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Writing your thesis

Stuff you need to get started.

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).

Latest updates

• Para: As of April 2013, Mendeley has been…
• §2.1. Zotero
• §2.2. Mendeley
•   Using a wordprocessor
•   Using L A T E X
•   Zotero
•   Mendeley
•   JabRef
•   EndNote / ProCite / Reference Manager

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 ( L A T E X ) is discussed in section 1.2, ‘Using L A T E X ’ 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.

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 L A T E X

The most common alternative to using a wordprocessor is the L A T E X document preparation system. This uses a typesetting program ( T E X ), so the formatting quality is much higher than a wordprocessor. Because L A T E X 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 L A T E X 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 T E X Users Group web site ( Windows , Macs , Linux , and instructions ).

The major difference is that L A T E X 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 L A T E X formats them for you.

Figure 1. Writing an article in L A T E X using the Kile editor

L A T E X 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

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 ( B I B T E X ), EndNote , ProCite , Reference Manager , etc.

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

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/ B I B T E X /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

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 L A T E X , 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 L A T E X 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

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.

Installing L A T E X for Linux

If you have an up-to-date distribution (eg RedHat, Debian, Ubuntu, etc) with a package manager (rpm, yum, Synaptic, etc), then just install texlive-full , plus the kile or emacs editor (your choice). You do not need to install from the DVD.

If you have an older system, or one without a working package manager, borrow the T E X Live DVD from the Electronic Publishing Unit.

The Firefox browser

Firefox is a free replacement browser for Microsoft Internet Explorer . You can download it for any Windows, Mac, or Unix/Linux computer. It has a huge range of useful add-ons and plugins, the most important of which for academic work is the Zotero bibliographic database mentioned above .

Writing your thesis

Stuff you need to get started.

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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How do i submit my thesis electronically.

From January 2020 all theses of research programmes must be submitted electronically. Submit one PDF copy of your thesis for examination  online here.

Paper copies of the thesis are no longer required, unless specifically requested by the Examiner. If your Examiner requests a paper copy of your thesis, you will be notified of this and required to submit a paper copy to the Graduate Studies Office.  

Along with your e-thesis you must upload a completed  Submission for Examination Form , where you will choose the level of access required for your final thesis. You must read the  Access Options Here , and agree the required level of access with your Supervisory Team. The Submission for Examination Form must be signed by all Supervisors and the Head of School/Department. 

After the examination, final submission of the thesis to the Library must also be done electronically. Log into  CORA  with your UCC IT account details (@umail.ucc.ie) and submit your abstract and thesis online. Hard copies of the final thesis are no longer required. 

Read full instructions for research thesis submission and examination here .

Applies to students on research programmes only. 

Please familiarise yourself with UCC's webpages for research students . 

• Not yet registered? Visit the Prospective Student Queries form .
• Already registered? Visit the Current Student Queries form .

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Theses: Research Theses Access Conditions

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Digitalisation of Theses Submission

UCC will move to digital submission processes for theses from all research postgraduates from 6th January 2020. Final theses will no longer be required in hard bound format for archiving in UCC Library but will be archived in electronic format in CORA .

Thesis authors will define how their thesis can be accessed when they set out access terms at time of submission of their examination copy to the Graduate Studies Office. For more information on examination copy submission see the Current Research Students section of the Graduate Studies Office website 

The access categories are described in more detail here and thesis authors can contact [email protected] for any clarifications.

Access categories for thesis authors

Open Access  

Your  thesis can be viewed and downloaded by anyone, once any embargo  you might have set   ha s expired. You would choose this option if you want to share your thesis openly online. A Creative Commons License should be applied to  an  open access thes i s to indicate how you wish to share your work and you can indicate this on the Research Degree Submission for Examination  form. 

Controlled Access  

Your thesis may not be viewed or downloaded openly on CORA. You would choose this option if you do not wish to share your work online at any time but wish to facilitate researchers with access to UCC Library to read your thesis. Any individual who requests access for research or private study will be granted permission once they agree to a copyright declaration. Access will be managed by library staff.   

Restricted Access  

Your  thesis may not be viewed or downloaded by anyone  at  any time . You would choose this option if your thesis contains sensitive or confidential materials throughout the entire thesis. This option is only to be selected in exceptional circumstances  and you will have to provide a justification for requesting the restriction. 

Your  thesis can not be  viewed or  downloaded by anyone from CORA  while an embargo is in place .  An embargo can be placed on an open access or controlled access thesis while you publish material from your thesis for example. You will be notified by email 2 weeks before an embargo is about to  automatically  expire   and you should contact  [email protected]  if you wish to extend the embargo. 

Redaction  

If there are parts of your thesis which you would like to redact permanently while leaving the remainder of your thesis available through open access or controlled access, you should indicate this on the   Research Degree Submission for Examination Form . You may consider redaction when you have used third party copyrighted material for which you did not receive permission for online use or to protect confidentiality or sensitive materials or data in your thesis.  

• Research Thesis Copyright Declaration Form Readers of e-theses made available under controlled access must agree to the conditions of use outlined in the form.

What do access categories mean for thesis readers?

Creative Commons Licenses

 A Creative Commons License will only apply to a thesis which has been nominated Open Access by the thesis author.  

License Types  

Creative Commons offers six copyright licenses and also provide  the  CC0 tool  which allows an author to waive all rights and place a work in the public domain. The information outlined here has been adapted from the Creative Commons website  

Attribution (CC BY)  

Attribution  ShareAlike  (CC BY-SA)  

Attribution- NoDerivs  (CC BY-ND)  

Attribution- NonCommercial  (CC BY-NC)  

Attribution- NonCommercial - ShareAlike  (CC BY-NC-SA)  

Attribution- NonCommercial - NoDerivs  (CC BY-NC-ND)

This license lets others distribute, remix, tweak, and build upon your work, even commercially,  as long as  they credit you for the original creation.  This is the most accommodating of licenses offered. Recommended for maximum dissemination and use of licensed materials.  

V iew License Deed  |  View Legal Code  

This license lets others remix, tweak, and build upon your work even for commercial purposes,  as long as  they credit you and license their new creations under the identical terms.  This license is often compared to “copyleft” free and open source software licenses. All new works based on yours will carry the same license, so any derivatives will also allow commercial use. This is the license used by  Wikipedia, and  is recommended for materials that would benefit from incorporating content from Wikipedia and similarly licensed projects.  

View License Deed  |  View Legal Code  

This license lets others reuse the work for any purpose, including commercially; however, it cannot be shared with others in adapted form, and credit must be provided to you.  

This license lets others remix, tweak, and build upon your work non-commercially, and although their new works must also acknowledge you and be non-commercial, they don’t have to license their derivative works on the same terms.  

This license lets others remix, tweak, and build upon your work non-commercially,  as long as  they credit you and license their new creations under the identical terms.  

This license is the most restrictive of the Creative Commons main licenses, only allowing others to download your works and share them with others  as long as  they credit you, but they can’t change them in any way or use them commercially.  This licence has been applied to UCC e-theses since 2013. 

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