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Managing Bibliographic References

26. August 2011 at 09:03
filed under Binäres Leben, Neues aus dem Elfenbeinturm
Tagged bibliography, bibtex, dropbox, english, idisk, ipad, papers, references, science, syncing

Being some kind of scientist, I read a lot of papers. And because I want to cite and therefore re-find some of these papers, they need to be organized somehow. Apart from the core data (author, title, conference/journal, year etc.), organizing should include notes, PDF documents, BibTeX-export and be synced to my iPad (To be exact: I want a part of the library synced to the iPad, not all 500 papers).

Papers

Of course, there’s software for that: Papers for instance. Papers looks good, has an iPad/iPhone app and syncs between them. So, I tried using Papers (2.0). To make it short, I didn’t like it very much. It all worked fine, but for some reason I didn’t like it. And it’s expensive: 59 € for the Mac app, plus 12 € for the touch app — too expensive for not being completely satisfied.

BibDesk

Before my Papers-experiment, I used BibDesk. BibDesk is essentially a BibTeX editor for Mac OS X. You can read and write BibTeX files. In addition, BibDesk can organize PDF documents (the feature is called AutoFile) and stores links between BibTeX entries and PDFs. Using BibDesk, you can specify additional (non-standard BibTeX) fields to be stored in the file. The only thing missing is the syncing with my iPad.

But today, I found the solution for that.

Syncing BibDesk Entries to the iPad

By entries, I mean PDF-papers (I don’t need full references on the iPad, because I only read on it). This how it works:

1. Point the location for AutoFile to some kind of web space (I use iDisk, but Dropbox or any kind of WebDAV should be fine).
2. Add a new BibTeX-field called “Sync”, make it boolean. This results in a checkbox at the bottom of each entry window.
3. Now, go back to the AutoFile preference pane. On the bottom, you can edit the format string, which controls the folders and file names of your papers. Click on “Advanced…”. Then, add the format specifier %s{Sync}[Sync][][]0/ to the beginning of your format string (BibDesk documentation). %s works a little bit like if then else: If the field “Sync” (the parameter in curly braces) is non-empty (true), the string “Sync” (the first parameter in square braces) is returned. In all other cases, an empty string is returned (the last two pairs of braces). The integer at the end can limit the returned string to a specific length or set it to unlimited (0).
   My complete format string looks like this:
   %s{Sync}[Sync][][]0/%Y/%t0%u0%eThis results in the following structure:

   Sync/
     2007/
       Title.pdf
       Title.pdf
     2008/
       Title.pdf
   2007/
     Title.pdf
   2008/
     ...
   

   Thus, in the directory “Sync” we have all PDFs that are marked as “Sync” in BibDesk. Under that, we have organized the papers by year. Papers not marked as Sync in BibDesk are stored year-wise at the top.

4. We want to sync the folder “Sync” on our remote disk to an iPad. I use GoodReader (3,99 €) for that (although I am sure that there are other options). GoodReader can be configured to sync a folder on the iDisk/Dropbox to the iPad. The sync goes in both ways, so if your annotating a PDF with comments and highlighting, the PDFs will be uploaded to the server next time you touch the sync button.

That’s it. Now we have configured syncing of marked BibDesk entries to the iPad.

Downside(s)

1. On the iDisk/Dropbox, the PDFs are moved to the Sync folder. This is not exactly what I want, but it’s close enough.
2. You have to manually start the syncing. There is no way of automatically push every change.
3. No automatic merging of changes: If you changed the PDF on the iPad and on the server and then sync, GoodReader will ask you which file to use.

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