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© 2002-2007 by
Chih Long Liu

Walkthrough for Stainfinder - 2

Configuring Stainfinder

Open the copy of the Stainfinder program stored on your web server with your favorite text editor. If you modify a copy stored elsewhere, be sure to upload it to your web server once you have completed your modifications. An example is shown below.

here for a larger view

Modify lines 22 and 23 so that they point to the correct location of your files on your web server. The exact location will depend on your server configuration.

Save the changes and close the text editor.

Configuring TreeView

Open the TreeView program and load your clustered dataset. If you have not already done so, proceed to the walkthrough for generating a clustered dataset of your TMA data. Alternatively, you may download the demo clustered datasets from the Downloads section and use that instead.

Go to the Setting menu and select "Edit URL strings". A screen like the one shown below will pop up.

On a new line, enter the URL string corresponding to the address of the Stainfinder program on your web server, plus the parameters. The screenshot above indicates the correct URL string for the demonstration database on the Stanford Genome servers. For example, if the Stainfinder program was stored in the cgi-bin directory of your server, and your server address was www.myserver.edu, you would specify the following:


You will notice that TreeView is passing whatever is specified in the UID column to the variable UNIQID. For example, if your UID column contained the following:


then it will send the following URL to your default browser (as a single unbroken line):

http://genome-www5.Stanford.EDU/cgi-bin/ TISSUE/demo/Stainfinder.pl?uniqid=1_4_1_1_34_1012_1.jpg! 164!bcl2!mib1!mum1!mum1

If you have configured Stainfinder and TreeView properly on your computer and on your web server, clicking on a TreeView link should bring up a screen similar to what you will get when you click on the link above.

Back to Step 1.

Step 3 - Using Stainfinder with TreeView

Return to the walkthrough overview.

Last edited by Chih Long Liu on January 17, 2007