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JabRef and ''BibTeX'' Bibliographies

Introduction

JabRef is an open-sourced, Java-based reference manager. It uses BibTeX as its underlying structure. BibTeX is essentially a LaTeX add-on for storing bibliography information separately from the formatting (in the same way that LaTeX allows separation of information and formatting).

Getting and Using JabRef

Enough of the intro - how do you use the .bib file containing the whole bibliography for the Journal Club? If you download JabRef (you will need a Java runtime environment, which is already installed on most machines), you can open the .bib file by going to File > Open database. This will display a list of bibliography entries, each corresponding to a paper considered for the Journal Club, as seen in the screenshot below.

Typical screenshot of a JabRef window in action. Click to enlarge.

If you double-click on a given entry, you can see additional information on the article, separated in the tabs illustrated in the image above. In this image, the General tab is selected. This is where external links, keywords, DOI and file links are configured. The other tabs are fairly easily figured out - the last tab allows the user to view the BibTeX source code (notice that it is simply text - we will use this in a bit).

Should you wish to add another entry, you can download citations from your favorite journal in a variety of formats (RIS, Endnote, BibTeX, etc), then import them to JabRef (File > Import into current database…). Of course, you can create a new entry, simply by going to (BibTeX > New entry). You may select the entry type, and then enter the information field by field in the tabbed detailed information screen, or you could directly enter the BibTeX.

Using the .zip File of Journal Club Papers

This is where things get slightly trickier. If you noticed, the .zip file contains both the bibliography, and a folder called Papers. The folder contains all the papers for the Journal Club in .pdf format. The bibliography (contained in the .bib file) has links to each of these papers (little icon on the left of each entry in the bibliography)! However, it is set to link to the file locations on my computer. Since the .bib file is just a text file, we can easily set this up to work on your computer.

  1. Unzip the JournalClub.zip file to some convenient location on your hard drive (on a Windows machine, something like C:/JournalClub/).
  2. Make sure your JabRef is closed (this is not necessary, but it will give you funny messages if you leave it open during the following operations)
  3. Open the JournalClub.bib file that was just unzipped in a text editor (such as notepad.exe, TextEdit.app, or VI).
  4. Perform a Find operation for the string Users/joffrey/Documents/2009Fall/JournalClub/
  5. Perform a Replace All operation and replace the above string with the directory where your Papers folder is located

Note: If you are on a Windows machine, you will require a colon in your file path. This requires you to type something like C\:/JournalClub/. Make note of the \: in place of the standard :.

Now, you should be able to open the JournalClub.bib file in JabRef, and click the links to the .pdf files and have them simply open with your default .pdf viewer.

For more information on JabRef, and a free and open-sourced LaTeX editor (LyX) which interfaces nicely with JabRef, see my personal physics site or my wiki.

Let me know if you have any issues – J


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groups/journal_club/jabref.txt · Last modified: 2009/09/01 00:04 by peters