The PHP file for a module can be edited, as you have done, to change certain text that appears on the list pages. The text on the detail pages, however, is dictated differently.
To have changes made to such text, you have to administer the 'interface creator'.
Use the 'admin' link on the front page to get to the link to administer the interface creator (or browse to .../interface_creator/admin.php -- the ... will be something like www.xyz.edu/mylab/stocks). On the following page, choose the right table (say, 'plasmids') at the top, and then follow the link pointed by 'To configure the interface of the table ... go to this page'.
On the ensuing page, choose the right field in the menu at the top. The options refer to the MySQL table field names. In your case, you can choose 'source'. You will be presented a form with a field for 'Label'. It should be shown filled with 'Source', which you can change to 'Reference'.
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Thanks for trying the software. I hope I am able to release a newer version with improved features, flexibility, and documentation.