I recently started my PhD and now try to find a convenient software for managing my literature research. What I want it to be able to do is:

  • Let me highlight PDFs
  • Add notes to PDFs
  • Add tags to my literature
  • (as a bonus:) load methadata and create bibtex files

I personally really like Mendeley as it does pretty much exactly that. At my institute we have a strict open source policy though, which excludes Mendeley. Is there an open source alternative to Mendeley, which runs under Linux Gnome?

Thanks for your input.


2 Answers 2


I have been in your shoes before and am currently looking for some form of pdf organization.

Here are a few alternatives : http://alternativeto.net/software/mendeley/

What I use, is dropbox. I even dropped Mendeley because it didn't sync well with android for annotations. I can favorite papers I need to have on my phone/tablet at all times and always have access to them. My fellow cohort feels the same way about the lack of pdf organization as we generally just print out what we need. I've been searching for years and the only thing I can come up with is paper.

Sorry this is isn't more useful, but from my experience, paper is really the way to go.


I would say that Zotero is an obvious alternative. It does all the things you mention and is free (in its basic form) and open. You can store the pdfs locally or buy cloud storage. It can be used to add multiple notes to papers, connect other files to papers (figures etc), add tags, and it will also allow you to extract metadata from pdf files. Individual papers or collections of papers can also be exported as Bibtex-files or other formats. You can run Zotero either as a web browser plugin or as a locally installed program, and it works on Linux.

Personally, I've mostly moved from Endnote to a mixture of Zotero and Jabref for my reference software.

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