop and display the genome browser.

ArrayViewer1.jpg

The owner of the browser may also include the links in a excel file, and viewers may click cells in the excel file to launch the genome browser session.

3. Embed the browser links in a excel

The owner of the browser may create an excel file, and use hyperlink function in excel to embed links to a cell as shown below. Once viewers received the excel file, they may simply click the cell to launch a Array Viewer or Array Studio to display the browser.

ArrayViewer.jpg