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Not sure if this is the right place to ask, but I am trying sync my pdf archive (of manuscripts) between several computers (OS X, Linux, and Windows).

I am currently using the Mendeley Desktop software on OS X (with pdf archive in my user directory), but it associates metadata with the absolute location of each file on the hard drive. Therefore, it is difficult to sync the archive (not just the metadata) across platforms. I read once that you can create a symbolic link to /home/ as @/Users/ on Linux to emulate the path you would have on OS X, but I would like a less kludgy solution (though this is clever) which preferably avoids monthly fees for remote storage, as my archive is quite large (~15 GB currently). I would rather pay for a suitable piece software (that extracts pdf metadata and manages them -- i.e., rename and allow search) than storage space, if there is such an option. So far I have found none suitable (though I was hoping for Zotero to step up, but please see below). Also, as discussed by several threads on the Mendeley forums, there are manuscripts which I prefer not to be hosted on their servers. My archive size exceeds my Dropbox quota; I am also using Dropbox actively for other things so I cannot allocate enough GB required to store my pdfs with my current account without upgrading. However, there would still be an issue as paths to the Dropbox folder set up on my machines each have different absolute path names (which Mendeley would not recognize).

I have recently downloaded Zotero Standalone as I heard Zotero can also manage and rename pdfs based on extracted metadata, but I have not been able to discover this feature in this software. This may still be lacking from the standalone version (Firefox has a ZotFile extension which does this, from what I gather).

Alternatively, is it feasible to try to move all of my pdfs to a folder like /var/pdfs/ on all of my machines, which then is easy to coordinate absolute path names? (Windows would still be a problem as Mendeley would not use cygwin paths, but I may be able to live with not syncing on my Windows machine).

I have several questions, which is whether 1) Zotero can indeed serve this functionality, 2) whether using the /var/ directory universally could be a solution, or 3) what other solutions have you found for your pdf archive?

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I am one of the founders of Docear, which is a new software for organizing, creating, and discovering academic literature. Today, we released version 1.0 of Docear after a ~2 year beta phase. If you are interested in reference management, you might want to have a look at Docear. The three most distinct features of Docear are:

  1. A single-section user-interface that differs significantly from the interfaces you know from Zotero, JabRef, Mendeley, Endnote, ... and that allows a more comprehensive organization of your electronic literature (PDFs) and the annotations you created (i.e highlighted text, comments, and bookmarks).

  2. A 'literature suite concept' that allows you to draft and write your own assignments, papers, theses, books, etc. based on the annotations you previously created.

  3. A research paper recommender system that allows you to discover new academic literature.

And Docear is free and open source and available for Windows, Mac, and Linux. More information can be found in our Blog, including a detailed explanation of what makes Docear superior to Mendeley, Zotero, etc. (at least in our opinion :-) ).

If you don't like reading, there is also a 6 minute introduction video on our homepage.

In case you are using a BibTeX based reference manager such as JabRef (and you don't want to switch to Docear), you might at least be interested in Docear4Word. Docear4Word allows you to insert references and bibliographies from BibTeX files to MS-Word documents. Hence, it makes writing papers much easier, since e.g. JabRef has no own MS Word add-on.

Finally, I would like to point you to a recent Blog post I wrote about what makes an evil reference manager. Maybe the post helps you deciding which reference manager to use (even if it's not Docear).

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Thanks - I look forward to this development, especially the addition of syncing capability. Currently I have switched to Zotero but would be open to another switch as Zotero is slow and crashes a lot, I've found. – crippledlambda Nov 17 '13 at 22:46

Mendeley allows you to sync across multiple platforms. I use it on multiple machines and devices. Each install should have it's own set of files and therefore allow you to access the PDFs without issue. If you by any chance are not synchronizing the files to Mendeley Web due to some reason such as space constraints, then this becomes difficult to assure proper sync across multiple platforms.

As for manuscripts and not wanting them to be indexed by Mendeley's research catalog, the easiest way is to tick the box at the bottom of the "document details" (right side panel) to make sure the document is excluded from there. Take a look at this blog post:

Disclaimer: I'm a community liaison with Mendeley and a PhD candidate using Mendeley since the beginning of my Master's degree.

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