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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:
o SciPlore Mindmapping may be substituted with FreeMind, MindManager, XMIND and most other mind mapping tools allowing to link PDF files
o Foxit Reader may be substituted with Adobe Acrobat
o JabRef may be substituted with any other reference manager supporting BibTeX (e.g. BibDesk, Referencer and Mendeley)
o 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 and other 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: March 2011

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 :-) .

You have read my mind. You have put into practice what I could envisage yet not even come close to develop.

You are helping to tackle the biggest obstacle to my research

I really like SciPlore’s approach. Connecting papers through a mindmap is genious!

I’m in the middle of my PhD and was becoming overwhelmed with the amount of information I need to manage. Nothing else was really cutting it for me and I stumbled on Sciplore.

Great software! Trying to get my adviser and all the graduate students in our lab to start using SciPlore. Keep up the efforts!

I very much enjoyed using Sciplore and was very impressed by its performance and options.

Congratulations on a great time saver and program to make PDF Bookmarks useful.

I’d like to thank you for the great work you’re doing.

I love your product

Great software, thanks!

Your tool is great

Thank you very much for the excellent software. SciPlore has helped me organise my notes and research while undertaking my Masters degree.

I was greatly surprised to find SciPlore, and it seemed to be exactly what I needed for my work

Just wanted to say that SciPlore is a wonderful program. I use it to organize my thoughts and my research. Can’t wait to see what’s coming!

Thanks for making SciPlore!

This tutorial is divided into three parts. the first part covers how to manage literature. The second part covers how to draft a PhD thesis. The final part covers how to write a PhD thesis and how to manage references.

But now, let’s start…


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