MacResearch

To organize the PDF of articles and papers, I use BibDesk... an open source bibliography-manager program.

http://bibdesk.sourceforge.net/

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I'm not telling you that you should believe me. Learn the facts, and the origins behind the facts, and make up your own damn mind. That's why you have one.

I like to use the app I found out about on this site. iPapers. This is a terrific app that lets you download pdfs directly via pubmed central. It stores the pdfs by naming them with the PID number which may be limiting if your your papers aren't indexed there.
Cheers
-Chris
see:
http://homepage.mac.com/toshihiro_aoyama/iPapers/

I looked at DevonThink for this purpose before, but realized that it doesn't match my needs at all. I am very happy with Bibdesk. It is an amazing little piece of software and exactly what I needed to organize my papers + Bibtex references.

Bookends is bibliography/citation management software that also manages PDFs very nicely. In general Bookends serves the same function as Endnote, but has a much nicer and more stable user interface. You can drag PDFs (or any other file, I believe) to a citation in its library, or in some cases download the PDF directly from the internet during a pubmed search. I've moved most of my saved PDFs over to BookEnds, and it's made management and searches easier.

Previously, I would use MS Word and Endnote or Bookends, but the software really started to be somewhat unreliable particularly when dealing with embedded images or cross-platform-compatibility, so I switched, not only from Mac to Mac/Windows/Linux, but also from dedicated applications to a more relaxed approach.

About PDF organization:

I found that I have to read PDFs and not "organize" them, so I spend more time reading than I spend time "organizing" them. That helps me really knowing about the stuff that's in them and remembering who wrote what. Then I use the OS to take care of me finding the PDFs again:

- so, PDFs are all read, and then renamed, so Miller P, Smith J (2005) Where to put literature. Journal 12(4):1-2 would become something like miller2005where_put_lit.pdf (advantage: sorting automatically, or by date, will give you a within-10-second-find of most what you remember);

- PDFs are then stored in crudely categorized folders, all of which reside in one folder that contains them all; so, it's not very difficult to define some broad categories and let that be it (advantage: you want to take one folder home to go over a particular subject, just copy the whole thing and go through it with your PDF reader);

- Beagle (Linux) or Spotlight (Mac OS X) or Google Desktop (Windows) automatically indexes the PDF files, so no need to worry, I can find them again later on any machine (advantage: no specific software is needed, OS does it for you).

About citations:

In order to store some meta-information about these articles, to add some reading notes, to add what I thought should be cited, and to have them ready for citation, I use Aigaion (free pHp/mySQL software; if you want, you can also use this to store your PDFs there). I can import bibtex entries using a text-import dialog field, or I can import bibtex-files, and use the search function:

http://www.aigaion.nl/

With this, I can get to the information from another computer on the same network, be it on a workstation in another room, or laptop computer, and also it doesn't matter whether I run some Unix / Linux or Macintosh OS X system.

In order to work on the documents, on Mac OS X, Windows or Linux, I use texmaker:

http://www.xm1math.net/texmaker/

Advantage - it really doesn't matter what system I run it on, as long as I install the necessary components.

So, I can use a particular computer like a Macintosh, but I'm really not restricted to it (using Powermac G5, or PC / AMD-Workstation running Suse Linux, or PC / AMD Laptop running Ubuntu or Windows XP) and so I can change system while not having to change working technique / workflow and can maintain a good focus on content.

So, first I copy all files into location, then I update the current PDF choice, then I update citations, then I update Text-File folders, and keep going through that cycle.

I use both JabRef and Bibdesk to manage my BibTeX bibliographies. I have found that JabRef excels at manipulating .bib files, for example, JabRef has the ability to automatically abbreviate or unabbreviate journal titles. I have found Bibdesk excels at importing bibliographic data and managing article collections, and so I currently use Bibdesk to manage my digital article collection. It will be interesting to see how both programs evolve in the near future.

Hi,

I use the excellent Papers app. It integrates searches for different repositories and automatically extracts lots of metadata. Major disadvantage at the moment is that it is very centered on journal papers, while there are more ways to publish. But they're working on that...

Dirkjan

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Ph.D. student Auditory Cognition Group
Artificial Intelligence, University of Groningen
Tel: +31 30 363 6955
j.d.krijnders@ai.rug.nl