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Is there any smart way to manage scientific papers for offline use in a linux system.

For example:

  • It should be possible to tag papers with customizable tags, sort them by tags and so on
  • if I see a new paper on arxiv.org and want to read it if I have more time, there should be a nice way to put it to my "read it later list" of my paper manager
  • the paper manager should allow me to store bibtex data
  • it should give an easy way to write down notes and comments to individual papers (supporting math-formulas)
  • support pdf and djvu
  • should be easy to backup

I don't need any integration to word-processing software.

share|improve this question
You may want to try asking on scicomp.stackexchange.com – Lorin Hochstein Mar 5 '12 at 22:15
@LorinHochstein Nothing to do with Computational Science. Possibly Academia, depending on where that's heading. Or TeX - LaTeX, for a (Bib)TeX-based solution. But the question is fine here. – Gilles Mar 5 '12 at 23:25
Jabref with some additional plugins fulfills most of your wishlist. – jofel Mar 5 '12 at 23:25
Take a look at gpapers.org – user6435 Mar 5 '12 at 23:34
Check out zotero.org, from poking around on their website it seems to support everything your requested. – André Paramés Mar 11 '12 at 23:36
up vote 3 down vote accepted

Mendeley Desktop (http://www.mendeley.com/) is pretty close to what you want; it supports tagging papers (although I haven't used this feature), adding nodes to papers, viewing/annotating PDFs, and it has web-based imports for several reference sites including arXiv: http://www.mendeley.com/import/. There is a Debian/Ubuntu repository to install the desktop client.

And of course, it can export to bibtex.

Note that it keeps your references on their server, and you might have to change some settings to get it to sync the PDF files with the references, but it stores the data under ~/.local/share/data/Mendeley\ Ltd./Mendeley\ Desktop/ so there is a local copy available.

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Does that mean, that I can use it offline? – student Apr 14 '12 at 7:05
It does work offline; you can add PDFs and references without synchronizing to the server. – Joseph Apr 14 '12 at 20:51
But I have to create a mendely account? – student Apr 15 '12 at 8:34
Yes, I think you need a Mendeley account; it's a web-based reference management system with a desktop client that can function offline. – Joseph Apr 18 '12 at 11:26

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