I use KBibTeX to manage my references database, but I used to use Jabref. Jabref has a handy feature that can automatically abbreviate journal names to their standard (ISO) abbreviation format. The built-in list of abbreviations is missing a lot of common biology journals, but I have updated it with many biology journals. You can get the most recent version of my abbreviations list from my Dropbox.
Abbreviate journal titles with Jabref
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