A new initiative by the NCCR on the move: a reference database on crisis and migration. Freely available on Zotero (obviously): https://www.zotero.org/groups/4873171/crisismigref/library
Mastering Zotero: an introduction video
I have compiled a video introducing the most important features of Zotero — the only reference manager you ever need.
The video covers different ways to get references into Zotero, mostly from websites, but I also show how to add PDF documents and to import references from a BibTeX or RIS document. For organizing references, we look at folders (a.k.a. collections) and tags; sub-collections and colourful tags are included. I show how to use the advanced search and saved searches, and we’ll see how the integrated PDF reader is very helpful to create notes from annotations. Collaboration using group libraries is covered, and I show how to cite your references in a word processor like Microsoft Word or LibreOffice.
Cleaning up Zotero’s “The attached file could not be found at the following path”
After an upgrade to one of the machines linked to my Zotero account, I got errors that some of the attached filed could not be found. Now, I attach most of my files, so I was pretty sure that the files were there. I also double-checked that the base directory was set correctly, and that it was set to relative paths (moreover, only some of the attached PDF were affected, so I knew that the basic setup was OK).
Using Zutilo (a plugin for Zotero), I could figure out that the problem of those attached files was that an absolute path was set. In fact, on the Windows machine (i.e. the machine that was upgraded and where Zotero was set up afresh), I could simply choose to select the file again to resolve the issue, but there were more than a handful of attachments involved.
So I used the Zotero Storage Scanner (another plugin for Zotero). I was useful to read the instructions, as the scanner plugin has no GUI and works in the background to tag broken attachments. On my machine, I got around 1 entry tagged per second, so adjust your expectations accordingly.
Because the scanner plugin tags the attachments/PDF and not the articles, I then created a new collection in Zotero. Selecting the #broken_attachments tag, pressing minus (to collapse all items), I then added all the items to that collection. This way, I was sure to select the entries for the next step.
Selecting all articles with broken attachments, enter Zutilo for the second time. This time, I needed to “Modify attachment paths”. There are two boxes, one after the other. So in the first one, I entered that part of the absolute path, that wasn’t needed (I copied this from Zutilo’s “show attachment paths”), like “D:\ZoteroPDF\” (without quotes). In the second one, I added “attachments:” (without quotes, but including the colon). On my machine, this took around 3 seconds for 2k items.
Because I did the fixes on the GNU/Linux machine (this will also apply to Mac), I used Zutilo once again to modify attachment paths: In the first box, I entered the backslash (“\” without quotes), and made sure to tick “change all instances”, and then in the second box I entered the forward slash (“/” without quotes).
Getting everything synced on the Zotero servers took a while, but all my attachments work again as they should.
More Support and Templates in SciFlow
SciFlow is an online editor for academics. They have recently updated and expanded the documentation, so should you ever get stuck, here’s how to. That said, the interface is pretty intuitive, so I’m not sure you’ll ever need to navigate to the support pages for basic editing.
There are some useful hints, though, like using zbib (Zotero) with Sciflow (instructions here). This gets pretty close to Authorea’s citation feature, and is also useful for collaborative texts (and doesn’t suffer from the slowness of direct Zotero/Mendeley connections if you have a large database of references).
The SciFlow team have also recently updated the Templates feature:
There are many journal styles to choose from. It’s not quite (yet) like typeset.io, but the social sciences are not well covered by typeset anyway. SciFlow offers some useful templates, but in most cases, it’s necessary to do some finishing before submitting to a journal. On the other hand, there’s a template for minutes — that’s useful for anyone working in a team, and who isn’t?
In most cases the generic templates will do, including the SciFlow templates which support many common citation styles.
Zotero!
If you aren’t, you should be using Zotero. It amazes me to see researchers ‘managing’ their references manually these days. It’s complicated, takes time, is prone to errors, and simply unnecessary. There are many options out there to manage your references, but you should look at the free and open Zotero. You can install it on all your devices, you’re not limited in the number of citations you can use, you can take it with you when you change workplace, and in fact you’re not even restricted to the feature of Zotero because you can use plugins. Seamless integration in word processors isn’t going to stand out from the competition, but getting stuff into Zotero takes no effort at all — it’s unparalleled easy with just one click in your web browser. You get free syncing, too. There really is no reason not to keep notes of what you are reading.
After grabbing Zotero, you probably want Zotfile, too. Zotfile manages your PDF versions of research articles. In my view, the most useful feature is the ability to extract highlighted text from the PDF. It’s so practical that I sometimes even don’t take proper notes (for the main points, you should store them in your brain anyway).
Image credit: Zotero, Zotfile
Didier Ruedin 