
Ask HN: How do you organize scientific literature? - ayu
I look for research papers frequently and it&#x27;s becoming difficult to manage them all.<p>My current system is a local directory synced between computers. There are subdirectories for fields of study, and each field has further subdirectories for topics of interest. Right now this is adequate. Problems it has:
1. Difficult to browse through topic directories
2. Need to manually rename papers to a common filename format (e.g. Author Year Title.pdf)
3. Can&#x27;t annotate papers<p>I&#x27;ve tried PaperPile, a web-based literature manager, and it generally works pretty well. However I dislike that it requires Google Apps login, and it costs money which feels contrary to the principle that knowledge should be free and open.<p>Calibre is a software usually used for ebooks that also seems promising for research papers. It&#x27;s licensed under GPL v3 and supports tags, search and metadata download (via plugin with some configuration). It doesn&#x27;t seem to have good annotation support.<p>I&#x27;m interested in ways you manage your scientific literature. If you could share them I&#x27;d really appreciate it!
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veddox
Check out Mendeley, ReadCube and Citavi.

ReadCube (www.readcube.com) is focussed on organizing your personal library,
though it also has an inbuilt PDF viewer with annotation capabilities and a
browser for searching PubMed, Scholar et al. It is cross-platform: Windows,
Mac, mobile - not Linux though. A very nice interface and the basic version is
free. The Pro license brings you cloud storage and syncing.

Citavi (www.citavi.com) is probably the ultimate desktop software for managing
scientific literature. Apart from organizing your library, annotating PDFs and
writing notes, it also has plenty of tools to help you write your own
articles. Unfortunately, it only runs on Windows and comes with a hefty price
tag (though many institutions have a site license - check if you are
eligible).

Mendeley (www.mendeley.com) might be the best choice for you. Like ReadCube,
it concentrates mainly on library management and paper annotation. However, it
also provides plugins for browsers and word processors that add some neat
functionality (such as automatic citation insertion for LibreOffice). It is
multiplatform (Windows, Mac, Linux, mobile) and free. Syncing is included in
the basic free plan, the premium plan gives you more storage space and
teamworking functions.

Sadly, none of the above is open source, and only Mendeley works on Linux.
Otherwise, take your pick :-)

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auxym
I used Zotero, mostly for it's automatic database filling feature (eg from a
journal website). I sort-of classified papers in in a directory-like structure
by topic. When it came time to find stuff, the search worked pretty well,
considering most papers had the abstract filled out in zotero and therefore
was indexed for searching.

Good support for shared libraries if you work with other people.

Combined with a plugin called lyz, it made for a very streamlined integration
in my thesis workflow (in lyx).

Bonus: free and open source.

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OopsCriticality
BibDesk for filing (and of course as a citation manager). Any notes for an
article I store as an identically named plain text file generated by text-to-
speech dictation while I'm reading, e.g., "page 7, column 2, VERIFY they used
0 point 1 molar thiosulfate, but I believe that 0 point 5 would be necessary
to reproduce their results". I rely on Spotlight to find things.

~~~
codles
I too use bibdesk. While the file format is open, I haven't found an
equivalent Windows editor. Do you know of one?

~~~
OopsCriticality
JabRef?

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Dmitry_Bryliuk
there is more arbitrary web-tool

it is possible to organize information into folders, properties and relations.
so you may implement arbitrary classification and efficiently search through
it. it is possible to make annotations. it is possible to share your
information to other people.

it is free.

however it requires google login and no file uploading - you may use your
google drive and post links.

[http://project-identity.com](http://project-identity.com)

I have started entering my own worth to read book list, if you can read
russian you may enter search request to get it: name: тема value: книги
которые стоит почитать

or browse user Dmitry.Bryliuk@ directly

