How to write a thesis (Bachelor, Master, or PhD) and which software tools to use

How to write a PhD thesis? This is not a trivial task. Related literature needs to be found, notes need to be taken and finally the thesis has to be drafted and written including the creation of the bibliography. Dozens of books exist about how to do a literature survey and how to write a PhD and scholarly literature in general (e.g. [1-9]). However, software tools that might help in doing a literature survey or writing a thesis are hardly covered by these books, if at all. This is surprising as many software tools exist facilitating the daily work of a PhD student.
In this tutorial we present a new method to reviewing scholarly literature and drafting a PhD thesis with mind mapping software, PDF readers and reference managers.  This tutorial focuses on PhD students. However, Bachelor and Master students can use the here presented methods as well to plan and write their thesis. What makes this tutorial special is the fact that everything – PDF files, the content of PDFs (bookmarks) and references are integrated with mind mapping and word processing software.

To make the tutorial better understandable we provide many examples for which we assume that you want to write a PhD thesis about academic search engines.

Please note that

• All tools presented in this tutorial are free and open source(except Microsoft Word)
• All tools presented in this tutorial are based on Java and run on Windows, Linux and MacOS (again, except Microsoft Word)
• All tools used in this tutorial may be substituted:
  • SciPlore Mindmapping may be substituted with FreeMind, MindManager, XMIND and most other mind mapping tools allowing to link PDF files
  • Foxit Reader may be substituted with Adobe Acrobat
  • JabRef may be substituted with any other reference manager supporting BibTeX (e.g. BibDesk, Referencer and Mendeley)
  • Microsoft Word may be substituted with OpenOffice or LaTeX or any other word processor that BibTeX support/plugins exist for

You will spend the next couple of years doing your PhD (or months if you are doing a Master or Bachelor). We highly recommend to read this andother tutorials to find out the way that is best for you to manage your literature and references and write your PhD. Spending a few hours now will save you days if not even weeks later. This tutorial will be updated from time to time to consider the latest features of the tools presented here.Last update of this tutorial: Mai 2010

Before starting, we present some user feedback that we got by email for our software and this tutorial. We hope it motivates you to read the complete tutorial :-).