Wednesday, May 21, 2008

Reference management system open thread

When I was a student, I used endnote to organize and manage all of my references. In hindsight, this was probably one of the stupider decisions that I made. It meant that as soon as I finished and left university, the index that I spent 4 years building turned into an unreadable file, and I was left with the 14 pages in the back of my thesis as the only hint as to what my filing cabinet of papers contained.

While it would be melodramatic so say that this was a main contributor towards my poor record in publishing mostly finished work, it is one more annoyance that I don’t really need. And this year I am trying to make a renewed effort to get some manuscripts out the door- both old stuff that is still relevant, and recent stuff from my old university job.

I’ve heard all sorts of odd-sounding names when the subject of reference management comes up- words with non-transparent meanings, like Zotero, or JabRef (the indexer of choice for smugglers on Tatooine?). I have no idea what any of these things are. So I’m asking y’all to pitch in. Do you use a non-institutional program to manage your references? If so what is it? And most importantly, is it the sort of thing that is accessible to a computer semi-literate like me?

14 comments:

wna said...

I can strongly recommend BibTex. I run the application BibDesk on a mac, but I'm sure there are Windows clients if that's your system. It's fairly accessible and flexible since references are stored as plain text, but still has the bells and whistles. And free.

Can be a little fiddly at times though.

Propter Doc said...

Ditto endnote problem. New Univeristy uses Reference Manager which I loath. I tried Zotero (a firefox plugin) but found it fairly unintuitive (i.e. I couldn't grasp it in about 2.5 minutes). I've used EndNoteWeb for a while, again requires institutional access, and have experimented with 2collab and connotea (but think they are more bookmark management than reference management).

Worse, you can't import from endnote to endnoteweb - what's the point in that?

So I have no real suggestions, except for the notion of watching this thread closely and seeing what ideas come up!

Sara said...

dont have much to compare it to since its the only one i used but JabRef is what I used for my thesis. It is pretty easy to use both with Latex and also just on its own to look up references.

Chuck said...

Sara, how's life? I haven't heard from you for a while. Enjoying the real world? Do you miss Lanthanides yet?

LatEx is a bit meta for me- I can't even remember which letters to capitalize. So I'd rather not use it just for the ref management plugins, and none of the stuff I'm working on now is going to require big equations either...

Schlupp said...

Ok, so BiBTex is a database format. It has some connection to LaTex, 'cause the latter uses it. But that's about it. JabRef is a clickety-click interface for BibTex written in Java, so should run everywhere.It works with BibTex, but claims to be able to import/export data in other formats. (Never tried this, since I use BibTex and LaTex. Which is why the word cloud for my papers contains mostly LaTex commands, BTW.) You can edit your entries by writing author names ... in appropriately labeled fields, so you don't have to know any BibTex. I played around with it a bit and quite liked it.

If you have an Apple, consider Papers. I like that it automatically does all the administration for the .pdf files on my disk.

ScienceWoman said...

I assume you don't want to pay for your own copy of EndNote? Can you find a student to buy you a student license (significantly cheaper)? My only experience is with Endnote, so I can't add much to the discussion of alternatives.

For some reason, I doubt that you run a Mac, but if you do, send me an email and I have something to help you out.

Mel said...

I have a copy of Endnote for students that was pretty cheap. Let me know if you are interested in obtaining a student copy of it.

John Wilkins said...

If you want to export data from Endnote to another reference management system, try this:

Find a copy of EN you can borrow. Open your library and select all (or all that you wish to export). Then, using the Output Style Manager, choose an export format - there's five on my install, including one for BibTeX. Then choose Export under File, and select the Output style you want. Save as Text Only, and there you have a file ready to import into your new reference manager.

Chuck said...

Thanks, John. I was just about to find all my .enls to put on a stick and take into uni for extraction via friends.

To everyone else:
Nick Gardner has put together a review blog on previous forays into this field. It is here.

Nick Gardner said...

Well, if by previous forays you meant by two lines saying I've tried this, and I've tried that, but you should really go read Andy Farke's blog because he's done a series on this, then I suppose that's what it is.

Also, more shameless plugging for Andy Farke:
The Open Source Paleontologist

Anonymous said...

Papers for mac, period. organizes your pdfs and can export to many different formats (including endnote). so if you have an actively expanding library, I recommend it.

-TLH

Chuck said...

And if I'm macless? Can I run it on my iPod?

I'm afraid that I'm not quite nerdy enough to have copied my scientific pdf library onto that particular device.

flickamawa said...

I like EndNoteWeb, because you can export easily directly to it from Web of Science, but I still have institutional access and as such don't know about the pitfalls once that's gone.

Schoko said...

If you really do not want to pay for a liscence, then try to import your files (after exporting as described by John wilkins) into connotea. this is a free reference manager build by the guys of the journal Science. It is not as smart as Endnote or Refmanager, but you can add, sort and search in your references. You can also do a bibliography, but this feature is not very sophisticated, as I was not able to find an output style manager or something like that... To sum it up: It is better than nothing and worse to try it.