Managing papers

Update: 2015 August 19th: I discovered the "Retrieve Metadata from PDF" feature in Zotero that can retrieve all the metadata from a PDF and adds all the relevant information. (This doesn't work for all PDFs but for the majority it works. Note that if you perform too many queries, Google Scholar will restrict you from performing further searches.)

Since last year, I have been managing papers using Zotero following a recommendation from Casey (thanks again!):

@davetangdotorg @benjaminlmoore start using @zotero, you won't be disappointed - does bookmarking + PDF management + citation all in browser

— Casey Bergman (@caseybergman) April 1, 2013

However in 2013, I stopped using it after I quickly exhausted the 300 MB free quota. Last year, I decided to give it another go by wondering whether I could incorporate DropBox with Zotero Standalone. I found this guide and simply set the "Data Directory Location" to the zotero folder I made inside my DropBox folder. And that was it!

I use Zotero Standalone a bit primitively though. I save a PDF of an article using a simple naming scheme; the file name contains the surname of the first author, followed by the journal it was published in, and the publication year (in addition I only use lower case and I never have spaces in my file names). For example I read Gene regulation for higher cells: a theory yesterday and saved the PDF as britten_science_1969.pdf. (So far I've only ran into the problem of having two identically named PDFs once [li_bioinformatics_2009] but the directory structure of Zotero is such that they don't collide.) Then I simply use the "Store Copy of File..." option in Zotero to store a copy of the PDF, which gets automatically uploaded to the DropBox server. To make it easier to search for my papers, I have various folders within Zotero and I also add "Tags" to each paper; the file name and the tags are searchable. Within Zotero there's also a pane to write down notes, which I sometimes use; I usually just highlight my PDFs.

I'm definitely not using Zotero to its full potential, since I'm using it mainly as a PDF manager; they have various other features like the Zotero Connector for Chrome (which makes it very easy to save references directly to Zotero), citation functions for word processors (I now write my manuscripts in Vim and $$ \LaTeX $$ so I don't use these features), and other goodies. Zotero Standalone is available on OS X and Linux (and Windows but I've finally stopped using Windows) and so far I haven't run into any problems on both platforms. To synchronise all my papers on different computers, all I had to do was set the data directory to my DropBox folder (assuming that I have DropBox set up on those computers).

Some of my colleagues use Papers, Mendeley, and EndNote but I've been happy with Zotero.