Where should I publish?

26 Apr 2018 / Leonardo Barichello

A common recommendation for those starting to publish in academic journals is try to go for the journal you read the most. Of course this could mean a highly competitive journal, in which case you may need to consider other options, but the idea behind this advice is that by reading papers from a journal you get familiar with its style, purposes and so on and, therefore, all this would reflect in your paper.

When I heard this advice my computer programmer brain thought: I could write a script to do this for me!

Since I use Zotero and Zotero is a very friendly open source software, I decided to try to write a script in Python that would search its database. After checking the tables, I could identify where the information I needed was (see the query below).

SELECT * FROM itemData INNER JOIN itemDataValues ON itemData.valueID=itemDataValues.valueID
WHERE fieldID=12 ORDER BY value

For those interested: 12 is the id for the "publication" field, which contains the title of the journal for "journal article" items.

You can use the query above in any software that can read SQLite (I recommend SQLiteBrowser on Linux). But if you are not experienced with such things, you can just download the script available on my github or here (this link may be outdated).

After unzip it, you will get a .py file. Save it on main Zotero's folder (you will see a zotero.sqlite file in it) and run the script. It depends on some very basic Python library, which I believe are installed in most computers being regularly used. The screenshot below shows the result.


Now, you just need to scroll the list and find the most common journal in your library (pay attention to small variations in the title of the journal - the script is sensitive to them). For me, it was the Educational Studies in Mathematics.

Presentation using beamer via pandoc

09 Apr 2018 / Leonardo Barichello

Beamer is a tool to create slide presentations using Latex. Since I was "forced" to use Latex for a project I am involved with, I am trying to use it as much as possible to get acquainted with its quirks; which, by the way, are a lot.

Some time ago I heard of Pandoc. A tool that allows you to export text created with markdown (supposedly the most intuitive way to format text without using an interfaced software such as Libreoffice). The idea of exporting my notes, such as below, directly to a slide(image further down) is very appealing to me, so I decided to combine both to generate a pdf presentation directly from my notes.

## The lesson plans

- 12 lessons plans grouped into 3 packs (one per term);
- Worksheets + Comments for the teacher + cut-outs;
- Topics covered:
    - equivalent fractions,
    - comparison of fractions,
    - addition and subtraction,
    - mixed numbers and improper fractions,
    - word problems.

slide generated with pandoc and beamer

You can check the complete file with my notes in markdown (actually, just a part of it - just enough to show the most important codes in markdown) and the resulting pdf presentation.

Once you have pandoc and latex (with packages to run beamer) installed, use just have to use the following command to compile the presentation:

pandoc inputfile.md -t beamer -o output.pdf

Basically, pandoc generates a latex file and then uses latex+beamer to create a pdf formatted as a presentation.

Some comments

  • The first block of content is the metadata, which generates the front page and set some parameters regarding the layout. The slide_level parameter determines how many sections and subsections (marked by # in the md file) are before something is an actual slide. The header-includes are some parameter to change the layout of the theme I used. The others are sort of self explanatory;
  • I really do not like beamer's default themes, so I used metropolis. It is well documented and very elegant. It has some limitations and small bugs, but it does work and looks really nice;
  • The standout slide (last one) did not work perfectly for me. When I used it in the middle of the presentation it affected the title of the next slide. I guess it is a problem in the interaction between pandoc and the theme;
  • Beamer does not offer fields for supervisors and funders, so I had to improvise. Apparently it is possible to solve this issue by tweaking the theme and I will try to do so when I get some spare time.
  • I decided not to use any reference system because in presentations I use to include just a few references, but bibtex should work as usual;

The complete presentation can be seen here.

Public Money, Public Code in Barcelona

23 Jan 2018 / Leonardo Barichello

Another reason to love Barcelona: City of Barcelona Dumps Windows For Linux and Open Source Software.

This is the first result of the Public Money, Public Code campaign headed by the Free Software Foundation in Europe. Let's hope it is not the only!


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!

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