What to use for research?

[warthog]

I'm working on my second graduate degree (after a six year hiatus), and I'm hoping to keep track of my literature search in a bibliographic database this time. What are people using these days?

I know bibtex exists and there are several front ends. I've been experimenting with web-based RefBase (since there is an e-build for it), but I'm not real happy with it. Regardless, it would be nice to have a web front-end that I could access at libraries and such. It doesn't appear that there are e-builds for the other web tools that I've found. Are they simply not popular?

I am also not sure if I should use openoffice. I've used openoffice writer for small documents, but never for anything significant. Additionally, I'm not sure how well it imports bibtex databases. Although I've done some searching, and it does appear that it's possible. I'm also looking at lyx, which I have used before for math papers, but I'm not sure if I'd want to use if for a more general paper.

So please give me your suggestions!

Thanks!

[dyeu]

I use Jabref, for the nice GUI and features. It can import entries from CiteSeer, and also from PubMed if you're doing medical research.

It is a desktop app, not a web-based one. But I just use NFS, SVN or other means to synchronise my bibtex files between my machines.

Alternately, vi does the trick I just can't stand to write a research paper or bibliography with OpenOffice or MS Office.

[warthog]

[timeBandit]

[karnesky]

[karnesky]

[warthog]

[karnesky]

jabref is an excellent program which I do use myself--it is hard to go wrong with it!

[karnesky]

The problem with italics appears to be because some gentoo installs only have Garamond Italic installed. I have no idea why. A work-around is to remove the occurrences of "garamond" from the css file. The fix is probably to either remove garamond italic or to install the normal font.

See also this post.
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[warthog]

[karnesky]

No problem. The official refbase-0.9.0 has been released and can be downloaded from sourceforge.
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[GNUtritious]

Wikindx (http://wikindx.sf.net/) is a great application.
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[karnesky]

[simon_irl]

i'm just entering my vote for bibus and openoffice writer. i wrote my thesis using writer. having the reference list linked to citations is great...and it's integrated with writer's bibliographic tools, so you can drop a citation (from your reference database) into your text as you write, and the document's reference list is automatically updated with the full reference entry (in apa format or whatever format you're using...there are many to choose from and they can be customised in any case). if you delete the citation later on as you're editing the text, the entry is removed automatically from the reference list.

this is the only functionality i particularly care about...it's a major hassle trying to keep hundreds of references in sync with a large document without this kind of automation. bibus and writer do it well enough. i agree that writer's large document handling could be improved, but again it's adequate: a document outline with sections that can have their own page styles etc. is enough to make writing a book-length text reasonably painless.

speaking of pain, it's not so many years ago that they were hunting down their references manually on library shelves, and typing up the thesis on a typewriter...

[karnesky]

Comparison of reference management software on Wikipedia features most of the programs mentioned in this thread & a few others.
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[simon_irl]

thanks for the link...i hadn't heard of zotero...will certainly test-drive it...if it does a decent job of extracting reference fields from online journal databases then i will use it (to grab records for bibus). it's also interesting to see that pybliographer now has limited openoffice writer integration...it didn't when i first checked it out...i may take another look and see how it compares to bibus.

[sybille]

Hi,

Sorry to dredge up this thread, but I thought someone might like to hear that the recent update to Zotero now allows for its database to be integrated directly into OpenOffice.org Writer documents. It works kind of like Bibus but with the Zotero database (and, for me, less worry about formatting issues).

In addition to the Zotero extension for Firefox, a Zotero extension for OOo needs to be installed. Get them here:
http://www.zotero.org/ (check out the docs here, too, and there are some helpful screencasts)
http://www.zotero.org/documentation/openoffice_integration

Once both are installed, you'll see a toolbar in OOo Writer with buttons that allow for inserting a citation (using the style of one's choice), inserting a bibliography, updating these, and setting preferences. I've only been trying with some "Lorem Ipsum" test documents and my existing Zotero database so far. There are a few quirks, but overall I'm finding the OOo extension is working fine. I'll be interested to try it with a longer master document containing the bibliography of a series of subdocuments containing the references.

Zotero itself works just great for me. One "big deal" with Zotero is that it uses something like screen scrapers (site translators) to automatically enter bibliographic information from compatible websites - and there are many - into its database. So it's possible to search for books at places like the Library of Congress (USA), SUDOC (France), various university libraries and so on and then import the information with one click of an icon in the Firefox address bar and maybe a little editing depending on how rigorous one tends to be. The system also works with a variety of online journal databases (JSTOR, etc.). There are a lot of other features which you can check out at the Zotero site.

One issue with Zotero right now is that it uses Firefox's Sqlite functionality and therefore the database is not multi-user. Apparently (see the warning at the bottom of the page), it is also necessary for everyone who wants to share a word-processor document that relies on a Zotero database to import the database into their own version of Zotero, which means that Firefox 2.0 + Zotero is a requirement even for MS Word users. So I don't see Zotero as a fully cross-platform and fully collaborative tool at this time. The next version of Zotero is supposed to include sharing/multi-user features of the "Web 2.0" sort and expected changes to the ODF format (and future versions of OOo) should help with the document-sharing part? In any case, I've listened to a podcast in which the Zotero team said that they already have funding for this "2.0" project, so it shouldn't be a permanent limitation. Zotero is developed by the Center for History and New Media at George Mason University.

Anyway, I think Zotero is just great and I wish I would have had something like it when I was in school. It's particularly useful for people doing research in the humanities and the social sciences, where LaTeX isn't an option. (For example, in the fields I'm involved with, publishers require submissions in the form of MS Word documents. My partner and I have been able to submit docs and pdfs exported from OOo, with an explanatory note about the formatting being potentially problematic in the doc version and the offer to send an odt formatted document as well.) Zotero does support lots of science databases, though, and it can export to BibTeX.

So maybe it will be useful for someone else, too.

(Edited for silly grammar errors.)