Translations: Chinese (thanks to Chen Feng) | Portuguese (thanks to Marcelo Cruz dos Santos) | Russian (thanks to Sergey Loy) | send us your translation 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 (or Docear) 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 or PDF XChange Viewer.
    • 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 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: November 2013 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 before you begin, you might want to have a look at this video of Docear, a great solution to manage academic literature.

How to Write a PhD Thesis (Part I): Literature Management

To write a good PhD thesis it is key to keep track of related work in your field. That includes that you know all the relevant studies, results, facts, ideas and so on in your field. Keep in mind, by the end of your literature review you will have read or at least skipped through hundreds of books and papers. You must be a genius to remember every interesting fact and idea you have read in a paper without any tools. Before the computer-age, academics could only rely on index cards, (post it) notes, highlighting pens, indices, etc. With computers, and especially mind mapping software, new possibilities evolved. In this part of the tutorial we explain how to search for literature with academic search engines. Then we show how you create summaries of your PDFs with bookmarks and keep on overview of all important information in our mind map. By the end, your mind map will contain literally all information that you have considered to be important. Whenever you want to know something, you can look it up in your mind map, and read in more detail about it by clicking on the link to the PDF.

Searching for (Electronic) Literature

A prerequisite for a good PhD thesis is to know what others have done in your field of research. But how to find this related work? Due to computers and the internet, searching for literature has changed dramatically over the last years. Instead of using catalogues in libraries, students can use full text search offered by academic search engines and databases such as Google Scholar, SciPlore and ACM Digital Library. In addition, academic search engines usually offer sophisticated ranking algorithms which help in finding the most relevant documents [10-12]. Dozens of academic search engines exist. Some are focusing on specific disciplines such as computer science and some are trying to cover several or even all disciplines. For the field of computer science, popular academic databases are Springerlink, ACM Digital Library and IEEE Xplore as well as ScienceDirect and to sometimes Emerald Insight (Wikipedia provides you with an extensive list of available resources). All these databases require a subscription to access their content. If you are lucky, your university has an agreement with these databases so you can access all their articles for free. Ask your supervisor or in your library which databases you have access to. Free alternatives are CiteSeer and SciPlore which provide you free access to many academic articles. Google Scholar is a special case: Often you can download the linked content for free but not always. In this tutorial we will focus solely on the management of electronic literature.

Storing Files in Folder Structures

Most academic search engines and databases offer to download scholarly literature in PDF format. The probably simplest way to store (and retrieve) these PDFs is a reasonable structured folder system. Each PDF can be stored in one folder which is labeled with an appropriate descriptor. It is usually helpful to give a meaningful filename to the PDF such as the article’s title. In case that one document fits into two or more categories, most operating systems allow creating a shortcut or alias for a file (see picure). Some feel this approach as being too structured and prefer tagging.

Possibility: Save PDFs for your PhD in different folders

Possibility: Save PDFs for your PhD in different folders


Tagging allows assigning multiple keywords (tags) to a file independently of where the file is stored. Based on these tags, users can retrieve the files from their hard drive. Popular tagging tools for the desktop are Tag2Find, iTag, and Punakea. There are also services allowing to tag and store academic articles online such as Connotea, CiteULike or Bibsonomy. However, for the approach we present in this tutorial we will focus on desktop tools and, more importantly, neither folder structures nor tags are important for the approach we present. Of course, a good folder structure never harms but you do not really need it.

Starting to Search and Storing Files in One flat Folder

In the beginning of your PhD you should just search for the most relevant keywords in academic search engines and store whatever paper you get on your hard drive. If you wanted to do a PhD about academic search engines, it might make sense to start doing some research about Google Scholar, one of the leading academic search engines. Let’s assume you have found a hand full of interesting PDFs and stored them in c:myliterature (don’t spend too much time with judging the relevance of a PDF. If the title or abstract sound interesting, store it).

Your first PDFs for writing a PhD thesis

Your first PDFs for writing a PhD thesis

Memorizing a PDF’s important information

What you really need to know as a researcher is: Where have I read which information? For your thesis it is worthless to know something but not where the information is from. Eventually you will have to reference the origin (ideally with page number). As a first stept, PDF readers are perfect to keep track of a PDF’s most important information. You need a PDF reader that can create bookmarks and ideally highlight passages and create annotations. If you have access to Adobe Acrobat that’s great (the free Acrobat Reader is not sufficient). Otherwise we would recommend the free version of Foxit Reader. Now, whenever you read an interesting PDF you create a bookmark for every statement that might be interesting for your PhD thesis. We would also suggest highlighting the interesting text directly in the document. Have a look at the picture.

Marking important information for your PhD thesis

Highlighting important information for your PhD thesis

This is the PDF of an article titled “Academic Search Engine Optimization (ASEO): Optimizing Scholarly Literature for Google Scholar and Co.”. It is about how to get your papers indexed and well ranked by academic search engines such as Google Scholar. If you write your PhD about academic search engines it might be interesting to keep in mind that this paper is the very first paper about academic search engine optimization. And also the definition of “academic search engine optimization” might be relevant later for your PhD thesis. Therefore you create a bookmark for each of this information (see the picture). It is up to you how detailed you make the bookmark structure. In the very beginning it might be appropriate to create just one bookmark that briefly describes the paper (e.g. “first paper about academic search engine optimization”). If you need more information you could come back to this paper later. It is easy to get lost with all the information you read. So, for the beginning, really, create bookmarks only for the very important information. When finishing reading the first PDF you proceed with the other PDFs in the same way.

Managing information from various PDFs

In the long run, it is not very helpful to have the information only in the PDFs. Here is where mind mapping joins the game. Mind maps were ‘invented’ by Tony Buzan in the 1970s [13]. A mind map is a diagram with a central topic and subtopics branching from it, like a tree (see the picture for an example). Usually a node in a mind map contains only one or two important keywords. Due to its visual structure a mind map is more effective for learning for many people. In this tutorial we use the mind mapping tool SciPlore MindMapping (Update: better use its successor Docear)  as it is especially designed for students and researchers. Please download and install it.

Example of a Mind Map

Example of a Mind Map

When you never did mind mapping before, the concept might appear strange to you in the beginning. And actually, mind mapping is not for everyone the best solution. But please, invest 30 minutes and we guarantee that the chance you will love it is really high.

Monitor all new PDFs in your Mind Map

We want to keep track of all the information you have read in one single place. Open SciPlore MindMapping / Docear and create a new mind map which you will use to manage your literature (press Ctrl+N). By clicking on the already existing node called New Mindmap this node is selected and can be renamed by either pressing F2 or just typing the new name, for instance My Literature. One of SciPlore MindMapping’s special features is monitoring a folder for new files. We use this feature to list all our PDF in the mind map. The aim is that whenever you find a new PDF on the Internet, you store it on your hard drive, and immediately it will be displayed in your mind map. Create a new child node by pressing the Insert key on your keyboard or selecting Insert | New Child Node from the menu. Call this node Incoming Literature. Now, right-click on that node, select Add PDF Monitoring Directory and choose your literature directory (e.g. c:myliterature). Now, all PDF files (plus DOC(X), TXT, RTF, ODT and XLS(X)) that are stored in the defined folder are displayed in your mind map’s Incoming Literature node. Other files are ignored. And the best – also the PDF bookmarks are imported. The following picture illustrates this.

Monitoring a folder for new PDFs that are important for your thesis

Monitoring a folder for new PDFs that are important for your thesis

That means, as of now the important information are not only in the PDFs but all together in a single place – your mind map.

Giving Structure to Your Mind Map and Literature

After you have read the first PDFs and created bookmarks, you should start giving some structure to the information: Create nodes for all the important categories you plan to do research in (you can change them later at any time). Then drag & drop the bookmarks from the incoming node to the appropriate categories. If you feel that one bookmark fits to several categories, just create a copy of it. The following picture shows an example.

Giving Structure to your Mind Map and Literature (and hence to the PhD thesis)

Giving Structure to your Mind Map and Literature (and hence to the PhD thesis)

Now you have a good overview of what you have read. On first glance this might seem similar to a folder structure on your hard drive and indeed it is. But there is one big advantage (and there will be more): In contrast to a folder structure you have not only sorted your PDFs but the PDFs’ contents by having direct access to the bookmarks in the mind map. Despite this, creating, deleting, renaming, copying and moving nodes in a mind map is much faster than doing this with folders in a file structure.

Deepening the Literature Review

Basically, you can go on as you did before. You find new PDFs, read them, create bookmarks, and sort them in your mind map. Let’s assume you want more information about a certain topic that is already in your mind map. For instance, about differences between academic and classic search engine optimization. Then you can just click on the node “Differences between ASEO and classic SEO” in the mind map.

Add more bookmarks if a PDF is relevant for the thesis

Add more bookmarks if a PDF is relevant for the thesis

The PDF will open on the right position and you can read on that topic and, if you like, create more bookmarks (in the current version, only the front page of the PDF is opened when clicking on the bookmark in the mind map). The new bookmarks can be easily imported by a right click and on the node and selecting Import Bookmarks.

Import new PDF bookmarks to the mind map to complement the PhD literature review

Import new PDF bookmarks to the mind map to complement the PhD literature review

After a while you will have a huge mind map with all the information that is important for your PhD thesis. You can use the search function (STGR+F) to find special nodes and (un) fold to get a better overview by selecting a node and pressing Space.

Making Notes

Another feature that makes mind maps superior to simple file systems is the possibility to add notes. To each node you can add any kind of text as a note and this note is shown in a separate window and as hover effect (see illustration).

Making additional notes in the mind map

Making additional notes in the mind map

How to Write a PhD Thesis (Part II): Structuring and Drafting the PhD Thesis

This is the second part of our tutorial about how to write a PhD thesis. In this part we cover how to structure and draft your thesis.

Typical structure of a PhD thesis in a mind map

Typical structure of a PhD thesis in a mind map

There is lots of good literature on how to exactly to structure your PhD so we will not cover this in detail here. However, either in your literature mind map or in a new mind map you start with a basic structure such as in the picture. 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. You might wonder why not doing this directly in a word processor. Simply, because it is much easier to move mind map nodes than sentences and paragraphs in a word document. Moreover, you have all the important information in your mind map already. And, in a mind map it will be much easier for you to restructure the thesis (we guarantee that you will have to restructure your thesis several times before you are really happy with the structure). You can also put all the administrational data in our mind map, as you see in the picture in the left half. For instance, deadlines of your PhD, important contacts and so on. The following shows how a final mind map for a PhD thesis could look like (nodes with a circle are folded and contain more nodes). You will notice that the related work section is very similar to your literature mind map. However, it is not the same. Most likely you will not use all the literature you have read. Accordingly, your literature mind map will probably contain much more information than your final related work section in your mind map / thesis. For finally structuring your thesis these information are not important. Therefore, we suggest using two mind maps: one for your literature in general and one for your PhD.

The complete draft of a PhD thesis in a mind map (nodes with a circle contain more sub nodes)

The complete draft of a PhD thesis in a mind map (nodes with a circle contain more sub nodes)

Keep in mind that your mind map for the thesis does not only include PDF links but you can write complete sentences. Again, have a look at the picture to get an idea how your final mind map should look like. Now, read in the third part how to finally write a phd thesis.

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

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 / Docear

SciPlore MindMapping / Docear 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 / Docear | Preferences and specify your BibTeX file. Then select SciPlore MindMapping / Docear | 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 / 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 SciPlore MindMapping / Docear to MS Word as shown on the following picture.

Copy bibliographic data from SciPlore MindMapping to your PhD thesis in MS Word

Copy bibliographic data from SciPlore MindMapping / Docear to your PhD thesis in MS Word

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

Creating an in-text reference in your PhD thesis

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

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 / 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 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. If you have any questions, please contact us or post a comment here in the Blog.


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