Part II: Structuring and Drafting the Thesis

This is the second part of our tutorial about how to write a thesis. In this part we cover how to structure and draft your thesis. There is lots of good literature on how to structure a thesis conceptually, so we will not cover this aspect in here. However, we will show you a practical way to devise, maintain and store the structure of your thesis in a mind map.

You start with devising a basic structure, which you can create in your literature mind map or in a new mind map, see the picture above for an example. You can then start drafting your thesis directly in the mind map. Create one node for each heading and one sub-node for each sentence (see picture below). You might wonder why not doing this directly in a word processor. Simply, because it is much easier to move nodes of a mind map than to move sentences and paragraphs in a text document. Moreover, you have all the important information in your mind map already. Thus, restructuring your thesis in a mind map is much easier and quicker than using a text document. We guarantee that you will have to restructure your thesis several times before you are really happy with the structure. Additionally, you may put all the administrative data related to your thesis project such as deadlines or important contacts into your mind map, as you see in the left half of the picture above.

The following picture shows how a final mind map for a PhD thesis could look like (nodes with a circle are folded and contain additional sub-nodes). You will notice that the related work section is very similar, yet not identical to your literature mind map. Most likely you will not use all the literature you have read. Accordingly, your literature mind map will probably contain more information than the final related work section in your mind map / thesis. Therefore, we suggest using two mind maps: one for managing all your literature and one for structuring your bachelor, master or PhD thesis.

Keep in mind that your mind maps are not limited to containing PDF links. You can add text, pictures or formula, you can insert icons, link to other files and webpages, highlight nodes and much more (see Docear’s User Manual for details). Again, have a look at the picture to get an idea of how your final mind map could look like. Now, read in the third part how to eventually write a thesis.

Part III: Writing the Thesis and Managing References

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

How to Write the Thesis

Every thesis project  will eventually come to the point where you start writing up everything that is in your mind map (see Part II of the tutorial) using the word processor of your choice. You could rightfully argue that typing every information twice, once in your mind map and again in your word processing software, is terribly inefficient. Docear offers a function to export your mind maps to Microsoft Word, OpenOffice, LaTeX, HTML, PDF, PNG, JPEG, SVG, and many other formats. However, we have to admit that the export function is not perfect. We suggest you try it to see if it fits your needs. Personally, we do not use the export function, but draft our paper in Docear, and then write the entire paper/book/thesis/… in the text processing software. While this process requires more work, it has the advantage of carefully thinking about the text again. You will find more errors and enhance the quality of the text greatly if you 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 have created a really, really good mind map. In practice, finally writing your thesis will probably take you a few weeks, because you will likely realize issues that you want to work on more during the writing process. Be assured that we know that a good export function is important, and that improving Docear’sexport capabilities is on our todo list. However, realizing this feature will not happen within the next few months or so.

Maintaining References

There is one important task that we have left out so far: The management of bibliographic data and creation of reference lists. For many people, this task is the most annoying in writing a thesis. Referencing a hundred or more publications in a thesis is quite common. Imagine you have to create a bibliography for 200 publications like the one shown in the right part of the picture. Now imagine, you manually created that bibliography and your supervisor tells you to use a different citation style, which means you would have to do it all over again. Alternatively imagine you have numbered your references manually (see left part of the pictures) and for some reason you have to insert another reference at the beginning of your thesis, thus renumber all references in your thesis.

Reference Management Software

We recommend using JabRef, which by default is integrated into the Docear suite, to manage reference data. Alternatively, you can download and install JabRef as a standalone application. JabRef allows you to maintain a database of bibliographic data in BibTex format. A brief step-by-step tutorial how to create a BibTeX database and new entries using the stand alone version of JabRef is available here and the complete manual here. For instructions on using the JabRef version integrated in Docear see the respective part in Docear’s User Manual.

You need to create a BibTex entry for each paper you want to cite. Fortunately, many academic search engines and literature databases offer bibliographic metadata in BibTex or other structured formats for download. Copying or importing this data into JabRef/Docear greatly speeds up the process. Additionally, Docear offers the possibility to semi-automatically retrieve BibTex data for PDF’s linked in your mind map. Eventually, your BibTeX database file will look like this.

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 Docear

Docear supports 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 Docear | Preferences and specify your BibTeX file. Then select Docear | Update reference keys in current 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 thesis. Read on…

Integrating BibTeX and Docear 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 Docear to MS Word as shown on the following picture.

That’s it, your thesis is done :-) To remind you what makes this tutorial (and the software Docear) 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 thesis 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. If you have any questions, please contact us or post a comment here in the Blog.


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