Software for Managing Your Bibliography?

Oliver Kayas asks: "I'm a newcomer to Linux specifically the Ubuntu distribution. I have been searching for software that will allow me to manage bibliographies for my thesis. I've come across Kile/Latex however, this only works on KDE and I am using Gnome. Under Windows I was using Endnote 8 which even allowed me to link references to documents on my hard disk so I could easily search for papers I just wanted to read. I know I could use an emulator such as Wine to use Endnote but that defeats the object of switching to Linux. I was wondering if you know of any alternatives?"

um...

[doja]

bibtex

Kile

[MarkRose]

Just install Kile. Programs that use libraries other than the GNOME libraries will work perfectly fine in GNOME. You'll need to install kdelibs and whatnot, but apt-get in Ubuntu will take care of all the necessary dependencies for you. Good luck!

Pybliographer

[swimin]

This? [pybliographer.org]

bibtex

[jefu]

I you are using LaTeX, use bibtex to manage the bibliography. It is not only easy to use, but can produce bibliographies in a variety of formats that are requested/required by various professional publications.

I think that citeseer [psu.edu] and other online resources often provide bibliographic information in bibtex format.

I think there are also ways to export/import various bibliographic formats into bibtex as well, which makes it easy to use bibliographies that are already compiled.

Mac OS

[Anonymous Coward]

For those that use MacOS, or those looking for a great model to copy for Linux, try BibDesk [sourceforge.net]

Re:bibtex

[jon787]

I can also recommend bibtex. Generally comes with LaTeX and is probably what your KDE program is doing anyway. LaTeX and bibtex can be done with any text editor. I recommend vim for a console editor and Nedit for a graphical one, both do syntax highlighting on LaTeX.

bibtex mode + reftex mode

[lost in place]

I have been there and done that. Here are my recommendations:

Use the TeTex distribution of Latex, available for just about every distribution (and unix-like platform).

For editing LaTex code I recommend AUCtex under emacs/xemacs. If you're not a *emacs fan you may balk at this, in which case I'm not sure what to recommend. AUCtex mode under *emacs is a first-rate method of editing and almost-WYSIWYG text processing.

For managing Bibtex bibliographies there are numerous graphical editors I've tried, but I've always come back to bibtex mode under *emacs. You're editing the raw text, but the commands for navigation, manipulation and clean-up are powerful enough that you won't miss the fancier graphical apps. Also, get reftex, which is like a bridge between bibtex and AUCtex. I have bibtex files with thousands of entries and I've found bibtex/reftex good enough to manage them.

Best of luck on your thesis...

Re:bibtex

[MrHanky]

If you use LaTeX, it's definitely the best option, but I'm not sure I'd call it good. At least not if you write in some weirdo language like Norwegian, where the standard styles are a bit different from the American, British, French and German styles you find in bibtex. I eventually hacked my own .sty from natbib to get the correct style for my thesis (I'm not quite sure I needed to, though).

Bibtex in itself is OK, but writing the bibliography file is a bitch. Perhaps what the OP was asking for was a good frontend?

Re:Mac OS

[zhiwenchong]

I second that. I use Bibdesk [sourceforge.net] and it is quite good -- very Mac like and much better than managing .bib files by hand. Furthermore it handles the .RIS (Endnote) and .BIB files that most electronic journal sites generate. I don't even type citations by hand these days - I just search for them on EngineeringVillage2 or Elsevier and drag the .RIS file into Bibdesk. Then I just drag the item into TeXshop and the citation is there.

As for porting it.... well, could be tough considering it uses the Cocoa framework.

However, since the poster is asking for a Linux solution, I can only think of web-based bib managers:

Cite-U-Like [citeulike.org] - a del.icio.us for journals, can export to Bibdesk.
Refworks [refworks.com] - if your campus has a subscription to Refworks, it's one of the best web-based bibliography managers around. It like the Bloglines of academic journals... well kind of...

Pybliographer looks promising too...

Crossplatform JabRef

[namtro]

I've just completed my thesis and have been quite happy with JabRef [sourceforge.net] which a Java based frontend to Bibtex. It's really quite flexible and works well with LyX [lyx.org], Kile [sourceforge.net], or WinEdt [winedt.com]. While I didn't need the capability, it can also import a whole bunch of formats.

Re:I know the article is asking about Linux...

[dmaduram]

I've been using Endnote for years, so I'm biased to it, but some of my peers use ProCite (http://www.procite.com/ [procite.com])

Your mileage may vary, of course :)

Try these two.

[Linuxathome]

Personally, I like using pybliographer (as was already mentioned) for my thesis. But also check out JabRef [sourceforge.net] which is written entirely in Java. So if you ever needed to go back to windows and still want to manage your BibTeX entries, JabRef may be a good option. Be careful moving back and forth between different bib managers because each one has its own convention in created keys (by default)--thus, the key for one entry in pybliographer will be different than the key referring to the same entry in JabRef. IIRC, both programs allow you to redefine how you want your keys to be configured, so if you define your own key structure, this problem is minimal.

If you're on a Mac, try out BibDesk. This user has a screencast (flash video demonstration) [hubmed.org] showing you how to export "BibTeX data and adding it to a BibDesk library, autofiling and associating a PDF file, adding the citation to a TeX file, then formatting a bibliography."

Re:Kile

[ezeri]

If you want to get KDE with Ubuntu http://www.kubuntu.org [kubuntu.org] is the place to go. If you want just a basic minimal install just "apt-get install kde-core" as root (yes it's more than just the base libs, but not that much).

Re:I know the article is asking about Linux...

[Merlynnus]

I used Reference Manager [refman.com] for my thesis. It integrated pretty well with Word and accepted reference citations from all the major online databases. The whole research group used it, and when I left, it was managing well over 3000 papers and assorted references. It comes with hundreds of reference formats for most major journals, and allows you to build your own format. The best feature with it, though, was the "Cite as you write" that allowed me to hit a key combo and then enter some identifers (like "Smith, 1996"). It would search through the database and offer the matches. Selecting the match put the reference in the correct place. Every once and a while, I'd generate the bibiography and it'd scan the document, pick up the references, format them in the text, and assemble the bibliography. Frankly, I don't know how I would have managed without it.

Re:Doesn't a word processor do this?!?

[mopomi]

OpenOffice.org does it, but last I tried, it needed work (pre-1.0 days).
Bibtex works great, and as far as I'm concerned is an essential part of LateX, which is an essential part of writing a thesis. . .

RefBase

[Bazman]

Try RefBase, and get everyone in your department to use it. Then you'll have a dept-wide database of references, just a few clicks away, and easily inserted into your LaTeX documents via BiBTeX. Its the way.

http://freshmeat.net/projects/refbase/ [freshmeat.net]

About:
refbase is a Web-based multi-user interface for managing scientific literature and bibliographic references. It offers powerful search tools and automatically generated citation lists.

http://www.refbase.net/ [refbase.net]

There's a few other similar projects listed on Freshmeat that may fit you better, just search for "bibtex".

Baz

bibTeX and LaTeX

[12dec0de]

I have written, among other things, two thesis papers, a couple of tech docs, a roleplaying game rule book and a security policy. And I allways use LaTeX.

And while I prefer (x)emacs with auctex for writing the document, that is not for the faint of heart. Use a front end, Kile looks like a good one for Linux (And just install the kde libs if you prefer a gnome frontend) Don't us Lyx, it is not real LaTeX. You may want to try TeXmacs, sounds good, I have not tried it.

For handling bibliographies, bibtex is unbeatable, but UI can be improved. Bibview is my method of choice, even though it does not have all the latest snazy look and feel features, as it is a Xaw Programm and you will probably have to have your packet manager install another lib.

Main adavantage of Bibtex is that you can get ready made entries while searching for sources. If you do computer science for instance there is The Collection of Computer Science Bibliographies [ira.uka.de] with allmost 2 million entries, many of which are linked to CiteSeer.

All of these programs come ready made on my prefered distribution (SuSE), and I gues they will be avaliable on yours as well.

Don't use Word or OpenOffice for anything larger than ~10 Pages. It will not make you happy, and when somebody tells you to change the format you will have to do it by hand. On each page. Repeativly.

Re:bibtex

[an_mo]

Bibdb is a frontend gui for bibtex. The GUI bit outdated, but nonetheless...