Using FOSS in academia: Part 1

A breakdown of FOSS for students and researchers in academia

Image by : 

opensource.com

x

Get the newsletter

Join the 85,000 open source advocates who receive our giveaway alerts and article roundups.

This article provides an overview of free and open source software (FOSS) that may be of use to students and researchers in academia, based on my own experience in psychology studies.

I use Ubuntu Linux, which is a FOSS operating system, but the software discussed in this article is multi-platform; in other words, it will also run on Apple Mac OSX or Microsoft Windows. There is so much FOSS available that this article only scratches the surface, but hopefully it will give some initial pointers to readers with an academic background but no previous experience of FOSS.

First, a simplified definition: FOSS is software that the user can copy, amend and distribute without getting special permission, and (in almost all cases) costs nothing to buy or use. Free software and open source software are similar, but the main distinction between them is that amended versions of free software must be distributed under the same license, while amended versions of open source software can be distributed under a different, non open source license. FOSS is a key part of modern IT systems—Google and Amazon run their services on FOSS, the addressing system for the Internet (DNS) is FOSS, and the UK Government has recently selected a FOSS format (ODF) as its preferred format for editable documents.

Office software

My first experience in using FOSS was with an office software package called LibreOffice. This includes, among other things, a word processor, spreadsheet, and presentation program, and is a good alternative to Microsoft Office. It is completely free, which is important if you are trying to cut costs as a student—a friend of mine had to buy a new copy of Microsoft Office when she got a new laptop because she couldn't transfer her existing copy across. With LibreOffice, this issue would not arise—when you need to buy expensive textbooks, spending even £70 on a student edition of Microsoft Office is not viable.

LibreOffice uses its own format (ODF, which is the UK Government's preferred option for editable office documents), but it can also open and save Microsoft Office formats, so you can collaborate with colleagues who are still using Microsoft Office (though you may have to save the document in the Microsoft format—Microsoft's support for ODF in different versions of Word is variable). Moving from Microsoft Office to LibreOffice should not be difficult—I rarely used Microsoft Word before I went to university, but all the library computers at the University of Kent use it, and I was able to work it out by knowing what I would click on in LibreOffice, so going the other way should also work.

Even though you and your colleagues can edit the same document on either office suite, complex layouts or spreadsheet macros may not transfer perfectly, and there can be subtle differences in layout and line spacing if you and your colleagues are using different fonts.

Writing essays

An important part of any undergraduate course is writing essays, so the less time that has to be spent on formatting the better. LaTeX is a versatile typesetting system that takes care of the mundanities involved in preparing text. Almost 5,000 add-on packages handle different publishing requirements, and one, apa6, formats documents in APA 6th Edition style.

In LaTeX you "mark up" the text rather than seeing it as it will appear—for instance, you type \textbf{mytext} to tell it to print "mytext" in bold later, rather than clicking a Bold button and seeing the text change to bold, as you would do in a word processor. This takes a bit of getting used to (though it is similar to the way webpages are marked up in HTML), but in the longer term LaTeX is a major time-saver—the APA styles are quite complex, and it can be difficult to remember what items are required on the title page, what format subheadings should have, and so on. LaTeX+apa6 chooses the correct format automatically—tables and graphs look especially good. Because LaTeX is so versatile, it may take some trial-and-error to get the effect you want, especially with tables. To help you get started quickly, there is an essay template on my website that should cover most of the basic requirements. A range of other document templates are available from LaTeX Templates.

LaTeX creates your essay as a PDF file, which looks tidier than word processor output. Most universities will, like the University of Kent, accept PDFs, and so will the widely-used anti-plagiarism software, Turnitin. If your lecturer needs to make comments directly on the PDF, many PDF readers will allow her to do this. The Preview PDF reader in Apple Mac OSX will annotate PDFs if you select Tools → Annotate, and other programs like Skim will allow you to export annotations into a separate file (useful if you are reading PDFs of journal articles!). For Microsoft Windows, you can use progams like Foxit PDF Reader or Nitro Reader.

Moreover, the PDF toolkit PDFtk allows you to split, merge and rotate PDFs—very useful if you want to put together a revision document by taking pages from a number of lecture PDFs and journal PDFs.

If you would like to experiment with LaTeX before actually installing it, you can use an online service like Overleaf, where you can create a LaTeX document in your browser and see its PDF output. Colleagues can collaborate on the same document, which is also under version control (see Part 2), so you have a complete history of any changes made.

Handling citations

An important section of any essay or research report is the literature review, which creates the huge task of keeping track of your citations. For this you can use JabRef on your computer, or Zotero if you want a web-based system. Both programs use the BibTeX format, which also allows you to include abstracts, notes and so on in your citation records.

BibTeX was designed to work with LaTeX, so if you put all your citation data into one JabRef file as you read each article, when you come to write your paper LaTeX will only insert into the bibliography the ones you have actually used. This saves a lot of time—you do not need to check your text to ensure that all your citations are in the bibliography, or check the bibliography to ensure that it does not include an entry for a source you have not cited.

Another time saver is that the apa6 package in LaTeX formats the citations properly—complex rules such as quoting all the authors of a paper on first appearance, but only the first on subsequent appearances, or using "and" in the text, but "&" in the bibliography, or adding "a" and "b" when there is more than one paper by the same author, are all done automatically without the writer having to think about them (or look them up in the APA manual!). Nevertheless, it is always a good idea to double-check the bibliography to ensure everything is coming up properly—sometimes less common citation types (for example, websites) have to be tweaked to ensure that everything is as required by the APA style guidelines.

Doing experiments

Two software packages allow a point-and-click interface to be used to build complex experiments.

OpenSesame can connect to eye-trackers and other external hardware, and has been used to present questionnaires, and to design experiments in gaze cuing, implicit association, attentional blink paradigms, computer mouse tracking, and so on. One interesting feature is that it can now run on an Android tablet, which opens up new possibilities for selecting or involving participants. For instance, you could take the tablet to a mother and toddlers group and ask individuals to do the questionnaire or experiment then and there. This may help find a demographic that is different from the WEIRD (Western, educated, and from industrialized, rich, and democratic countries) university students (Brookshire 2013) that we usually see in psychology research, and may help make the process faster and more efficient, rather than having to wait for people to go to the laboratory.

PsychoPy is a stimulus presentation and control program, and can be integrated with a wide variety of hardware. It has been used for work on reaction times, Stroop experiments, contrast detection, and so on.

In my next article on this subject, I'll look at software to help you with statistical analyses and various options for sharing and presenting your research.

About the author

Lois Donnelly - I'm currently doing an MSc in Psychology at the University of Kent, Canterbury, having just graduated from my BSc in the summer. I've been using open source software as long as I can remember, and find it very useful in my research. I have even converted my boyfriend to Linux!