Zotero

07 Nov 2017 / Leonardo Barichello

If you are starting a more "professional" academic journey, as a master or PhD student, I strongly recommend that you use a reference manager to help you organize and keep track of the things you read.

The two main roles of a reference manager are: a) help you organize papers and books you read and b) facilitate citation and referencing when producing your own text. The most common options I know are EndNote, Mendeley and Zotero. The first is paid and proprietary. The second is free (of charge) but not open source (although very friendly with users). The latter is free (of charge) and open source, so it is my choice!

zotero's logo

Below, I will present basic steps to set up Zotero, recommend some good practices, offer some specific tips that are useful for me and, finally, make some comments on advanced features.

The only limitation that is worth mentioning is the fact that Zotero does not have a built-in pdf reader, as Mendeley (I do not know about EndNote). So, every time you open a PDF stored on your collection, Zotero launches the reader on your system and you have to make notes, highlightings and annotations in it. I actually prefer this way (I like my PDF reader - Okular), but some people may prefer a built-in reader to stay always inside the same environment.

Most of the info in this post is also on this pdf that I used in a presentation at the 2017 PGR Conference - School of Education, University of Nottingham. Feel free to use and distribute it :)

Before the instructions, some comments on the interface. On the left you have the organizational features: collections (similar to folders) and list of tags (on the bottom). On the middle you have your entries (each entry can have sub-items such as the actual pdf file, notes written on zotero, images, etc). On the right you can see the metadata of the entry selected in the middle column (basic info such as authors, title, journal, etc), notes (you can use this features to attach your comments on the entry for instance), tags and a list of related papers. Note that Zotero can fill the basic info for you, but the other tabs have to the generated by you.

scheenshot of Zotero

Setting it up

  1. Download and install it;
  2. Go to Tools → Add-ons → Extensions, and activate the integration with LibreOffice or Word;
  3. Go to Edit → Preference → Sync, and create an account to be able to use groups and access your references in different devices;
  4. Go to Edit → Preference → PDF Indexing, and install the plugin that enables Zotero to get metadata from PDF files;
  5. Go to Edit → Preference → Cite, and mark Use classic Citation Dialog to have access to more options when adding a citation on LibreOffice or Word. I really think this is better than the "modern view";
  6. Create a basic set of Collections (in the column on the left), such as “For the future”, “Unread”, “Favourite”, "Thesis", etc;
  7. Decide if you are going to save all your pdfs in Zotero or not. The advantage of using Zotero for that is that you can easily find the pdf once you found the entry. The disadvantage is that the way Zotero organize the files is not so intuitive, so it is a bit complicated to find a pdf without Zotero.

Using it

The three ways to add a source are:

  1. Using unique IDs, such as DOI or ISSN (click on the wand button). By far the easiest way and recommended if you plan to collaborate;
  2. Dragging and dropping a PDF into the software (then, use the option Extract metadata from pdf after right-clicking the pdf). It does not work sometimes (it depends on how the pdf was generated);
  3. Copying (control+C) the bibtex metadata (from Google Scholar, for instance) and using the option File → Import from Clipboard. Most websites offers bibtex format, but sometimes it is not complete (specially on Google Scholar).

In terms of organization, I recommend to use lots of tags (easier to combine) and be more selective with the Collections. Finally, check regularly the “Duplicated Items” collection to avoid surprise in the future when writing.

Specific tip

This is a suggestion I read online a long time ago and found very useful during my PhD.

Zotero allows you to create collections and subcollections, which can be flexibly reorganized and renamed according to your wishes. My suggestions is: create a structure of collections that mimics the structure of your thesis. Of course you are going to change your mind during the process, but you can reorganize the collections as well to keep some resemblance.

I found this useful to recollect in the future, when you start to actually write up your thesis, the papers you read in the beginning of your research. So, when you get to your Methods section, let's say, you can check the references on your Methods collections. This way, you do not have to rely on your memory.

Advanced features

Zotero's Advanced Search is extremely powerful, allowing you to create searches combining collections, tags, search on all the fields of an entry with regular word searches. Also, it allows you to save the searches in case you want to use them in the future. This can be very powerful if well utilized.

Also, Zotero organizes the metadata in a readable and intelligible database. That is the part I love about open source! If you need to fiddle with the metadata in a way that is not supported by the software, you can open this file using any database tool and read it! And script it!

Freeing (a little bit) my mobile

27 Oct 2017 / Leonardo Barichello

Last week the crowdfunding campaign for Librem 5 finished and they achieved their goal! Actually, they exceeded it in 42%, with more than 2 million dollars raised when the goal was 1.5 million. This was a huge achievement and since they are going fully open (hardware and software) and think this could be the beginning of linux's on mobiles. Although open software may never get a significant market share on mobiles, I am very glad that this option will exist and will be viable!

My only issue with the Librem 5 is its price. I do not like mobiles, I have one because it is convenient. So, I would never pay 600 dollars in such a device. My latest devices is a second hand Nextbit Robin that costed me 130 pounds. The device was chosen because it is considered (by some reviewers) as one of the best to run Lineage OS and because I could find a second hand in good conditions.

Unfortunately, as I use some google services and I could not make the mobile work as I needed without the basic google apps. So, my solution was to install OpenGApps (the micro version), which allowed me to use Gmail, Google Calendar and Play Store with no hustle. I know there is a lot of proprietary code behind these apps and services, but I feel this is a viable step towards openness. The micro version does not include Google Maps, which was important for me since I was getting really bothered by its alerts tracking my location even when I was not actively using the app.

My next step was to install F-Droid, an Android app repository for free and open source. My intention is progressively identify good apps that may enable me to get ride of all google apps. So far, here are some recommendations:

Sparse RSS: basic rss reader to gather news and blog posts. The look is not that great, but it does what it is meant to do. The only annoying feature is that the user has to provide the full address to the rss file (it does not detect it from the basic url of a blog, for instance).

Pretty Good Music Player: folder based music player. Simple, intuitive and functional. The problem for me is that it is not possible to close the app from the status bar and I like this feature.

Vanilla Music: music player that offers the possibility of navigating your collection according to artists, albums and so on, but also according to folders. The status bar provided is very useful and functional. I am very satisfied with this app so far.

Any new app, I will post here.

BarraQDA - NvivoTools

20 Mar 2017 / Leonardo Barichello

Nvivo is the proprietary software most widely used by researchers to analyse their qualitative data. The software is very mature and offers a wide range of tools available through clicks. However, it has some problems:

  • It does not run on Linux;
  • It offers no way to extend its features;
  • It does not export to friendly formats.
  • Although most big universities offer free license to their researchers and students, Nvivo is quite expensive if you have to pay for it;
  • Finally, it is not open.

This list of reasons made me develop a software to help me organize and analyse the data I collected during my PhD research. But this post is not about my baby. Instead, I want to talk about BarraQDA - NvivoTools.

This set of tools allows you to export projects built on Nvivo to some more flexible (and open) formats. The options are RQDA (an open add-on to R that enable text coding) and a "standardized SQL format" that is coherent with current schemes for qualitative data and very user-friendly for non-experienced programmers.

Recently, I used the script to convert Nvivo to SQL to help a colleague generate a report ordered by an criteria that was not supported by Nvivo. Once exported, I opened it using SQLite Manager on Firefox and run a query doing what she needed. Lovely!

If you are stuck with Nvivo, you may consider these scripts to get some freedom if you need...



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