Summary

If this is your first year as a postgraduate in UCC, welcome to the world of research. If you're returning after the summer, welcome back. This is a short note to bring you up to date on some tools you may need for your research, especially for writing your thesis.

This may sound like it's a long way away yet (unless you're just about to submit) but a little time and effort spent getting properly equipped now is going to save you a lot later on. Using the right software in the right way, you can cut up to 2–3 months off the writing time for the average 4–year PhD, and pro rata for other degrees—like being given a free extension.

The two most important tools discussed here are your document preparation software (wordprocessor or other software) and your reference management software (bibliographic database). There may be other special software for your own discipline, but your supervisor will advise you on that.

There are translations of this page at http://students.studybay.com/?p=190 (Armenian, by Gajk Melikyan) and http://science.webhostinggeeks.com/latex (Serbo-Croat, by Anja Skrba).

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Para: As of April 2013, Mendeley has been…
§2.1. Zotero
§2.2. Mendeley

Section by section

1. Document preparation software

Most people use a wordprocessor because it's only software for writing that they have ever come across. Unfortunately, most wordprocessors were not designed for academic or technical writing, or for doing long or complex documents like theses. There are several alternatives, the most popular of which (LATEX) is discussed in section 1.2, ‘Using LATEX’ below.

1.1. Using a wordprocessor

Using a wordprocessor for your thesis

Follow the UCC requirements for theses: set the margins and line-spacing correctly.
Use a common serif typeface for readability (eg Times, Garamond, Charter, Georgia etc). Avoid using sans-serif typefaces like Verdana, Arial, Helvetica, Avant Garde, etc for the text. Set the text size to 11pt or 12pt.
Be consistent: don't format the same kind of thing one way in one place and a different way in another. The best way to avoid this is to read the rest of this list!
Learn how to use the built-in named styles to automate your formatting (details: OpenOffice, Word) and how to create your own in a template: this alone can save days of fiddling around with the font menus.
Never add manual line-breaks or page-breaks until after you have written it all and really finished editing. Otherwise you'll find that any late changes and corrections will mess up all your formatting again and again.
Use the built-in cross-reference mechanisms (details: OpenOffice, Word) rather than typing them by hand. That way when you move bits of your text around while editing, you won't have to waste time tracking down and manually changing every cross-reference.
The same applies to the automated Table of Contents (details: OpenOffice, Word), List of Figures, List of Tables, Index, Glossary, etc (if you need them). Don't even think of typing them by hand, otherwise you'll spend forever trying to keep them up to date.
Most important of all, use a reference manager (bibliographic database) to keep track of all the articles, books, papers, websites etc that you read. This lets you add citations formatted correctly for the style your discipline uses, and ensures that they all appear in your References section correctly sorted and formatted.

Most wordprocessors are designed for simple office documents like sales reports and business letters. To use a wordprocessor successfully for long or complex documents like theses you need to put in a lot of effort. It can sometimes also be difficult to get ‘business’-style wordprocessors to do some of the important academic tasks (eg decent mathematics, multiple footnote series, apparatus criticus, or mixed right-to-left and left-to-right languages) without a lot of additional software.

There are two wordprocessors in common use, OpenOffice (which is free) and Microsoft Word (which isn't). Both do the same kind of thing in the same kind of way, with minor variations.

Wordprocessor	OpenOffice	Word
Maker	Sun Microsystems	Microsoft Corporation
Computer	Windows, Apple Mac, Linux, Solaris	Windows (a Mac version exists but is different; Linux can run the Windows version using WINE)
Cost	Free	€83.95 inc VAT and 2Gb memory stick
Licence	Open Source (freely copyable)	Commercial (restricted)
From	`http://www.openoffice.org/`	`http://www.studentsoftware.ie/`

There are dozens of other wordprocessors in existence but they are not supported in UCC. Few wordprocessors were ever designed for academic use; one still seen occasionally is NotaBene, but it has proved unfeasible to obtain support for it.

Please do not use obsolete or unsupported packages (eg Microsoft WordPad or Works, Apple MacWrite, Lotus Notes, etc) because we won't be able to provide any help with them.

If you decide to use a wordprocessor, you can make life easier for yourself and others by making use of automation (see the panel ‘Using a wordprocessor for your thesis’).

1.2. Using LATEX

The most common alternative to using a wordprocessor is the LATEX document preparation system. This uses a typesetting program (TEX), so the formatting quality is much higher than a wordprocessor. Because LATEX already knows about how to format long or complex documents, it is also much easier to save time through automation and keep your layout consistent.

The LATEX DVD is available free of charge for any desktop or laptop computer by contacting the Electronic Publishing Unit or you can download the software yourself from the links at the TEX Users Group web site (Windows, Macs, Linux, and instructions).

The major difference is that LATEX is not a wordprocessor; it's a typesetter. Instead of fiddling with formatting menus, you just label the parts of your document as you write: title, author, heading, list, table, figure, citation, etc, and LATEX formats them for you.

Figure 1. Writing an article in LATEX using the Kile editor

LATEX comes with all the automated facilities mentioned above for styling, cross-referencing, citation, Table of Contents, List of Figures, List of Tables, References, Index, Glossary, etc. It also includes automated mathematical formatting, and features for typesetting multilingual and bidirectional text, linguistics, music, chemistry, engineering, and dozens of other formats; multiple footnote series, parallel columns, and the apparatus criticus.

The unit runs free training days, and there is extensive online and printed documentation as well as forums for users in UCC, Ireland, and worldwide.

2. Reference management software: bibliographic databases

Gathering references for reading and citation takes up a large amount of time when you're researching and writing a thesis. It is very important that you record everything you read and may want to cite. You need a quick and effective way to capture and store the proper details (author, title, date, publisher or journal, volume, issue, etc). And you need a quick and effective way to get them into your document formatted in the style your discipline requires. There are hundreds of styles: Harvard, MLA, IoP, IEEE, Legal, AMA, APA, Kluwer, Elsevier, etc—all fractionally different; and you also need to be able to reformat your references if you publish in different journals.

Reference management software makes your job easier and more accurate because it saves you doing it all manually:

You can capture full references from online sources such as web pages, library catalogues, and journal databases;
You can import and export whole files of references to and from other systems;
It stores and labels all the pieces making up a reference separately and unformatted, so it can automatically insert and reformat both the citation and the full reference.
You can choose the citation and reference style according to the rules of the format that you must adhere to.
You can add citations with a mouse-click anywhere in your document.

Never just type references into your document and format them by hand, especially if you just copy and paste them from another source (online or offline). This is completely pointless and a serious waste of your time. The formatting of citations and references demanded by academic work is detailed and exacting, something which computers are very good at doing if you give them the right information (and wholly useless if you give them the wrong information).

There are many reference management programs available; the following sections describe those in most common use. See the Wikipedia page on reference management software for some good explanations and comparisons.

2.1. Zotero

Zotero was developed by the Center for History and New Media at George Mason University. It is available both as a standaline program and as a plugin for the Firefox web browser (install that first). Download and install Zotero from http://www.zotero.org/. One click grabs the full biblographic details of any journal, library, or book page that you visit and adds it to your reference list. It recognises the reference data that libraries and publishers embed in their pages, so when you go browsing for your sources, you can add items to your collection at any time.

Figure 2. Using Zotero to save a reference from a catalogue search, and insert the citation into a document

Screenshot of using Zotero to save a reference

Screenshot of OpenOffice adding a citation from Zotero

It has plugins for OpenOffice and Word so that you can cite any document in your collection just by clicking on it (see Figure 23 above). You can copy your references to a USB stick if you've been working on a shared (lab) computer, and you can also export selected references to other reference managers like JabRef (BIBTEX), EndNote, ProCite, Reference Manager, etc.

Figure 3. Exporting your Zotero collection for use in another system

Screenshot of Zotero exporting references

There are also facilities for backing-up or storing your reference data in the cloud, so that you can continue working on them even when you're away from your own computer.

2.2. Mendeley

The Mendeley Desktop is a free bibliographic manager which runs on all modern systems (Windows, Macs, and Linux). Their web site describes it as ‘like iTunes™ for research papers’. You can import and export references in different formats, including the three most important import formats, RIS/BIBTEX/EndnoteXML, and all the popular citation formats like Harvard, Chicago, IEEE, MLA, etc. It also lets you share them with your colleagues, so it makes collaborative work (multi-authored papers) much easier because you can all be certain that you are citing the same works the same way.

Figure 4. The Mendeley desktop exporting citations in Chicago style

Screenshot of Mendeley exporting a citation in Chicago style

Like Zotero, it has plugins for Word and OpenOffice (in fact it re-uses the same plugins for efficiency), so you can just click and cite while you write.

It can synchronise with Zotero, so you can use Zotero for gathering your references, and Mendeley for managing them.

⇛ As of April 2013, Mendeley has been taken over by Elsevier, who have been the subject of much criticism for many years over dubious business ethics in respect of scholars, and who are also the target of an academic boycott. Users will need to make their own decision about whether or not they wish to support Elsevier by using Mendeley.

2.3. JabRef

JabRef is an Open Source (free) reference manager designed for use with LATEX, but also able to import references from databases like SilverPlatter, Medline, Ovid, ISI, and file formats like EndNote; and to export references to Zotero, EndNote, and a wide variety of other systems including SQL and MODS databases, Microsoft Office 2007, web pages, and spreadsheets.

Figure 5. Using JabRef to add a citation to a LATEX document

Screenshot of JabRef adding a citation to a LaTeX document

In common with all reference management systems, inserting a reference is a single-click operation (see Figure 5 above).

2.4. EndNote/ProCite/Reference Manager

Three popular, competing bibliographic databases all from the same company (Thomson). All of them powerful, but enormous, complex, and very expensive for personal use. The differences are largely in the range of online features and support for obsolescent file formats.

Figure 6. Using EndNote to add a citation to a Word document

Screenshot of EndNote adding a citation to a Word document

EndNote has become a de facto standard in some academic and research fields, partly driven by the fact that Thomson is the supplier of a valuable citation-measurement service, which is used in many institutions to judge the relative importance of research output.

Writing your thesis

Stuff you need to get started