Slashdot Mirror

← Back to Stories (view on slashdot.org)

Software for Managing Your Bibliography?

Posted by Cliff on from the publication-tools dept.

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?"

26 of 77 comments (clear)

  1. um... by doja · · Score: 2, Informative

    bibtex

  2. Kile by MarkRose · · Score: 4, Informative

    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!

    --
    Be relentless!
    1. Re:Kile by ezeri · · Score: 2, Informative

      If you want to get KDE with Ubuntu http://www.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).

      --
      There are 4 boxes to use in the defense of liberty: soap, ballot, jury, ammo. Use in that order. Starting now. - Ed Howd
  3. "this only works on KDE and I am using Gnome" by Uncle_Al · · Score: 3, Insightful

    I really do not understand this. How come everybody is so binary* when it comes to Linux desktop applications?

    All the time I see someone say something along the lines of "Is this great program X also available for KDE/GNOME?"

    Newsflash: You do not need to run the other desktop. You just need to install some base libraries.

    Yes, it will look a little bit out of place. But is that such a big problem for you? Take the best of both worlds and be happy...

    * yes it is a very bad joke. My appologies.

    1. Re:"this only works on KDE and I am using Gnome" by Bester · · Score: 2, Insightful

      This is the kind of attitude that is damaging to linux.

      If you are trying to get a user to switch over one of the important things you can point out is that linux works like windows. You want that program, well just download it and install it. None of this screwing around trying to compile it, downloading a million different libraries trying to find the right one

      Most desktop users and new switchers are just not interested in compiling a program to get it to run. They want it to "just work"(tm).

      Charles

    2. Re:"this only works on KDE and I am using Gnome" by agraupe · · Score: 2, Insightful

      Installing aa library happens at the same time as installing the software. I have never had to look for a library when installing something, because apt-get/yum/portage/etc. does it for me. Just like Windows programs may install DLLs they need, linux programs will sometimes require libraries. These are usually available as binary, and as such, do not require compilation, or, if you are using a distro with apt-get or a similar system, no extra work beyond installing the application at all.

    3. Re:"this only works on KDE and I am using Gnome" by pla · · Score: 2, Insightful

      If you are trying to get a user to switch over one of the important things you can point out is that linux works like windows.

      "So, um... Why would I switch?"
      "Well, you get Linux for free."
      "I got Windows for free too, with my new PC"
      "Yeah, but not really free, you actually paid for it"
      "Hmm, that sucks... But should I just throw that money away???"
      "Okay, Linux also has a lot of free software for it..."
      "Like WinSite? Or TuCows?"
      "Well, yes, but also free as in speech, not just beer!"
      "Uhh... You mean like taht whole 'I speak, it types' thing?"
      "Mmm, no. With Linux programs, you usually get the source code."
      "What do I do with that?"
      "Well, you can modify it to make new versions of the program yourself."
      "I can barely use Excel, that sounds even harder."
      "If you don't want to, you don't need to code, but you at least have that choice."

      (Thinks for a moment)

      "Riiiiiiight - So instead of using software I already paid for, with a basically-sane and consistent interface, I should switch to something that I need to manage these library things in, just to get an interface that clashes with itself, for theoretical benefits that I can't actually use? Thanks, but I'll stick with Windows."

      (Awkward silence)

      "Say, have you considered a Mac?"
      "Don't go there."
      "Gotcha."


      And we wonder why people don't switch?

  4. Pybliographer by swimin · · Score: 3, Informative

    This?

  5. bibtex by jefu · · Score: 4, Informative
    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 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.

    1. Re:bibtex by jon787 · · Score: 3, Informative

      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.

      --
      X(7): A program for managing terminal windows. See also screen(1).
    2. Re:bibtex by MrHanky · · Score: 3, Informative

      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?

    3. Re:bibtex by an_mo · · Score: 2, Informative

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

  6. Humm... by Spock+the+Baptist · · Score: 2, Interesting

    Well I could mention that the Mac is great for thesis, but I'll not go there.

    I've been there and done that, writing a thesis that is, but that was in the dark ages(1992-1997). I just used the footnote feature of Word 5.1. Kept each chapter as a separate document, with multiple copies for backup. Even kept a floppy buried in the back yard in a sealed container in case the house burned down.

    Back in the day there were not nearly so many online journals etc. as there are today. So, keeping PDFs of articles was not an issue. You just kept photocopies, and referred back to them.

    A possible workaround is to keep your journal articles organized in a folder. That way they'd be easily found.

    What format are your articles in?

    --
    "Oh drat these computers, they're so naughty and so complex, I could pinch them." --Marvin the Martian
  7. Mac OS by Anonymous Coward · · Score: 3, Informative

    For those that use MacOS, or those looking for a great model to copy for Linux, try BibDesk

    1. Re:Mac OS by Spock+the+Baptist · · Score: 2, Interesting

      Just downloaded it. Very nice! Wish that I'd had this back in the day.

      BibDesk is GNU. Someone ought to be able to take the source code and brew up a nice version that will work with either KDE, or Gnome.

      --
      "Oh drat these computers, they're so naughty and so complex, I could pinch them." --Marvin the Martian
    2. Re:Mac OS by zhiwenchong · · Score: 5, Informative

      I second that. I use Bibdesk 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 - a del.icio.us for journals, can export to Bibdesk.
      Refworks - 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...

  8. bibtex mode + reftex mode by lost+in+place · · Score: 3, Informative

    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...

    1. Re:bibtex mode + reftex mode by hprotagonist0 · · Score: 2, Insightful
      AUCtex mode under *emacs is a first-rate method of editing and almost-WYSIWYG text processing.
      OK, I love AUCtex. I wrote my thesis in emacs using AUCtex. But it's not WYSIWYG. It's not even close. Word is WYSIWYG. LaTeX, AUCtex-mode or not, is marked up text. Have you ever had to insert a diagram? Or change a margin, for that matter?\\
      {\em This} is not {\large WYSIWYG}. Neither is this equation: $y=\int_0^T x(t) dt$. Sorry.
      --
      "A witty saying proves nothing." --Voltaire
    2. Re:bibtex mode + reftex mode by menscher · · Score: 3, Funny
      {\em This} is not {\large WYSIWYG}. Neither is this equation: $y=\int_0^T x(t) dt$. Sorry.

      That's not an equation... THIS

      \int d\eta_1^+d\eta_1\cdots d\eta_N^+d\eta_N e^{-\sum_{i,j} \eta_j^+A_{ji}\eta_i} \eta_{j_1}\eta_{i_1}^+\cdots\eta_{j_n}\eta_{i_n}^+ = \det A \sum_{k_1\cdots k_n} \epsilon_{j_1j_2\cdots j_n}^{k_1k_2\cdots k_n} A_{k_1i_1}^{-1} \cdots A_{k_ni_n}^{-1}

      is an equation!

      Apologies... Crocodile Dundee was on TV today.

  9. Crossplatform JabRef by namtro · · Score: 4, Informative

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

  10. Re:I know the article is asking about Linux... by dmaduram · · Score: 2, Informative

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

    Your mileage may vary, of course :)

  11. Try these two. by Linuxathome · · Score: 4, Informative

    Personally, I like using pybliographer (as was already mentioned) for my thesis. But also check out JabRef 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) 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."

    --
    Linux at home
  12. Re:I know the article is asking about Linux... by Merlynnus · · Score: 2, Informative

    I used Reference Manager 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.

  13. Re:Doesn't a word processor do this?!? by mopomi · · Score: 2, Informative

    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. . .

  14. RefBase by Bazman · · Score: 2, Informative

    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/

    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/

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

    Baz

  15. bibTeX and LaTeX by 12dec0de · · Score: 2, Informative
    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 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.