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How to Write a PhD Thesis (Part III): Writing the PhD Thesis up and Managing References

This is the third part of our tutorial series about how to write a PhD thesis. In this part we finally explain how write up a PhD thesis and how to manage references.
How to Write the PhD Thesis

There is not much to say about eventually writing up your phd thesis. Basically, all you need to do is taking some word processing software of your choice and start writing everything up that is already in your mind map (see Part II of the tutorial). You could argue that this is inefficient because why should you type everything twice, once in your mind map and then again in your word processing software. And you are right. Therefore, we are working on a function that lets you export a mind map perfectly to MS-Word and OpenOffice. However, this will not happen in the next few months or so. And it has also advantages to do the part of the work twice. You will find much more errors and enhance the text much more if you are forced to write your thesis after you have structured it in great detail in the mind map than as if you had started directly in the text document.

In theory, you could write your thesis within a few days if you had a really, really good mind map. In practice, it probably will take you a few weeks because when finally writing the thesis up you will realize some issues you want to do some more work on.
Maintaining References

There is one important part we have left out so far: The management of bibliographic data and creation of reference lists. This is probably the most annoying part in writing a PhD thesis. It is not unusual that a thesis is referencing a hundred or even more publications. Imagine you have to create for 200 publications the bibliography list as shown in the right part of the picture. And imagine, you did this and then your supervisor tells you that you have to use a different style and you have to do it all over again. Or you have numbered your references manually (see left part of the pictures) and for whatever reason you have to insert another reference at the beginning of your thesis and therefore renumber all references in your phd thesis.
Example of a reference list in a PhD thesis and its use in the full text

Fortunately, this can all be done automatically (more or less).
Reference Management Software

Download and install JabRef. With JabRef you can maintain a database of all bibliographic data of the publications you want to reference. Eventually, your BibTeX database file will look like this.
Managing Bibliographies for a PhD thesis with JabRef

Managing Bibliographies for a PhD thesis with JabRef

A brief step-by-step tutorial how to create your first BibTeX database and create new entries is available here and the complete manual here.

So what you need to do is creating an entry for each of the papers you want to cite. This is still a lot of work but that’s how it is. To integrate your BibTeX data with your mind map (and finally MS Word, OpenOffice, …) one more step is necessary. You need to link the corresponding PDF to the BibTeX entry. This can easily be done by drag & drop the PDF from your literature directory to the BibTeX entry.
Integrating BibTeX (JabRef) with SciPlore MindMapping

SciPlore MindMapping has support for BibTeX (no other mind mapping software can do that). That means whenever a node in your mind map links a PDF (or PDF bookmark) the BibTeX key will be displayed as an attribute. To do so, just go to SciPlore MindMapping | Preferences and specify your BibTeX file. Then select SciPlore MindMapping | Update reference keys in current mind map.
Displying BibTeX keys and title in a mind map

Displying BibTeX keys and title in a mind map

You now see the title and BibTeX key of the linked PDF file as attribute. This way you can easily see where the information in your mind map is from. If the information is annoying you, select View | Attributes | Hide All Attributes (the attributes are still stored in your mind map, you just won’t see them any more). You might not realize this right now while reading this text but actually this feature is fantastic. It will allow you to very easily create a reference list for your PhD. Read on…
Integrating BibTeX and SciPlore MindMapping with Microsoft Word

To automatically create reference lists in MS-Word, based on BibTeX, you need a plug-in. We recommend BibTeX4Word. The installation is anything but user friendly and also requires the separate installation of MikTeX but it is definitely worth the effort. If you have installed BibTeX4Word you can simply copy and paste the BibTeX key from SciPlore MindMapping to MS Word as shown on the following picture.
Copy bibliographic data from SciPlore MindMapping to your PhD thesis in MS Word

Then you can copy the BibTeX key from SciPlore MindMapping with a right mouse click and paste it into MS-Word (click on the red +).

Creating an in-text reference in your PhD thesis

After copying the BibTeX key to your word processor you just need to click on the reference list icon and there reference list is created automatically (you can choose out of hundreds of reference styles such as APA, IEEE, ACM, Harvard, …)
Create a bibliography (reference list) for your PhD thesis automatically

That’s it, your PhD thesis is done :-) To remind you what makes this tutorial (and the software SciPlore MindMapping) special in contrast to other software tools and tutorials is the fact that everything – PDF files, the content of PDFs (bookmarks) and references are integrated with mind mapping and word processing software. Imagine, for instance, you would not have the BibTeX keys in the mind map (or wherever else you draft your PhD with). You would have to manually make some notes where the information is from and later look the bibliographic data up in you reference manager. And without having PDF bookmarks you could hardly read in more detail about something that interests you. You might have a note somewhere (maybe even with the page number the information is from) but to look it up would take some time. With PDF bookmarks it takes 2 seconds.

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