JabRef
The program
Introduction
JabRef is a free, open source reference manager based on BibTeX, a universal referencing format that works particularly well with the LaTeX document markup language. Note that you don't actually need to learn LaTeX to use JabRef, as programs like LyX serve to provide you all of its power (to produce beautifully formated PDF documents) while being easy to use and clean. Additionally, you can use your JabRef bibiliography with OpenOffice and Word (see below). Note: this is not meant to be a comprehensive wiki, just a help file to get you started with using JabRef and BibTeX. For very detailed information, see the actual JabRef documentation.
Installation
Go to the Jabref homepage and click on Download (the latest stable version) onto your desktop and open it (you need to have Java installed.
Creating a bibliography
Finding references through Medline
Open the Jabref program, go to 'File -> New database', browse to find a place where to keep your bibliography and give it a name ending with '.bib'. Alternatively, if you already have a BibTeX bibliography, use 'File -> Open database'.
To search for a reference online, go to 'Web Search -> Fetch Medline' (or type F5) and in the new side pane that opens type the keywords you are interested in and click 'Fetch'. A list of references that has been found will come up: find the references that you want and, under the field 'Keep', click on their boxes and then on 'Ok'.
Prego! Now you have some references in your bibiliography.
Editing references
To change an entry just double click on it. You will see various tabs: 'Required Fields' (typically contains all the fields necessary for your reference to be sufficient for citation), 'Optional Fields', 'General' (particularly useful for keywords, web-links, PDFs and other comments), 'Abstract' (very useful to quickly glance at the content of an article), 'Review' and 'BibTeX source'
These tabs are useful to edit your references to your liking, such as copy-pasting a missing abstract from PubMed.
If Medline fails
In the rare case when Medline (PubMed) fails, you can create a new reference by clicking on the green plus on the icon bar. Select your reference type (usually 'Article', 'Book' or 'Inproceedings') and either complete the various fields yourself or find the BibTeX source in...
Google Scholar
Go to Google Scholar. Click on the 'Scholar Preferences' link (tiny thing next to Search button) and scroll down to check-on 'Show links to import citations into BibTeX' and 'Save Preferences'.
Search for an article in Scholar, say 'luck vogel working memory' and click on the click on the 'Import into BibTeX' link underneath. Copy the strange text within and paste into it into your empty article's 'BibTeX source' tab-field.
Importing from EndNote
I have never used EndNote, but apparently you can export EndNote references into BibTeX for use in JabRef.
Using groups
One most useful tool available to you on JabRef is the ability to organise your references into groups, subgroups, sub-subgroups, you get the idea! To toggle the group menu, click on 'View -> Toggle groups interface' or type 'Ctrl + Shift + G'. The interface will appear on the side pane, containing the macrogroup 'AllEntries'. In the groups interface click on the white page to create a new group. Name your group and select how you will decide reference inclusion into the group (manually, keyword, search) and the hierarchical context of the group (e.g. whether to include entries contained in subgroups). Now you can drag-and-drop each of your references into one or several of your groups.
Sorting your pdf's
The bibliography can allow you to have all your papers at the reach of your finger. My preferred way is to have all the PDF files in a sub-folder with your actual '.bib' file. For instance, create a 'PDF' folder wherever you have saved your bibliography. In JabRef, go to 'Options -> Preferences' and select 'External programs' from the left-hand list. The first field is called Main PDF directory, which you can change by clicking on 'Browse', browsing to the folder where you keep your PDFs and click Ok.
To link your references to your PDFs, the easiest way is to name your PDFs according to the 'Bibtexkey' field in the 'Required fields' tab of your reference, which may look something like 'Luck1997'. Then, go to the 'General' tab of your reference and click on the 'Auto' button - if you have done everything correctly, the name of your PDF file should appear in the 'Pdf' field and you should be able to access the PDF by clicking on the relevant icon in your reference list. Alternatively, if you like to name your articles in a specific way, simply go to the 'General' tab and click on 'Browse' to find the correct PDF; again, it is recommendable and easier to keep this in the PDF folder, allowing you to transfer your whole bibliography easily between machines (and to back it up quickly!).
Using your bibliography
Usage with Lyx
Under construction! Come back soon.
Usage with Word
Again, I have not used Word for scientific writing, as I have found it quite a heavy, clunky program, but given that many journals apparently only accept .doc format submissions, there's a walktrhough of how to use JabRef in Word.
Usage with OpenOffice
Again, there is a walkthrough for using JabRef with OpenOffice, which natively supports the BibTeX format and allows you to save documents in '.doc' format, so this may be a good compromise if you want to use BibTeX but need to submit your papers as a '.doc'.
Page created by AlejandroVicenteGrabovetsky. Please feel free to contribute so I can add an 'acknowledgments' section 