By Grant Jacobs 18/01/2017

Three free tools for filing research papers and browsing the web.

If you’re in research—be it scientific work, writing a book, or similar—you’ll be spending a lot of time gathering material on-line and filing it.

There are a lot of tools out there, and everyone has their favourites. Let me introduce three I use (along with others*).

I collect and read a lot of research papers. I also like to track other’s writing on science. It’s nice to be able to file both research papers and websites under the same tool and filing scheme.


Zotero will file research papers and web pages direct from the web browser. In their blurb they say, “You can add PDFs, images, audio and video files, snapshots of web pages, and really anything else.” In that way Zotero can serve as your one point to bookmarking all your research content. (One thing it can’t do, as far as I know, is to file selected text from a web page, as apparently EverNote can.)

There are two editions of Zotero – one that files your stuff to Zotero’s server, and one that stores them locally using a stand-alone application. I use the latter, and don’t have experience of the former.

Once you’ve installed Zotero, a new icon is added to your web browser. Click on that and the current web page will be filed to Zotero. If the web page is a research paper, Zotero will try file the PDF for the paper, too.

You’ll find that the icon for Zotero will change, depending on what it thinks the web page is, reflecting what it will store.

For all things Zotero, head over to

One quick tip: if you find Zotero won’t file a page from the web browser menubar icon, right-click (control-click) the page: the pop-menu should include ‘Save Page to Zotero’. If you select this, Zotero will save a snapshot of the page.


Zotfile bills itself as ‘Advanced PDF management for Zotero’.

It’s is an add-on for Zotero that let’s you do do more with PDFs in Zotero, including those Zotero has just gotten. Realistically if you’re using Zotero for research filing, get Zotfile.**

You can,

  • Attach New Files to Zotero Items Sometimes you want to add the PDF of the research paper later, perhaps because it was from a subscription-only journal you didn’t have access to and had to get a copy from the corresponding author. This let’s you do that. It also provides a work-around for those research journal papers that Zotero can’t automatically grab and download the research paper PDF from. You can have Zotfile watch a folder (directory) for new PDFs.
  • (Batch) Rename and Move Attachments based on Zotero Metadata You can have them filed into a file structure of your choice, for example, naming the file from the authors, titles, journals, publishers, etc., filed in folders (directories) named by year, journal, etc.
  • Sync PDFs with your iPad or Android tablet I have no experience of this, but I can imagine this is useful to those with tablets, who would prefer to read the PDFs on their tablet.
  • Extract Annotations from PDF Files You can select text in the PDF, and have it filed as notes in Zotero.

There’s more that could be said, but that’s enough for today!

For Zotfile, head to

While we’re on the subject of PDFs, if you’re using Mac OS X don’t forget to check out Skim, a free PDF reader and note-taker for OS X. I introduced Skim at Code for life about five years ago; the basics are still be the same.

(I could write more on Zotero and Zotfile, as I have (old!) notes with detailed tips on how to use them. In the meantime I’d just like to introduce these tools. Let me know if more information might help!)


Some may remember that Opera once offered an excellent free web browser, with their own web page rendering engine. The company has now been sold to a Chinese outfit. A team has set up a start-up to develop a new free web browser, Vivaldi. They posted their first full release late last year.

Vivaldi is aimed at those who use web browsers a lot.

One of Opera’s big strengths was being able to get in and tweak many settings to tailor the web browser to your needs. Vivaldi does the same.

Vivaldi can use most Chrome browser extensions. Chrome is Google’s web browser. Among these is the Chrome Zotero extension. To see what extensions you have, type vivaldi://extensions into Vivaldi’s web address text box. You’ll also be offered a link to the Chrome extension store.

To get Vivaldi, it’s at

Featured image: Portrait of Jean Miélot. They note,

Burgundian scribe (portrait of Jean Miélot, secretary, copyist and translator to Duke Philip the Good of Burgundy, from a copy of his compilation of the Miracles de Notre Dame NOTE: NOT IN FACT A MONK AT ALL, though a canon of Lille Cathedral.), 15th century. The picture is greatly detailed in its rendering of the room’s furnishings, the writer’s materials, equipment, and activity.

Source: Wikimedia Commons, public domain.


* I try (!) to use to different web browsers for different things. When I’m downloading a lot of papers or building up material, I tend to look for a stable browser. Safari links well with the rest of Mac OS X (or iOS), but in my experience it crashes a lot if you try have open more than a trivial number of tabs. When it crashes it ties up the system, forcing me to force quit everything reboot — a major interruption to the work flow. Hence looking to a stable browser when I’m doing work! If I’m just catching up on social media, and generally browsing, Safari is fine.

** Zotero has added some of Zotfile’s features over time; it may pay to keep an eye on that, as it’s a tiny bit faster to do things without Zotfile, as Zotfile takes a (usually brief) moment to fire up and do it’s thing.

0 Responses to “Filing research papers and web browsing: Zotero, Zotfile and Vivaldi”

  • Great post Grant, thanks for reviewing these. I used Zotero ages ago but ended up with EndNote on account of the Word referencing functionality (and access through a university). However EndNote isn’t great at keeping track of websites etc.. I’ll be having a closer look at these.

  • You can get a bibliography into Word with Zotero, apparently. I haven’t done this myself as I haven’t gone back to pick up Word (I should, but I never get to it!) There’s a plugin or something for that – I’d have to look it up.

  • A new version of Zotero has come out during the year. I probably won’t get to reviewing it, but there is an updated tutorial and a slide show in this blog post:

    Another tool for tracking & filing stuff available on Mac OS X is EverNote, which some rave about.

    One thing EverNote claims to do that Zotero won’t: file selected scraps of text from websites. I keep meaning to suggest it to the Zotero team, as it seems to be it’d be great for filing quotes you want to use from wherever – newspaper articles, etc. One poor man’s substitute is to cut’n’paste the relevant text into the notes Zotero lets you write about filed entries. Another is to file the webpage with a snapshot of it, and highlight the saved text, but I’ve never explored that.