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]

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.

Cool, I was just checking out JabRef. I just wish it had some sort of internet lookup feature, where I could type in a book's ISBN, and it would look up the rest of the information so I don't have to type it all in. Just getting lazy

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.

that's a great idea; maybe I'll just do that instead of trying to get along with RefBase.

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

Yeah, I was looking at using Kile or one of the other tex/latex frontends. I really don't want to spend a lot of time learning codes, although I really almost killed myself last time I attempted to put together my graduate research project using MS Office. That's something I'll never do again!

Thanks for the feedback!

[timeBandit]

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

Yeah, I was looking at using Kile or one of the other tex/latex frontends. ... I really almost killed myself last time I attempted to put together my graduate research project using MS Office. That's something I'll never do again!

Then by all means, if you're not already very comfortable with OpenOffice, avoid it.

I like it a lot, prefer it over Word and it's certainly up to the task: I've done book-length projects replete with photos, figures and whatnot. But it's nuts to tackle a project that size if you're at odds with your tools. So if MS Word didn't work for you, I'd say OOo Writer is similar enough to dredge up some bad memories.

Good luck with the second grad degree. I've toyed with the same idea of late but don't know what I want to be when I grow up.

[karnesky]

What are people using these days?

I use (and contribute both code and money to) refbase as a central web-based system. I also use various desktop clients, depending on what I'm using to author papers. I particularly like Zotero (a new plugin for firefox 2), Jabref, and bibus. I also use the in-build manager for OO.o & manage some bibtex by hand.

I've been experimenting with web-based RefBase (since there is an e-build for it), but I'm not real happy with it.

I didn't make that ebuild, but I've suggested fixes for it. Is there anything, in particular, that you don't like? refbase-0.9.0 will be released very soon & you're welcome to try the release candidate:
http://arc.nucapt.northwestern.edu/~kar ... rc1.tar.gz
This adds MUCH better import of references & also adds some nice features like export to OO.o and embedded metadata for use by extensions like Zotero or LibX.

[karnesky]

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.

As for the actual document creation process, I author in whichever format the journal prefers. This is usually either MS Word DOC (bleh!) or LaTeX (yea!). Some will only accept a single format. Also check what your colleagues use. I have colleagues who will only edit documents which can be read by Word. If you are using LaTeX or some other format, you may have to convert to RTF and/or DOC. This can be done (see, especially, latex2rtf and tex4ht), but results aren't "perfect" & you may have to explain that it will be prettier when the reviewers get PDFs and when it appears in print.

[warthog]

I use (and contribute both code and money to) refbase as a central web-based system. I also use various desktop clients, depending on what I'm using to author papers. I particularly like Zotero (a new plugin for firefox 2), Jabref, and bibus. I also use the in-build manager for OO.o & manage some bibtex by hand.

I didn't know about Zotero; it looks promising. At the moment I'm leaning towards Jabref. It seems to do a pretty good job for me. I'm also using OO.o's bibliographic database for small assignments. But every time I use OO.o, I find I'm more concerned with how the material looks, and I'm therefore not having as much time to spend on the content.

I didn't make that [refbase] ebuild, but I've suggested fixes for it. Is there anything, in particular, that you don't like? refbase-0.9.0 will be released very soon & you're welcome to try the release candidate:
http://arc.nucapt.northwestern.edu/~kar ... rc1.tar.gz
This adds MUCH better import of references & also adds some nice features like export to OO.o and embedded metadata for use by extensions like Zotero or LibX.

I didn't appear to have any problems installing refbase, and I haven't spent a lot of time evaluating it, but my initial impressions are that it is probably overkill for what I'm trying to do, and some of the features of 0.80 are not working for me, but it could be that I didn't perform the installation correctly. In any case, the features that are not working are (1) bibtex exprort gives me a blank screen, and (2) uploading PDFs fail (I think that's related to directory permissions related to my install), and (3) I haven't found a way to produce the APA-style "cite", although that's not as important. Lastly, the italics are very difficult for me to read! I'm sure there must be some setting to turn off the italics, but I haven't found it yet. I'm sure some if not all of my problems are related to my install. I may go ahead and give your release candidate a try. Are there any installation instructions provided with the RC? I haven't looked at the tgz yet.

BTW, thanks for replying to my post. I really appreciate the suggestions, and thanks for putting effort into refbase. I can definitely see that it's a very useful tool even if it doesn't work out for me.

[karnesky]

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

In any case, the features that are not working are (1) bibtex exprort gives me a blank screen

You can check wherever you log your php errors (or set error_reporting = E_ALL, display_errors = On in php.ini). The most common cause of this is using the wrong path to bibutils when you installed refbase. This is improved ih 0.9.0: install.php will now search your path and auto-fill the correct path for your system. Also, if you have 'safe_mode' on in php.ini, then you'll need to put the Bibutils programs within the directory that's specified in 'safe_mode_exec_dir'.

uploading PDFs fail (I think that's related to directory permissions related to my install)

Again, check your error log. It can also be because of php.ini settings (file_uploads On, reasonable values for post_max_size and upload_max_filesize.

I think that both of these are most likely configuration issues you'd run into with any Apache/MySQL/PHP app. I can, of course, understand that it isn't worth the headache if a desktop-based solution would workf for you, though.

I haven't found a way to produce the APA-style "cite", although that's not as important.

Right--The lead developer has a bias towards polar and marine biology & the styles match the journals they use. Customizing styles isn't that hard & the J. Glacial style is pretty close to APA. We probably should include some of these "universal" styles, though.

Lastly, the italics are very difficult for me to read! I'm sure there must be some setting to turn off the italics, but I haven't found it yet.

This can be controlled with the CSS. The italics aren't intentional & are most likely cause by a different font family. You can see the screenshots to see the intended style. You can also look at my installation, which uses the monobook skin from mediawiki (used by wikipedia). I agree that italics isn't desirable (and they're probably not intended), so will mention it on the dev list.

I may go ahead and give your release candidate a try. Are there any installation instructions provided with the RC? I haven't looked at the tgz yet.

Yes--the README will direct you to the important files (INSTALL and/or UPDATE). I'm sure you could get any additional help in the forums on sourceforge.

BTW, thanks for replying to my post. I really appreciate the suggestions, and thanks for putting effort into refbase. I can definitely see that it's a very useful tool even if it doesn't work out for me.

Well, thanks for trying it & for your feedback. I hope that it can work for you or at least that your experience can improve it for other people. I also hope that whichever tools you finally decide to use work out wel for you.

[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.

[warthog]

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.

Yep, that was my problem. I yanked all ocurrences of 'garamond' from the css file, and it now looks much better. I also installed 0.9.0, but I'm having some php problems when I try to add a record. I need to turn on php error logging and do some additional investigation when I get time.

Thanks!

[karnesky]

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

[GNUtritious]

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

[karnesky]

I haven't found a way to produce the APA-style "cite", although that's not as important.

Right--The lead developer has a bias towards polar and marine biology & the styles match the journals they use. Customizing styles isn't that hard & the J. Glacial style is pretty close to APA. We probably should include some of these "universal" styles, though.

I committed a APA style file to the refbase subversion repository.

[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.

[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/ope ... ntegration

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.)