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However, at this point in my life, the computer is the means, not the ends. When I just need to get work done, Linux just isn't the tool.

Rubbish. I use GNU/Linux daily for academic, professional, and personal use without ever needing to use Microsoft Windows. If an academic course requires Microsoft Windows it is a sure sign of an ill-conceive lesson plan and curriculum. That said, since I paid for a copy of Microsoft Windows when I bought my latest computer, I chose to replace it with Xubuntu Linux and install Microsoft Windows as a virtual machine instance via Oracle VirtualBox.

LibreOffice's support for MS Office file formats is pretty good. It's usually only when a new version of MS Office has just come out, you know, when they deliberately break backward compatibility, that problems arise. But those issues arise for MS Office users too.

BTW, Zotero https://www.zotero.org/, the FOSS academic bibliography and citations manager, works much better with LibreOffice than with MS Office :)

BTW, the Zotero https://www.zotero.org/ plugin for LibreOffice works much better in LibreOffice Writer than in MS Word.

Personally I have found Mendeley frustrating to use anyway. Seemed more interested in shiny features than working well. Wasn't very good at maintaining its bibtex file (which could be a problem using it with other programs) and expected you to have digital references only.

JabRef is a great multiplatform reference manager which combines excellently with Docear for writing a paper/thesis/dissertation (Docear lets you organize your references and annotations as part of your outline). I have also found it worth it to run PDF-XChange Viewer under WINE. It is unfortunately not open source but it supports any feature you can think of for annotating PDFs and integrates nicely (with a bit of non-windows setup) with Docear.

Zotero is another great reference manager. I have also heard good things about BibDesk (OS X only).

I don't use firefox either, so good thing there's been Zotero standalone for several years now (you get offered both the firefox and standalone equally prominently on the download page: http://www.zotero.org/download/) along with plugins for chrome and safari. There's also several guides online to setting up either zotero standalone or the firefox version in 'portable' mode on a usb stick, although I haven't tried that myself.

I used Endnote because of a few cool capabilities.

- You would copy/paste text-citation mix to a new document (from several previous papers/thesis of yours) and it would order the citation numbers (as in IEEE and numbered format) and produce a final reference list. - You could have multiple types of documents (Journal, Conference paper etc.) - The numbers were always in the order of usage, - The formats could be changed and the whole document would be updated immediately. - The database could be saved on a cloud storage (and be available on all PCs) - You could download Endnote files on IEEE, Elsevier (scopus, sciencedirect) and other websites.

How does Zotero fare in the features I mentioned? I used it a few years ago but it lacked integration with MS Word, so I just gave up on it.

It does all of the above, and then some.For starters its has an interface that makes sense, unlike Endnote's which is a random pile of features accrued over the years. Capturing sources takes just one click within your browser. The only exception from your list is that the journals don't provide citation style files (you refer to them as Endnote files) for zotero. However this doesn't matter. You can find pretty much any style you want at http://www.zotero.org/styles. I think they have the formatting files for several thousand journals and the list keeps growing. One very useful feature of Zotero is the ability to have multiple groups with which you can share different libraries online. It comes handy both for collaborative writing and for teaching. I switched from endnote couple of years ago, when Zotero wasn't nearly as mature as it is now and i haven't looked back.

I believe all the features you mentioned are included in Zotero, and it can do indexing across pdfs it stores. You should check it out as they are rather responsive to updates and it is open source (and free!) Also, since it is a Firefox plugin, it can detect that you need to be behind a proxy automagically when appropriate, and so it makes adding new citations quite easy. I'm not a developer on it, but just a rather happy user! The only thing I miss from EndNote is an easy way to search Pubmed and pull citations that way, but I suspect they are working on it (or may have added it?) because I've seen other people request this feature in the forums.

I believe all the features you mentioned are included in Zotero, and it can do indexing across pdfs it stores. You should check it out as they are rather responsive to updates and it is open source (and free!) Also, since it is a Firefox plugin, it can detect that you need to be behind a proxy automagically when appropriate, and so it makes adding new citations quite easy. I'm not a developer on it, but just a rather happy user! The only thing I miss from EndNote is an easy way to search Pubmed and pull citations that way, but I suspect they are working on it (or may have added it?) because I've seen other people request this feature in the forums.

I believe all the features you mentioned are included in Zotero, and it can do indexing across pdfs it stores. You should check it out as they are rather responsive to updates and it is open source (and free!) Also, since it is a Firefox plugin, it can detect that you need to be behind a proxy automagically when appropriate, and so it makes adding new citations quite easy. I'm not a developer on it, but just a rather happy user! The only thing I miss from EndNote is an easy way to search Pubmed and pull citations that way, but I suspect they are working on it (or may have added it?) because I've seen other people request this feature in the forums.

Zotero. I have never used EndNote, so I can't compare, but I have used Zotero for a while now. It works really well. It is also cross-platform compatible, and so works on Mac, Linux and Windows. I use it with Firefox, but there is a standalone version as well. It works with Word, Open/Libre Office, and anything else (if you are willing to not have the automated keeps track of references bit). It will also import your EndNote database.

Have a look, and give it a go.

I've been adding these titles to my http://www.zotero.org/ collection and searching my library's catalog. If not in there it will be on http://www.worldcat.org/

Use it as a plugin in your word processor?

From the Zotero site:

The word processor plugins are distributed as Firefox extensions, which provide integration support to Zotero and install the necessary components into the word processors. After you have installed a plugin from this page, Firefox will prompt you to install later versions automatically the same way that it does for Zotero.

I agree that Zotero is awesome. I just wish it wasn't tied so closely to Firefox.

Use it as a plugin in your word processor?

You seem to have missed Zotero (it's up there in the comments somewhere) which is a FOSS plugin for firefox. It keeps an offline database, and for nearly any site (e.g. journals) you click one button on the URL bar and it downloads the citation including full pdf so you can read it whenever. It will also let you perform full text searches of your database, and can be configured to perform OCR on scanned documents. Best of all, it's trivial to make bibtex (or many other formats) bibliographies.

I use that in combination with TiddlyWiki for personal typed notes not associated with a journal article/textbook, and Xournal for annotating documents and taking notes with my tablet computer. When annotating documents (textbooks, journal articles) just configure xournal as your pdf viewer and you'll be able to save every annotation you make. TiddlyWiki has a ton of plugins to do whatever you need, including a GTD (Getting Things Done -- it's a book) variant that's probably comparable to Emacs Org-mode, LaTeX math (I wrote that one -- use it every day), and many more.

The one drawback to all this is that I have no way to automatically organize my handwritten notes from xournal. Though they're computer files, my organization for them is horrendous. I still fantasize about some kind of hybrid mutant of TiddlyWiki, OCR (that can magically read my handwriting and equations), and xournal that would let me do all this on a pen-based tablet...

You're right, I didn't include Zotero in that comment! Having looked at it before, my impression of Zotero was that it is a (very competent) reference manager / source collection. Is it more than this? TiddlyWiki sounds familiar too - this is a subject I've dallied with before, so perhaps I came across it previously :-). I'll have another look at Zotero and TiddlyWiki and see if I can get it to do the categorisation thing I'm looking for that I mentioned in my other comment. Cheers!

You seem to have missed Zotero (it's up there in the comments somewhere) which is a FOSS plugin for firefox. It keeps an offline database, and for nearly any site (e.g. journals) you click one button on the URL bar and it downloads the citation including full pdf so you can read it whenever. It will also let you perform full text searches of your database, and can be configured to perform OCR on scanned documents. Best of all, it's trivial to make bibtex (or many other formats) bibliographies.

I use that in combination with TiddlyWiki for personal typed notes not associated with a journal article/textbook, and Xournal for annotating documents and taking notes with my tablet computer. When annotating documents (textbooks, journal articles) just configure xournal as your pdf viewer and you'll be able to save every annotation you make. TiddlyWiki has a ton of plugins to do whatever you need, including a GTD (Getting Things Done -- it's a book) variant that's probably comparable to Emacs Org-mode, LaTeX math (I wrote that one -- use it every day), and many more.

The one drawback to all this is that I have no way to automatically organize my handwritten notes from xournal. Though they're computer files, my organization for them is horrendous. I still fantasize about some kind of hybrid mutant of TiddlyWiki, OCR (that can magically read my handwriting and equations), and xournal that would let me do all this on a pen-based tablet...

http://zotero.org/

As a Ph.D. candidate who writes scientific software at a large research university in the US under NIH grant funds, I can say that simply adding more developers to a scientific software project is an unrealistic solution to the problem. Having been to a conference of developers for a well-known chemistry software package (which will remain nameless) I have seen firsthand how seemingly good intentions can quickly turn into an epic battle of conquest and control of the software. Add in the huge egos and arrogance of these scientists (some very famous in their field), and you wind up with software that no one wants to develop due to problems that have nothing to do with funding or lack of qualified developers. This is probably one of the main reasons new scientific software is created in the first place.

There are examples of problems in every solution. Zotero is a great example of F/OSS working beautifully, exemplifying researcher collaboration to develop a research collaboration tool. With some standardization and better communication between the F/OSS community and the research industry, I think we can open the door to more of Zotero and less of your chemistry software example.

This. They're supposedly working on other browsers, but for now, Firefox is the only way to get this addon, which is truly marvelous (I'm a student, I would know).

Zotero

I'll consider switching to another browser when Zotero is ported.

I decided not to do comp sci after I hurt my wrists during my senior year in high school, and I'm now a graduate student in solid state physics. I found a project which involves a lot of fabrication, so I don't have to spend all day on the computer. I occasionally have to write code to interface with equipment, and do a decent bit of word processing. It's not too bad although I manage all my citations in zotero ( http://www.zotero.org/ ) which is an excellent program but unfortunately mouse-intensive. Mostly I just read papers, although I do also spend a lot of time working on scanning electron microscopes and similar systems (these almost universally have horrible input systems, see for example all the knobs on http://www.nano.lth.se/data/nanometer/files/image/sem.gif )

Have you looked at Zotero? It may do what you want -- I think it does import and export Bibtex, but if what you want to do is manage citations and bibliographies, it may do what you need without any importing or exporting. You can insert citations into your doc and then change your mind about the formatting en masse. Ditto the bibliography.

This requires both the Zotero Firefox plugin and the Zotero OpenOffice plugin. Dunno if it is compatible with 3.2.

Zotero might be worth a look. It's a Firefox plugin (open-source), mainly designed for keeping track of a collection of academic litterature. It allows you to organize the papers in folders, tag, annotate, and share the papers and annotations with others, all easily available in the FF gui. You can export lists of references to Word/OpenOffice/TeX when writing papers, they can be autoformatted to a wide range of citation styles.

It works really well (with full-text search) for storing web pages/pdfs. I don't know how well it works for .odt etc. Even if your purpose is not that of the typical university researcher it might be useful. For instance, recently I've liked using it for storing job ads, and my corresponding applications.

Zotero may well be what you're looking for. Much better and more open source than EndNote (mentioned above).

But with a real tablet computer and a stylus (e.g. Lenovo x-series tablets), in addition to erasing you also get a pencil that can cut & paste, resize, move, add space in the middle of the page, highlight, color, change the color of already written text, and annotate pdfs (in case the lecturer hands out slides in pdf format), and undo.

It's called Xournal. I frakking love it. Completely changed the way I work. Now I don't have to carry a backpack full of printed articles.

I also use Zotero. It's a bibliographic database add-on for firefox, and it will store full-text pdf's. If you set up xournal as your default pdf viewer, you can annotate and store the annotations for papers. So I no longer carry any printed paper or notes anymore.

If you're in science or engineering and deal in diagrams, equations, and journal articles, this beats the crap out of paper & pencil.

I hope to see more real tablet computers this year. Everyone has decided to stop manufacturing tablets with high-resolution screens, and use wide screens too, which means in portrait mode your tablet is blocky (can't read subscripts of equations) and too tall (because it's 16:10 rather than 4:3). So while the iPad sucks on all the above points, I hope it spurs some new & interesting tablets this year. Pen input (wacom) also needs improvement, especially near the edges of the screens where precision is lost.

Anderson responded, "All those are my screwups after we decided not to run notes as planned, due to my inability to find a good citation format for web sources... "

Zotero, brother: a plugin for Firefox. Makes citing online sources a breeze in any format you care to mention.

Trevor's blog also had this post:
http://www.zotero.org/blog/help-zotero-by-donating-to-the-center-for-history-and-new-media/
which says that all tax-deductible donations made in June will be matched twice-over. This seems like a good opportunity to congratulate the team for making it through their legal hurdles & to support the development of great free/open source software.

I use it daily & it has never crashed. Firefox occasionally crashes (but that has usually been due to the flash plugin). Have you posted anything at the Zotero forums about your issue? They do have a good error reporting tool too.

Does Word beat out BibTeX yet?

Nothing beats Zotero, and AFAIK that doesn't work with Word. (In brief: a Firefox extension that recognizes citations to papers on the web and lets you add them to a list of references which can be exported to BibTeX.)

The cost is beside the point.

I am a long-time Linux (and much more recently OS X) user, and if I am presented with a piece of software that requires Windows to run it, I usually prefer to just do without.

Fortunately in my discipline (biotech) developers are beginning to realise there are alternatives - for instance, Geneious is a stupendously fine example. It's definitely not free, but it is available on multiple platforms, which is a big step away from where we were a couple of years ago.

Compare this with Endnote which is rapidly losing ground to Zotero because the developers refuse to cooperate with the *nix world.

Zotero is a firefox extension that can grab reserach papers directly from the journal or library web sites. It organizes the papers in collections, has keywords (they call them tags), can automatically index the PDFs. The metadata is stored also on a remote server and you can browse through it using a web interface. You also get a Word and Openoffice plugins to insert citations in the papers you write. The plugins are a little rough around the edges, but are usable. The references formatting is very robust and comes with styles for a lot of journals.

Mendeley is stand alone application. I haven't tryed it yet,but is seems to have very similar functionality.

Zotero might be useful.

I'm writing a substantial work in pod (perl's doc format) using git for vc at the moment, with 5 authors.Works fine, painless, reviewing changes is easy and everything is pretty low friction. Plain text is so much easier to work with than anything else I've ever come across.

So move over to academic work, I find word's track changes a pain to work with, especially with more than 1 other author compared to good old diff -u.

So I'm going to try to write my next big work with Pandoc using citeproc and Zotero for citation and collection management. I'll get back to you in three years time to tell you how it went.

Yes--I'm talking about trademarks and I didn't say anything about copyrights. I agree that a trademark is not a copyright, but they can both be infringed.

As I said, Thomson requested their trademark not be used in the Refer/RIS option and in the most recent complaint, they want the court to enjoin against further "inappropriate use" of this trademark (such as using it to describe .ens style files).

I happen to think that Thomson is on weak ground in these two claims, due to fair use of the mark.

If Thomson's reading is accurate, though: I fail to see why Thomson would think that Zotero is infringing their "EndNote" trademark when it describes Refer files, while google is using the same trademark to refer to the same filetype. Trademark law says that marks must be licensed and protected zealously. (This is why we have "Iceweasel"--Mozilla must defend their "Firefox" mark, or risk losing it.) Either Thomson is not zealously protecting their mark against the likes of google (which can mean that it becomes unregistered), or they are misusing their trademark registration by asking Zotero to stop using it (and could also lose the mark).

My main issue with it is that there's no method of syncing or consolidating and index or database between multiple comps.

There is a Zotero beta available which does provide synchronization support (its called 1.5 sync preview, available here http://www.zotero.org/documentation/sync_preview.)

For those not familiar, let me give a short advertisement for Zotero. I'm a Mac user, and I recently switched from Safari to Firefox just for Zotero. Zotero makes it possible to add a citation entry to my library with one click in Firefox. Another nice feature is Zotero's ability to determine citation information for loose PDF's. And did I mention that Zotero is free?

They are claiming that the defendants contracted not to reverse-engineer Endnotes and then did so, breaching the contract.

They haven't, they reverse engineered the file format for it's styles. Users can create and export these from within Endnote. You probably only need a corpus with known data to successfully reverse engineer the format. Looks to me like that was exactly how it was done.

svn co https://www.zotero.org/svn/extension/branches/1.0/ zotero

Never know what idiotic (or corrupt) judge might grant a preliminary injunction forcing them to remove the source.

I hoped that I kept the article summary relatively free of my personal opinion, which I will indulge in this comment:

Thomson Reuters has too many asshats.

Let us set aside the fact that academic software and those who develop academic software should embrace interoperability and knowledge sharing.

I'll even set aside that, despite the (rewritten) title, Zotero has many fundamental differences from EndNote.

The complaint is, in the words of Bruce D'Arcus, "a nuisance lawsuit designed to intimidate." Zotero's style repository contains no EndNote .ens styles and seems to contain no styles derived from those styles. CSL styles are created manually and through an online style creator. There is no way to get a new CSL style from an .ens file--the Zotero beta had mapped fields internally to allow .ens files to be used independently of CSL (but even this feature has been disabled in the trunk). Zotero thought about copyright issues surrounding this feature and came to the right decision--not to distribute .ens files or .csl files derived from .ens files, but to retain the feature to work with user-provided .ens files (similar to the way OpenOffice.org can open and save MS Office files).

I have decided not to purchase EndNote and I am asking my employer to do the same, unless the suit is dropped. I intend to donate at least as much as an EndNote license costs to George Mason University, the Software Freedom Law Center, the Electronic Frontier Foundation or any other applicable entity that both defends Zotero in this case and solicits donations. (I don't know any organization who has stepped in on this case yet, but I imagine that one of these organizations can provide some sort of legal support in the future.)

I encourage you to stop purchasing Thomson products too. There are plenty of reference managers for all platforms (some proprietary, some free/open source) that you can choose instead, not the least of which is Zotero.

Disclaimer: I am a developer of refbase, a free and open source reference manager that might be seen to compete with Thomson Reuters's EndNoteWeb. I have and continue to use many reference managers. While I have many technical complaints about the EndNote products, they aren't the worst technical products. Thomson may be the worst socially, though--in addition to inane and baseless lawsuits, they are very slow to respond to general feedback.

I hoped that I kept the article summary relatively free of my personal opinion, which I will indulge in this comment:

Thomson Reuters has too many asshats.

Let us set aside the fact that academic software and those who develop academic software should embrace interoperability and knowledge sharing.

I'll even set aside that, despite the (rewritten) title, Zotero has many fundamental differences from EndNote.

The complaint is, in the words of Bruce D'Arcus, "a nuisance lawsuit designed to intimidate." Zotero's style repository contains no EndNote .ens styles and seems to contain no styles derived from those styles. CSL styles are created manually and through an online style creator. There is no way to get a new CSL style from an .ens file--the Zotero beta had mapped fields internally to allow .ens files to be used independently of CSL (but even this feature has been disabled in the trunk). Zotero thought about copyright issues surrounding this feature and came to the right decision--not to distribute .ens files or .csl files derived from .ens files, but to retain the feature to work with user-provided .ens files (similar to the way OpenOffice.org can open and save MS Office files).

I have decided not to purchase EndNote and I am asking my employer to do the same, unless the suit is dropped. I intend to donate at least as much as an EndNote license costs to George Mason University, the Software Freedom Law Center, the Electronic Frontier Foundation or any other applicable entity that both defends Zotero in this case and solicits donations. (I don't know any organization who has stepped in on this case yet, but I imagine that one of these organizations can provide some sort of legal support in the future.)

I encourage you to stop purchasing Thomson products too. There are plenty of reference managers for all platforms (some proprietary, some free/open source) that you can choose instead, not the least of which is Zotero.

Disclaimer: I am a developer of refbase, a free and open source reference manager that might be seen to compete with Thomson Reuters's EndNoteWeb. I have and continue to use many reference managers. While I have many technical complaints about the EndNote products, they aren't the worst technical products. Thomson may be the worst socially, though--in addition to inane and baseless lawsuits, they are very slow to respond to general feedback.

I hoped that I kept the article summary relatively free of my personal opinion, which I will indulge in this comment:

Thomson Reuters has too many asshats.

Let us set aside the fact that academic software and those who develop academic software should embrace interoperability and knowledge sharing.

I'll even set aside that, despite the (rewritten) title, Zotero has many fundamental differences from EndNote.

The complaint is, in the words of Bruce D'Arcus, "a nuisance lawsuit designed to intimidate." Zotero's style repository contains no EndNote .ens styles and seems to contain no styles derived from those styles. CSL styles are created manually and through an online style creator. There is no way to get a new CSL style from an .ens file--the Zotero beta had mapped fields internally to allow .ens files to be used independently of CSL (but even this feature has been disabled in the trunk). Zotero thought about copyright issues surrounding this feature and came to the right decision--not to distribute .ens files or .csl files derived from .ens files, but to retain the feature to work with user-provided .ens files (similar to the way OpenOffice.org can open and save MS Office files).

I have decided not to purchase EndNote and I am asking my employer to do the same, unless the suit is dropped. I intend to donate at least as much as an EndNote license costs to George Mason University, the Software Freedom Law Center, the Electronic Frontier Foundation or any other applicable entity that both defends Zotero in this case and solicits donations. (I don't know any organization who has stepped in on this case yet, but I imagine that one of these organizations can provide some sort of legal support in the future.)

I encourage you to stop purchasing Thomson products too. There are plenty of reference managers for all platforms (some proprietary, some free/open source) that you can choose instead, not the least of which is Zotero.

Disclaimer: I am a developer of refbase, a free and open source reference manager that might be seen to compete with Thomson Reuters's EndNoteWeb. I have and continue to use many reference managers. While I have many technical complaints about the EndNote products, they aren't the worst technical products. Thomson may be the worst socially, though--in addition to inane and baseless lawsuits, they are very slow to respond to general feedback.

I hoped that I kept the article summary relatively free of my personal opinion, which I will indulge in this comment:

Thomson Reuters has too many asshats.

Let us set aside the fact that academic software and those who develop academic software should embrace interoperability and knowledge sharing.

I'll even set aside that, despite the (rewritten) title, Zotero has many fundamental differences from EndNote.

The complaint is, in the words of Bruce D'Arcus, "a nuisance lawsuit designed to intimidate." Zotero's style repository contains no EndNote .ens styles and seems to contain no styles derived from those styles. CSL styles are created manually and through an online style creator. There is no way to get a new CSL style from an .ens file--the Zotero beta had mapped fields internally to allow .ens files to be used independently of CSL (but even this feature has been disabled in the trunk). Zotero thought about copyright issues surrounding this feature and came to the right decision--not to distribute .ens files or .csl files derived from .ens files, but to retain the feature to work with user-provided .ens files (similar to the way OpenOffice.org can open and save MS Office files).

I have decided not to purchase EndNote and I am asking my employer to do the same, unless the suit is dropped. I intend to donate at least as much as an EndNote license costs to George Mason University, the Software Freedom Law Center, the Electronic Frontier Foundation or any other applicable entity that both defends Zotero in this case and solicits donations. (I don't know any organization who has stepped in on this case yet, but I imagine that one of these organizations can provide some sort of legal support in the future.)

I encourage you to stop purchasing Thomson products too. There are plenty of reference managers for all platforms (some proprietary, some free/open source) that you can choose instead, not the least of which is Zotero.

Disclaimer: I am a developer of refbase, a free and open source reference manager that might be seen to compete with Thomson Reuters's EndNoteWeb. I have and continue to use many reference managers. While I have many technical complaints about the EndNote products, they aren't the worst technical products. Thomson may be the worst socially, though--in addition to inane and baseless lawsuits, they are very slow to respond to general feedback.

Windows XP disables write caching on USB flash drives. You can remove them without the Safely Disconnect procedure if you are not writing to the drive when you remove it. The downside to this is that it makes the USB drive painfully slow if you are writing lots of small files to it. It took me about 2 hours to write 30 megabytes to a USB flash drive when backing up my Zotero http://www.zotero.org/ data, for example.

Anyone who makes documents with bibliographies should check out Zotero, but OpenOffice.org users in particular can benefit from the Zotero extension for inserting citations directly in odt documents. Like EndNote, but better.
http://www.zotero.org/

(Yes, there is a Zotero plugin for MS Word, too, for those unfortunate people who are stuck with that. :-))

I imagine something like a FireFox plug-in with a 'Remember This' button and some options for category, keywords, annotations, etc.

True, but at least Firefox lets me pick which extensions I run.

My problem with Opera has never been about the compliance. I used Mozilla from the beginning, ran Konqueror frequently, and toyed around with Safari on the mac when it was in its infancy. Sites that "don't work" don't seem to irk me as much as other people.

Opera is fast. Noticably faster I'd argue, than anything else I've used on Windows or Linux (not much experience with the Mac end of things).

But I don't use Opera. It feels bloated. Sure it's fast, but the UI feels awkward and clunky. There were a few releases a two or three years ago that yanked out most of the cruft, but they seem to have gone back to their old ways of including too many features. Even though these features are actually useful and well-implemented, I find that I don't need many of them, and that they get in the way too often, which is completely overwhelming for a new user.

Zotero is an insanely useful Firefox extension that I find myself using more and more. However, I'm damn glad it's not built-in to the browser, because most people simply don't need it.

Firefox's initial rise to popularity came from the fact that the author forked the Mozilla tree, and ripped everything out that was unnecessary, resulting in a lean, fast browser that was charmingly simple to use. (Unfortunately, like Opera, as time has gone on, a lot of that crap has been put back in, but that's a story for another day)

Firefox 2 includes a critical new underlying database engine--SQLite--which enables new kinds of extensions, such as the free, open-source citation manager and digital research tool Zotero.

One of my favorite aspects of Firefox 2 is the new features for developers, including storage with SQLite. This enables neat things like the new Zotero extension, which stores bibliographic data (a'la Endnote, but with automatic recognition of metadata by programs like refbase and on sites like google scholar).

• Bibus
• refbase
• Zotero

I am also in need of good citation support & am a bit of geek about it (I am a co-developer of refbase).

There are a few issues with your post.

An office suite is A LOT more than a bibliographic management system & it would not be a small task to implement it in XUL in Firefox. There have been a number of online word processors & they haven't yet seen great success.

The other thing is that Endnote is not that great of a bibliographic manager & there are more serious attempts to replace it. Zotero for Firefox will be worth watching. The new MS XML format has metadata support for citations. And OO.o has the bibliographic project to add citation support to OO.o. Bruce D'Arcus's blog is worth following.