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Software for Managing Your Bibliography? 77

Posted by Cliff 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?"
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Software for Managing Your Bibliography? More

Software for Managing Your Bibliography?

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  • um... (Score:2, Informative)

    by doja ( 36500 )
    bibtex

  • Kile (Score:5, Informative)

    by MarkRose ( 820682 ) on Saturday June 18, 2005 @06:55PM (#12853220) Homepage
    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!

  • "this only works on KDE and I am using Gnome" (Score:3, Insightful)

    by Uncle_Al ( 115529 ) on Saturday June 18, 2005 @06:56PM (#12853225)
    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.
    • "Newsflash: You do not need to run the other desktop. You just need to install some base libraries."

      No doubt! Asking about good software for bibliographys is a good enough question, but why didn't "Cliff" edit out the part about Kile and Latex not working on GNOME?

    • 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

      • 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.

      • ...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).

        That's the lovely thing about distributions like Debian (which I use) or Ubuntu. If I want to see the libraries that a program depends on, or what other packages depend on the one I'm

      • 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
        • Q: "Like WinSite? Or TuCows?"
          A: "You mean time limited, cripled, and full of ads and nag screens? No, nothing like WinSite or TuCows.
          Completely free, unencumbered, unrestricted, nag free, ad free, forever. And you get the source if you want, but you probably don't care about that"

          Switching to Linux is worth it just to escape the insane world of Windows shareware where people seriously expect you to pay $50 for the crapy semi functional app they spent 2 hours in VB on.
          At least in the open source world the

          • Switching to Linux is worth it just to escape the insane world of Windows shareware where people seriously expect you to pay $50 for the crapy semi functional app they spent 2 hours in VB on.

            But you know what? There is a lot of that "Windows Shareware" which simply isn't available on Linux, free or otherwise. And it's those crappy shareware applications which are often the stumbling blocks for end users to switch to anything.

            In particular, card games. Yes, Linux has Solataire in all its variations

    • For real. I run k3b and Kedit flawlessly, and I run iceWM.
    • i was just about to say the same thing. just because he used gnome there was no reason that he could run a application which use QT.

      also "WINE is not a emulator" if the windows application is perfect for your needs AND if it runs well with wine (i dont know if it does) then why not use it. using a program that was built for windows isnt such a bad thing.
    • Dude, he's a newcomer. Why do you expect newcomers to understand this, when it's really quite counter intuitive? As a newcomer, how do you know that running GNOME and KDE apps side by side isn't as crazy as running Mac OS X-apps next to Windows XP apps?

      As you quote in the subject line, it seems apparent that he believes they cannot run side by side.

      Just tell him in a friendly way (not including newsflashes). ;)

      The joke was pretty good, tho.

  • Pybliographer (Score:3, Informative)

    by swimin ( 828756 ) on Saturday June 18, 2005 @07:00PM (#12853242)
    This? [pybliographer.org]

  • bibtex (Score:5, Informative)

    by jefu ( 53450 ) on Saturday June 18, 2005 @07:03PM (#12853256) Homepage Journal
    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.

    • Re:bibtex (Score:4, Informative)

      by jon787 ( 512497 ) on Saturday June 18, 2005 @07:20PM (#12853331) Homepage Journal
      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.

    • Re:bibtex (Score:4, Informative)

      by MrHanky ( 141717 ) on Saturday June 18, 2005 @07:55PM (#12853506) Homepage Journal
      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?

    • I use tkbibtex as my gui front end for bibtex. It seems like a ok little program.

      And while you are using Latex, you might want to consider LyX as a gui front end for latex. It lets you see your equations and figures and tables...

  • Humm... (Score:3, Interesting)

    by Spock the Baptist ( 455355 ) on Saturday June 18, 2005 @07:07PM (#12853274) Journal
    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?

  • Mac OS (Score:3, Informative)

    by Anonymous Coward on Saturday June 18, 2005 @07:07PM (#12853278)
    For those that use MacOS, or those looking for a great model to copy for Linux, try BibDesk [sourceforge.net]

    • Re:Mac OS (Score:3, Interesting)

      by Spock the Baptist ( 455355 )
      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.

      • Re:Mac OS (Score:5, Informative)

        by zhiwenchong ( 155773 ) on Saturday June 18, 2005 @08:11PM (#12853563)
        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...
      • I'm not sure what you mean by "BibDesk is GNU", but in any case it isn't. It is BSD licensed (according to its SF.net page [sourceforge.net], and is not a GNU project [fsf.org].

        -Peter
        • Opps...

          It's the previous version that was under GNU.
          • You keep using that word . . .

            But seriously, I think you mean "distributed under the terms of the GPL" (or just "GPLed" for short).

            GNU is a project to create the core of a UNIX-compatible platform. I don't think that BibDesk ever fell under the auspices of that project.

            They promulgate their license, but some random person or group distributing their software under the terms of the GPL doesn't make it GNU software.

            -Peter
      • Yup, BibDesk is Gr8. BibTex mode in emacs is ok too. My institution has a site licence for Endnote, but BibDesk is much much better for all sorts of reasons.
  • Just use it with any text editor. There are two great choices avaliable for Linux: vim in a terminal, or gvim in X.
  • ...but aside from Endnote (as it's a terrible, terrible program), what *good* biblio programs are out there for Windows?

  • bibtex mode + reftex mode (Score:3, Informative)

    by lost in place ( 248578 ) on Saturday June 18, 2005 @07:29PM (#12853368)
    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...
    • 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.
      • {\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.

      • OK, I love AUCtex. I wrote my thesis in emacs using AUCtex. But it's not WYSIWYG. It's not even close.
        {\em This} is not {\large WYSIWYG}. Neither is this equation: $y=\int_0^T x(t) dt$. Sorry.

        OK, fair enough. And AUCtex with the preview-latex [sourceforge.net] package isn't really WYSIWYG either, but I'll claim it gets you pretty close. It calls out to latex to typeset important stuff (equations, tables, figures, images) and inserts the results into the buffer. I claim those are the most important elements to see. All t

  • Crossplatform JabRef (Score:4, Informative)

    by namtro ( 22488 ) on Saturday June 18, 2005 @08:33PM (#12853647)

    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.

    • Indeed, I second JabRef. And because it's Java you can easily recommend it to anyone who uses bibtex files regardless of their operating system. The moderators don't seem to agree with you at the moment, though :(
    • Jabref [sf.net] is also able to manage your PDF and PS files. It's great if you want to keep an electronic archive of the papers you cite.

      Definitively the best bibtex editor I came accross.
    • I highly recommend JabRef. I've been using it for a while now and it just works. Basically if you don't know. JabRef will format everything as a bibtex file so that you can use it easily with Latex. You can also export your bibliography database as an endnote database if you want and a couple of others.

      For actually writing your thesis, I just use a text editor for Latex code...I find that it makes much more sense to do this than to use Kile. My fav. is Nedit, it highlights the syntax and everything...you


  • If not, change word processor...

    Managing footnotes & creating a bibliography
    goes back to Lotus Manuscript (my fav, under
    DOS, in a previous life & era...)

    Is there any value in separating out either
    of those two functions, ie, from our modern
    word processing software?

    I don't think so...
    • Is there any value in separating out either
      of those two functions, ie, from our modern
      word processing software?

      I don't think so...
      A lot of folks that publish scholarly material like to use a bibliography database to save time finding and refinding references to works they cite. This functionality is not provided in any word processor that I am aware of currently.

      As a result, EndNotes and other programs have come to the rescue. They help you manage a library of citations for when you need to c
    • 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. . .

  • uhm, bibtex??????? (Score:1, Insightful)

    by Anonymous Coward

    I've come across Kile/Latex however, this only works on KDE and I am using Gnome.

    LaTeX is like, what, 20 years old? You definitely need to brush up on LaTeX and bibtex. they are indispensable.

    I've been using LaTeX and friends since, hmm, 1992 or so, still works fine on my latest Gentoo box, it's just a plain text format.

  • Try these two. (Score:5, Informative)

    by Linuxathome ( 242573 ) * on Saturday June 18, 2005 @08:43PM (#12853702) Homepage Journal
    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."
    • I've been using jabref for my thesis for over a year now, and I highly recommend it. I evaluated every Free software bibliography manager available about a year and half ago and jabref was the best hands down. Maybe pybliographer has improved since then...
  • Kile is just a KDE-based frontend. Other frontends I know of are lyx (X11) and ts (Tcl/Tk). I don't use latex, though, so I can't say if they'll do what you're looking for or not, but you won't have to install any KDE stuff to use them.

    That said, as many have already pointed out, you can use KDE apps under Gnome as long as you have the dependencies satisfied, which shouldn't be a big deal with apt-get.

  • I know I could use an emulator such as Wine to use Endnote but that defeats the object of switching to Linux.

    And the object of switching to Linux is... what, exactly?
  • I'm writing my thesis using LaTeX (invaluable for equations, but it's kind of a bitch to change formatting) and I'm using BibTeX. You create a list of items like:

    @inproceedings{jiaying,
    author = {Jiaying Shen and Victor Lesser and Norman Carver},
    title = {Minimizing Communication Cost in a Distributed Bayesian Network Using a Decentralized MDP},
    booktitle = {Proceedings of the Second International Joint Conference on Autonomous Agents and Multiagent Systems},
    year = {2003},
    isbn = {1-58113-683-8},

  • I do allot of internet research for my own purposes so I don't need to keep a list of sources. What kind of software is out there to aid in research? There has to be a better way than dumping all my notes and links into notepad. Or some advice on how other people organize information while researching would be extremely helpful.
  • Openoffice has the possibility to work with a bibliography database in a way that is a lot like the combination of Endnote with Word. This works quite nicely.
  • Anyone know of any reference manager that works with OpenOffice, GOffice or KOffice rather then LateX.

    I'm just guessing there would be someone who'd like that somewhere.

    I know I could use one for OpenOffice, would pave the way for implementing OpenOffice 2.0 (when it's ready) at my work, otherwise I'll be stuck supporting various iterations of MS Office.

  • RefBase (Score:3, Informative)

    by Bazman ( 4849 ) on Sunday June 19, 2005 @08:29AM (#12855711) Journal
    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
    • 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.

      I think I'd prefer to have a dept-wide BibTeX database instead (under revision control using CVS or whatever). That's the way people have worked since the seventies (first with refer(1), then increasingly with BibTeX) and I would hate if some web-based thingy broke that toolchain. Hopefully this RefBase

  • bibTeX and LaTeX (Score:3, Informative)

    by 12dec0de ( 26853 ) on Sunday June 19, 2005 @10:20AM (#12856069) Homepage
    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.

  • I know I could use an emulator such as Wine

    WINE is an acronym for Wine Is Not an Emulator.

    Brett
  • I just finished my thesis and I used NoodleBib. It worked out great for me and my classmates, as we had around 75 entries in NoodleBib. It proved really beneficial in switching styles, (MLA to APA) it was as easy as 1 click of my mouse. It was also very easy to input reference data as well as download it (it provides your bibliography in a word document or a text file).

    NoodleBib is a web app, so there is no issue of getting it to run on your computer. See if your school has it for free (mine did) for s
  • - User has working functional programs under windows
    - User switches to Linux
    - User finds program that does half of whats needed
    - User now spends 90% of time looking for alternatives while working around half assed linux implementation
    - User asks slashdot. Now 100% of time is spent reading flames on kde/gnome/etc and being told to hack the code.
  • I was in need of a software package that allowed me not just manage the bibliography information, but also include notes, commentary etc on an article item.

    So I tried a Wiki, where I have one page per article, a <pre></pre> block of bibtex-formatted bibliography data and the rest is commentary, links etc. Then I have a script/plugin that goes through the pages and dumps the stuff within the <pre></pre>-blocks to a file. Instant .bib.

    On a positive side this worked out pretty well. T
  • MyOPIA [sourceforge.net] is a web based (LAMP) system written by a guy from the University College London. Haven't managed to get it working here yet however...
  • The Medical College I work for is considering using Refworks - it is a webbased system - seems pretty strong and it is not platform dependent. http://www.refworks.com/productinfo.shtml [refworks.com]

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