Bibdesk
Here’s one for the academic geeks… After many years of using Endnote, I’ve finally switched to using BibDesk to organise my references. This will probably make me sound prehistoric, but when I did my PhD I used 3 x 5 index cards in a box to file my references. This had certain advantages—-you could pop down to the library with a stack of blank cards and fill the details in as you did your reading—-but they were hell to search. Things were fine if you could remember the first author, but if you only knew one of the authors, or part of the title, you were sunk. And then there was the whole dropping the entire box on the floor and having to resort the references thing—-not a good use of time.
So, when I switched to Endnote, it felt like a huge step up. There has always been a bit of a reference manager divide between the Physical Sciences and the Biosciences. Physicists, mathematicians and engineers tend to use LaTeX to write their papers (because of the all the equations, for one thing), so naturally use BibTeX to organise their references. Biologists tend to use Word (ack), and so use Endnote. I wish that this wasn’t the case, because BibTeX has a lot to recommend it. The files are just structured plain text, so there’s no fear that years of research will be locked into a corrupted, proprietary format. For the same reason, it’s easy to send colleagues snippets of text that can just be pasted into their *.bib files, already in the right format.
I’m writing in LaTeX much more now, so I felt that the time was right to switch. Endnote has felt more and more elderly, bloated and unloved over the years, and I’m happy to see the back of it. BibDesk is Open Source, and has great Applescript support, so even if you’re not using LaTeX, you can fairly easily knock up a script to print out your reference list nicely.
While I’m on the subject of references, I’ve also really got in to using CiteULike. It’s similar to del.icio.us, but geared towards academic references. It has tags, and the social nature of the system means that you often pick up interesting references by surfing other people’s tags. We have a reading group at work, and it’s really handy to list and tag the papers we’re going to read on CiteULike, so that everyone has the full information. As a bonus, it’s really easy to import or export references as BibTeX (or Endnote, but I haven’t tested that).
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Wow, this is defintely one of the most exciting blogs out there. I shall be paying you a visit more often if that's aight by you of course.
BTW, I came here by via a link on pandora's blog ----- Hey, a nice surprise - I already check your blog occasionally and here you've mentioned my project!
Welcome to the BibDesk nation - please feel free to suggest changes and comment on our future plans - there's a users list and a wiki you may be interested in. See http://bibdesk.sf.net/ for all the links, of course.
by Michael McCracken @ 25/05/2005 10:06 pm • Permalink •
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This is interesting. I have been thinking of trying out a Mac at home with the new Mac Mini, and was curious what the LaTeX process was like. It seems that things are much nicer on the Mac than Windows!
I still have a few concerns about switching:
by stressedacademic @ 26/05/2005 10:05 am • Permalink •
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Dave: Thanks!
Michael McCracken: Hi! You've built a great piece of software there. If I have any ideas I'll let you know, but it's working just the way I want it to at the moment
stressedacademic: (rubs hands) Aha, a potential convert...
I say go for it :-D
by bsag @ 26/05/2005 5:06 pm • Permalink •
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Me big NoteBook fan too. Checking those status boxes is the nearest I'll ever get to being organized! I won't allow myself to get any more organized
I used to be an OmniOutliner-er, but I think NoteBook is slightly more relaxed about life, somehow.
by pete @ 27/05/2005 1:06 pm • Permalink •
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Very interesting post. I shall have a look at BibDesk
I used for a long time Filemaker for story both my notes and bibliographical references. Having switched back from PC to Mac last year, I first tried Scribe. After discovering Devonthink, I decided to try completely "live" in it, at least for most of the research side of my academic activity. I now store all my bibliographical references in DT, and make the most of its wiki capability. I have had a few posts on this little experiment on my blog.
by Pascal Venier @ 27/05/2005 11:06 pm • Permalink •
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I moved from Endnote + Word to JabRef + LyX a couple of years back when I dumped the Sony laptop (a pig to run linux on) and bought a shiny new Powerbook. I've not looked back.
by DTL @ 29/05/2005 12:05 pm • Permalink •
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Yes, yes, yes ... Bibdesk is just terrific. Works a treat. And you are dead right to emphasize the virtue of never being locked into a proprietary file format. We (academics) don't shout about that loudly enough. (A very sore point, having been a dedicated FrameMaker user until Adobe dropped it for the Mac ...)
And yes, Notebook is terrific too -- in fact I think I first heard about it here, and it's invaluable (or at least, definitely worth the amazing bargain education price: so many thanks for the pointer).
by Peter Smith @ 01/06/2005 10:06 pm • Permalink •
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Pete and Peter Smith: Yes, Notebook is a real keeper. I like the fact that it's so flexible and open ended. The other day I was taking some notes on a PDF article in Notebook, and realised that I could take a screenshot of one of the figures then drag it in to Notebook to refer to it later without having to open the PDF file.
Pascal Venier: I think you'll like BibDesk. I like DevonThink too, but I think that having a dedicated reference manager would be a big advantage.
DTL: I've had a go on LyX, and quite liked it, though I'm just as happy writing plain LaTeX in a text editor.
Peter: (re: file formats) I think it's really important to keep our files in an open format. If not for our own peace of mind, someone else might want to re-analyse our data in future.
by bsag @ 02/06/2005 5:07 pm • Permalink •
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Oh by the way - did you know that NoteBook can do TeX and LaTeX? Just start a cell with %tex or %latex and type your stuff - then look on the menu.
Weird, eh?
by pete @ 04/06/2005 7:06 am • Permalink •
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pete: No way! But I tried it and got an error. I'd love it if it worked for me. I wonder what the problem is...
by bsag @ 05/06/2005 3:06 pm • Permalink •
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