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

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

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.


[1] A. Fink. Conducting research literature reviews: from the Internet to paper. Sage Publications, Inc, 2009. [2] J.L. Galvan. Writing literature reviews: A guide for students of the social and behavioral sciences. Pyrczak, 3 edition, 2005. [3] Judith Garrard. Health sciences literature review made easy: the matrix method. JONES AND BARTLETT P, 2006. [4] Chris Hart. Doing a Literature Review: Releasing the Social Science Research Imagination. SAGE Publications, 1998. [5] L.A. Machi and B.T. McEvoy. The Literature Review: Six Steps to Success. Corwin Press, 2008. [6] D. Ridley. The literature review: a step-by-step guide for students. Sage, 2008. [7] John M. Swales. Telling a Research Story: Writing a Literature Review. University of Michigan Press/ESL, 2009. [8] Rudi Studer, Richard V. Benjamins, and Dieter Fensel. Knowledge Engineering: Principles and Methods. Data and Knowledge Engineering, 25 (1-2): 161–197, 1998. Elsevier. [9] Steffen Staab and Rudi Studer, editors. Handbook on Ontologies in Information Systems. Springer-Verlag, 2004. [10] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Citation Counts (An Empirical Study). In André Flory and Martine Collard, editors, Proceedings of the 3rd IEEE International Conference on Research Challenges in Information Science (RCIS’09), pages 439–446, Fez (Morocco), April 2009. IEEE. doi: 10.1109/RCIS.2009.5089308. ISBN 978-1-4244-2865-6. Available on [11] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: An Introductory Overview. In Birger Larsen and Jacqueline Leta, editors, Proceedings of the 12th International Conference on Scientometrics and Informetrics (ISSI’09), volume 1, pages 230–241, Rio de Janeiro (Brazil), July 2009. International Society for Scientometrics and Informetrics. ISSN 2175-1935. Available on [12] Jöran Beel and Bela Gipp. Google Scholar’s Ranking Algorithm: The Impact of Articles’ Age (An Empirical Study). In Shahram Latifi, editor, Proceedings of the 6th International Conference on Information Technology: New Generations (ITNG’09), pages 160–164, Las Vegas (USA), April 2009. IEEE. doi: 10.1109/ITNG.2009.317. ISBN 978-1424437702. Available on [13] Toni Buzan. Making the Most of your Mind. Pan Books, 1977.
By | 2016-10-16T20:50:46+00:00 March 2nd, 2010|HOW TOs, sciplore mindmapping|73 Comments


  1. Linux March 18, 2010 at 16:36 - Reply

    I can’t find a PDF reader to create bookmarks with Linux. Any hints?

    • Joeran March 20, 2010 at 19:11 - Reply

      the latest version of foxit reader can do this. read here

    • Tux July 17, 2010 at 03:33 - Reply

      KDE’s Okular can insert bookmarks and highlight text. It runs on GNOME too. Both KDE and GNOME can coexist on a box Ubuntu.

    • ooolavr August 10, 2011 at 04:19 - Reply

      As appeared somewhere on this site as well as on the Web, jPDFbookmarks is IMHO the most appropriate and established software for embedding bookmarks and notes into PDF files on Linux.
      Okular is a nice allowing to visually add bookmarks, highlights and notes to the PDF file BUT those are linked with current user only so can’t be transferred and get visualised on other computers, that is, Okular stores all those modifications in the user’s home dir, not in the PDF file itself.

  2. DEHarry April 16, 2010 at 10:50 - Reply

    I am just about to start my PhD. Thank you very much for this tutorial, it is really helpful and on first glance sciplore mindmapping looks great!

  3. martina May 4, 2010 at 02:51 - Reply

    does there exist also a german version of this tutorial?

    • Joeran May 4, 2010 at 03:01 - Reply

      no sorry, there is no german version of this article.

  4. mrslucy May 5, 2010 at 18:25 - Reply

    i found this tutorial two month ago, tried sciplore mindmpping, and finished my literature survey for my BSc yesterday. Your software is awesome! awesome! awesome! It helped me so much! Thank you!

  5. Tim Olsen May 7, 2010 at 23:32 - Reply

    Thanks. This is fantastic. I was just thinking how valuable it would be to have this… and then I found you on wikipedia.

    One question. I have a PDF that already has a ton of bookmarks in it (a dissertation) — What’s an easy way to remove those, so I can start fresh?

    • Joeran May 7, 2010 at 23:52 - Reply

      you can delete bookmarks in a PDF e.g. with foxit reader. alternatively create a node in your mind map (e.g. “trash”) and move the imported bookmarks into that node. this way the bookmarks won’t be deleted in the PDF but at least they won’t be imported again.

  6. sangeeta May 17, 2010 at 19:17 - Reply

    how to delete Map and what is reference key.
    Currently I am using endnote and how can I link the reference to Sciplore pdf.

    Also, is it possible to get the pdf into one folder with a click from each reference in endnote rather rafting each reference to copy it.

  7. Craig Embleton July 23, 2010 at 09:19 - Reply

    The in (wordprocess) text references are given as numbers that refer to the bibliography references. Can this tool enter in text references in the Harvard format of (Author, date)?

    • Joeran August 5, 2010 at 11:35 - Reply

      SciPlore MindMapping does not directly create reference lists. Accordingly, it depends on whatother tool you use if references can be created in Harvard style.

  8. gsagri04 August 10, 2010 at 16:50 - Reply

    This is great article and software too.. I am using freeplane for mind mapping- basically to organize whatever I understood from research article. But this software seems to be good for researcher like me. It is hard to organize PDF when collection become huge. Thanks for the great software not only similar to freeplane but also supports Mendeley- one of the best PDF organizing software. I thank the developer for making good software for researches (nobody bothers about researchers, one who bothers makes money- was slogan with reference to Endnote or VectorNTI ).


  9. Dima August 10, 2010 at 22:11 - Reply

    Any hints, how I can create bookmarks on mac, besides Adobe software? Apparently there is no Foxit Reader for Mac.

    • Joeran August 11, 2010 at 16:43 - Reply

      no sorry, I only know of Adobe Acrobat for Mac. If you find an alternative, please tell me.

    • Melanie September 27, 2010 at 19:30 - Reply

      I don’t know if you are still checking back to this site, but the latest version of preview (s/w standard on mac o/s) does bookmarking and highlighting.

  10. msel September 22, 2010 at 09:19 - Reply

    For mac (also for windows and linux) you might use the program jpdfbookmarks. I’ve just try it in a windows environment. This program can also be used in a mac environment because it is written in java.

    Another good alternative for windows is PDFX-Change Viewer. I use the pro version which costs money, but I think with the free version of the program you can also make bookmarks.

    • Joeran September 23, 2010 at 17:14 - Reply

      thank you very much. i will have a look at the websites

  11. A_Rauf September 24, 2010 at 12:29 - Reply

    ohhh…I was really lagging behind in terms of my Master dissertation….and now with this I am very hopeful to meet the submission deadline.. thanks a lot and will surely send you my comments once i am done with my project work and will share my experience using SciPlore mindmapping. Great service by all developers and their team. congratulations.

  12. Michael September 30, 2010 at 18:27 - Reply

    I just recently stumbled upon Sciplore Mindmapping and I love the idea. I directly tried it out, but stumbled onto two rather annoying problems:

    1. When I select a directory (along with it’s subdirectories) to monitor my PDFs and import them, they are re-imported at each start-up. As a result I end up with the entries being duplicated EVERY time.

    2. The second thing is perhaps not so much a problem than a question:
    Assume I already have a PDF and with it’s bookmarks imported into a mindmap. Now if I add more bookmarks to that PDF is it possible to just import the added bookmarks. I didn’t find an “Update Bookmarks” option and if I do “import bookmarks”, it imports ALL the bookmarks, which is unnecessary and if the PDF has many bookmarks very annoying…

    I hope somebody can help me with this as it is kind of putting me off from reallying digging into Sciplore and doing everything with it.
    Thanks and best regards,

    • Joeran October 2, 2010 at 18:14 - Reply

      regarding 1: this definately is a bug. i have sent you an email.

      regarding 2: thx for the suggestion, i added it to our todo list. maybe we will have implemented this in beta 13

      • Michael October 4, 2010 at 15:50 - Reply

        Unfortunately I didn’t get your email regarding the bug.
        Perhaps you could send it again?

        • Joeran October 5, 2010 at 11:03 - Reply

          I sent it again (maybe it’s in your spam folder?). Anyway, ths is what I wrote:

          Are you sure you are using the latest beta 11 from our website

          If so, please could you send me the mind map this happens with? or
          ideally, create a new and simple mind map in which this problem
          occurs and send this to me.

  13. Michael September 30, 2010 at 18:32 - Reply

    Another thing:
    It would be nice, if one were able to select the PDF viewer that is used by Sciplore to open the PDFs. I am working in Linux and used Wine to install the “Foxit Reader”, which does work great.
    Nonetheless I don’t want it as my default viewer for the whole system, as it’s not part of Linux and it takes long to start up. I’d prefer just starting “Foxit Reader” from inside JabRef and Sciplore for adding bookmarks and else use the default viewers from Linux.
    Is there any way this is possible?
    Best regards and thanks again,

    • Joeran October 2, 2010 at 18:17 - Reply

      I also added this suggestion to our todo list. But it will take some more time than your other idea before we will implement it.

    • jpz July 28, 2011 at 12:24 - Reply

      ——— PDF-Xchange + Wine = bookmarking PDF reader in SciPlore under Linux ———

      Hi all,
      I found this workaround which may be useful to Linux users that want to use a bookmark enabled PDF reader within SciPlore.

      1) download the free version of PDF-Xchange, (a viewer that allows bookmarking and has a very nice search tool) from here:

      2) install PDF-Xchange so it runs under Wine

      3) Copy the following lines, paste them to a text file and save it as or something similar.
      ———————————–Copy from line below ———————————————
      # Purpose: To convert Linux-style filename to Windows-style to pass as an argument
      # to wine when starting PDF Reader
      #assuming you use the default installation folder in Wine
      App=`eval wine “‘C:Program FilesTracker SoftwarePDF ViewerPDFXCview.exe'” “‘$Filename'”`
      ———————————–Until line above ———————————————
      path to PDF-Xchange executable may be different, check it for your system..

      4) Change properties of the script you just saved to make it executable

      5) In SciPlore open “preferences” under ‘tools” menu to open the Freemind properties window and click on the HTML tab/button

      5) Go to the input box labeled “Default Browser Command Other Os” and replace the text “xdg-open {0}” with “dir-where-u-saved-yr-script/ {0}”

      6) Click Save in the Freemind properties window. Sciplore will prompt you to restart to enable the changes but this was not necessary for me.

      Now when you click on a PDF in your mindmap it will be opened with PDF-Xchange!
      The script is a modified version of a Foxit script found here:

      However Foxit would not work within Scilore in this way, failing to open the pdf, although it worked within Nautilus (the Gnome file manager)
      Both work fine with PDF-Xchange though!

      Good luck!

  14. Cindy November 2, 2010 at 03:36 - Reply

    I Love YOU!!!

  15. […] […]

  16. […] “How to write a thesis (Bachelor, Master, or PhD) and which software tools to use” – […]

  17. Jair Wen December 16, 2010 at 08:12 - Reply

    Hello, I tried SciPlore on the Mac OS X 10.6.5. It seems can not load highlight markers from pdf modified by Acrobat X in the same system. However, bookmarks are imported smoothly.

    • Joeran December 18, 2010 at 09:39 - Reply

      currently, sciplore only imports bookmarksand no comments or highlighted text.

  18. Anna January 4, 2011 at 16:13 - Reply

    Hi, this sounds great. I have already started writing my PH.D. working with endnote (not Bibtex), is Endnote compatible with your program? Or is there a way how I can move my reference-files to your program? Thanks!

    • Joeran January 10, 2011 at 19:29 - Reply

      sciplore mindmapping is not compatible with endnote. and if you google, switching from endnote to e.g. jabref seems to be difficult. if you find an easy way i would be very happy if you told me and i would publish it on our blog

  19. Andrea January 17, 2011 at 22:40 - Reply

    Hi, this is a great blog and extremely helpful however I have a quick question about using JabRef to cite things in MSword. I followed the instructions to use my JabRef citation database with MSword but am having trouble getting the citations in the form I would like. I need to cite according to American Sociological Assocation standards and can’t seem to find a format file that works. The furtherest I have gotten is going to the package manager in MikTex and downloading packages that are suppose to contain new formats. Is this how I should be doing this and if so do you know of a packages for ASA citation.

  20. Benjamin Ryba March 3, 2011 at 17:33 - Reply

    Hi, really nice and helpfull programm. I have a question and maybe an idea for new implementation:

    1. I use the latest version (14 Beta) but the bookmarks don’t really guide me to the correct page. I always get to the starting page of the PDF. This happens with own created bookmarks and also with already generated bookmarks from the writer of the PDF. (I use foxit reader)

    2. In my opinion the mindmap structure is prefered to use it with LaTeX. If there’s a way to export the different nodes with downwardly used sections similar to LaTeX (chapter/section/subsection …), an easy, first usable text could be generated. The whole formatting for the text have to be done in the header of your writings so you don’t have to think about. you just have to export in a .txt. Maybe one have to define what is “text” and what are headlines. Do you tink that could work?

    Thanks so far.


    • Joeran March 3, 2011 at 18:23 - Reply

      hi benjamin,

      the feature to jump to the bookmarked page is not yet implemented. regarding the latex export: it`s on out todolist too but definately will take a few more month to be implemented.

  21. kamran March 29, 2011 at 22:32 - Reply

    I installed the SciPlore, but when i start it, i get this message :”freeMind.Main.freeMind cann’t be started” !
    What shold i do? Help plz

    • Joeran March 30, 2011 at 14:37 - Reply

      have you installed the latest Java version from ? if you still have this problem please contact us at feedback A.T sciplore. org and tell us your operating system

  22. Gretchen March 31, 2011 at 03:42 - Reply

    I’m not sure I completely understood the process described here. From what I understood:
    First, you make a mindmap of the literature you collected and organize it by topic perhaps. Then, you make a second mindmap more according to how you want the paper/arguments to build up. I guess what I don’t understand is how the second mindmap works (in general, I do understand mindmapping). Do you copy nodes from the first map? What if I just want the bookmark, when I copy it to the new mindmap will the bibliographic info come along with it?

    I hope you can answer my questions/confusion, and thank you in advance.

    • Joeran March 31, 2011 at 09:56 - Reply

      eventually it`s up to you. if you have just a “small project”, e.g. a bachelor or master`s thesis you could do everything in a single mind map. if you have a larger project (e.g. a phd and several additional papers) you might want to use two mind maps. one for the literature management and one for each paper. and yes, you can just copy nodes (and bookmarks) between mind maps and reference information will be kept.


      • Gretchen April 1, 2011 at 03:59 - Reply


        Thank you for your reply – and after using the maps, I realized I already had the answer to one of my questions.

        By the way, I’d like to mention that I agree with Michael (Oct 2010) #2, that it would be handy to have the option when updating bookmarks to choose between “all” and “new” (currently all are imported again).

        Thanks again!

        • Joeran April 1, 2011 at 12:03 - Reply

          right click on a bookmark and select “PDF Management -> Import new bookmarks” – this should import new bookmarks only.

  23. sanspm July 12, 2011 at 13:59 - Reply

    Hi, I have a few questions related to the “monitoring folder” function:

    1) what’s the difference between “smart” and “thorough” update of monitoring folder? I deleted some pdfs from the folder being monitored as a test and even after trying the “thorough update” the information from the deleted files remained – I expected data from deleted files to have also been deleted.

    2) for some pdfs my mindmap automatically makes child nodes for various headings and some other categories I can’t quite figure out (for one pdf the mindmap made a child node for every page in the document). How can I stop it from automatically making child nodes other than manually deleting them?

    1) add a section in the help mindmap on monitoring folders and on reference management (some information is on the web-based manual, but there is nothing in the mindmap itself.

    2) you use the term “monitoring directory” in most places and “watch folder” in one instance, but then in the mindmap software it’s actually called “monitoring folder”; consistency in the terms would probably be helpful when people are searching for information

    • Joeran July 12, 2011 at 15:23 - Reply

      what’s the difference between “smart” and “thorough” update of monitoring folder?

      “smart” checks the file date (last modified) of PDFs and compares this to the date of the mind map. only PDF being modified later than the date of the last incoming folder update are analysed.
      “thourough” checks all PDFs for bookmarks which might take a long time.

      I expected data from deleted files to have also been deleted.
      this will be possible in one of the next versions of SciPlore MindMapping (Docear). However, I would appreciate if you could post your wish here too

      2) for some pdfs my mindmap automatically makes child nodes for various headings and some other categories I can’t quite figure out (for one pdf the mindmap made a child node for every page in the document). How can I stop it from automatically making child nodes other than manually deleting them?

      in the menu select “SciPlore MindMapping – Preferences – PDF Management”. There you can select which kind of annotations to import. If you don’t want to import any annotations (un)select “SciPlore MindMapping – Import Annotations from PDFs”

      regarding your suggestions: yes, we will do this, thank you! If you have any further questions feel free to use our new forum

  24. sanspm July 12, 2011 at 14:49 - Reply

    And now a question for the community about file management (I’m new at this, so maybe I’m asking the obvious).

    I’m using:
    – Mendeley because it grabs the metadata and renames the files automatically
    – Foxit reader to easily import bookmarks into SciPlore MindMapping
    – “Folder Monitoring” in MindMapping, but I want to monitor a folder that contains only the files that I’ve actually read and marked up

    I imagine the following, but doesn’t seem very efficient:
    1) download files to a folder, e.g.”journal downloads”

    2) have Mendeley rename the files and save in “Documents library” in “Mendeley Desktop”; delete version in “journal downloads”

    3) open and read the file in Foxit, re-save in another folder, e.g. “read documents”; delete the version in “Documents library”??

    Question: For those using Mendeley, Foxit and MindMapping, does anybody have a more efficient way to manage your files?

    Thanks for any ideas!!

    • Joeran July 12, 2011 at 15:31 - Reply

      Why not doing the following:

      1) Download new PDFs to c:allmypdfs
      2) Specify this directory as a “watched folder” in Mendeley and create a monitoring node for the same directory in the mind map. That means you will have all your PDFs in Mendeley (with the correct meta data) and in a node in a mind map
      3) Double click PDFs you want to read in your mind map. They will open in Foxit Reader. Create comments and other annotations
      4) Import the annotations to the mind map, sort them, remove the link to the PDF from the monitoring node in the mind map. Then you will have all your other unread PDFs in the monitoring node left and the read PDFs in the other nodes of your mind maps.

      Of course, on your hard drive everything is in one folder, but does this matter?

  25. Zhuang Xuhui August 16, 2011 at 04:30 - Reply

    Thanks very much.

  26. Dissertation Literature Sources September 29, 2011 at 20:38 - Reply

    […] […]

  27. Kurt November 9, 2011 at 11:46 - Reply

    Hey there!
    I am runnign into a problem. I will use a lot of literature sources. The pdfs during my dissertation work will run up in the hundreds at least. So I found it almost unusable when I expanded the folder in the mind map because of the all the pdfs (let alone the additional bookmarks), So what I did was start breaking down the Node : “incomming literature” into sub headings – however when I do this then I assume the path for each individual pdf, that is put into a sub node, has a broken path to the “monitoring folder” which then then creates deadlinks from the pdf to the bookmarks.

    I have also tired first structuring my folders on my pc to match the mind map structure I want – but I still get the broken link problem.

    Anyhelp? Is there a way to move nodes around (and into newly created ones) within the monitoring folder node?

  28. John November 9, 2011 at 18:29 - Reply

    You might want to check this PrepLit software out for preparing the literature review. PrepLit is a research tool that can search through your PDF collection
    and help doing the literature review. It does not just let you search
    PDF files with a lot of extraordinary research search options, but
    also helps you through the entire literature review process. The
    search results can be managed which a lot of carefully designed
    features such as: saving, exporting to open with Microsoft Office or
    Open Office, ranking, etc. It can make the time-comsuning search
    possible and save very big amount of your time. Free license of
    PrepLit is available for educational institute, blogger, journalist,
    and public speaker. More information on Preplit

  29. qahtan March 27, 2012 at 15:55 - Reply

    good paper for any student PHD or master

  30. Wilbart May 26, 2012 at 13:30 - Reply

    Hi there, this is a helpful post, this will give ease to those people who are having a hard time writing their thesis. I think we share the same views as well. I created a blog with step by step guide on making a research. Of course they are free, that is why I put it on a blog. If you have time, visit it…

  31. Sunya July 6, 2012 at 06:59 - Reply

    I am Just starting to write my PhD Thesis. I find the tutorial immensely useful.

  32. Stephanie August 28, 2012 at 02:23 - Reply


    I noticed Foxit is only available for Windows. I’m new to Macs, but in case anyone else had that problem, you can use the built in Previewer. Sorry if this is redundant, I didn’t want to read through all the messages.

  33. amit rajput August 29, 2012 at 21:49 - Reply

    i am just starting phd .i find this useful

  34. idris ahmed abaker September 11, 2012 at 11:23 - Reply

    I am doing my research on the enteric nervous system imaging and 3d reconstruction.I want to get use of this programe

  35. Muhammad Moiz September 20, 2012 at 19:46 - Reply

    I am very Happy to review this. it gave me lot of courage. & hve solved my problems.

  36. md tanweer alam September 22, 2012 at 05:19 - Reply

    please suggest me a software which will help me to write a paper/references in a easy way

  37. Joseph Ayerhan November 11, 2012 at 17:42 - Reply

    i need it for my paper

  38. ALAM November 20, 2012 at 17:55 - Reply

    Salam ,
    I desire to know how to make a questionnaire for my thesis,

  39. Mohamed January 6, 2013 at 10:52 - Reply

    please suggest me a software which will help me to write references in a Ph.D

  40. Derek July 24, 2013 at 08:32 - Reply

    This is very timely advice in writing a thesis, thanks for sharing!

  41. Matt August 22, 2013 at 09:22 - Reply

    I have just gone through the tutorial, and am strongly inclined to adopt the approach you outline as I undertake writing my thesis, but a few questions:
    1.I recently purchased the program, PapersApp. Should I entirely ignore that program if I use your suggested approach?
    2. I tend to read journal articles in printed form, and have many that I’ve highlighted, etc. I’ve considered reading digital documents and highlighting PDFs, and recognize the benefits of doing so, but haven’t done so yet because I’ve been unsure about which PDF reader to use, and how durable any mark-ups I make to files will be. Additionally, I’ll have to go through all of the papers I’ve read and transfer my highlights to the digital files. Will Foxit Reader (which you recommend) perform essentially the same mark-up and organizational functions as Papers?
    Thanks very much.

    • Norman Meuschke September 24, 2013 at 19:32 - Reply

      Dear Matt,

      I apologize for the late reply and hope my answers will still be useful to you.

      Concerning your 1st question:
      I am not familiar with the PapersApp and the features it offers. Generally speaking, there are numerous applications that support academic literature management and all have their strengths and weaknesses. So, I can’t tell you which one is right for you. However, to my knowledge, Docear, which is the successor of our mind mapping software, is the only integrated tool for academic literature management based on mind maps. If you would like to use our approach, i.e. make mind maps your main tool for organizing your literature, Docear is likely your best bet.

      Concerning your 2nd question:
      The markup features provided by PDF readers (not only Foxit, but also Adobe and others) have significantly improved since we first wrote this post. Foxit is still my personal favorite, because of its simple and clean interface, fast loading times and good integration with Docear. PDF annotations (highlights, comments etc.) are stored within the PDF, so they’re as durable or persistent as the file itself. Foxit has a nice feature I haven’t seen in any other PDF reader so far: it lets you export your annotations in a special XML-based format called FDF. Furthermore, Docear allows you to automatically import all annotations you made in a PDF into your mind maps. I hope that answers your questions. I suggest, you check out the Docear suite to see whether it fulfills your organizational needs.



  42. Li September 15, 2013 at 06:34 - Reply

    Hello,I am so interested in SciPlore Mindmapping.But I can not find “Update reference keys in current mind map” when I integrated BibTeX (JabRef) with SciPlore MindMapping.I can not any get reference keys from Jabref.
    I sincerely expect your reply.
    Thanks very much.

    • Norman Meuschke September 24, 2013 at 19:00 - Reply


      Thanks for your interest in SciPlore MindMapping. The development of our mind mapping software has been transferred to Docear, which is a separate project solely dedicated to advancing the mind mapping suite. Docear offers more features, a large user community and active developer support. We suggest you give it a try.

      Best, the SciPlore Team!

  43. Katherine Evans September 27, 2013 at 09:46 - Reply

    I would like to say THANKYOU.

  44. Somebody Anon November 24, 2013 at 13:45 - Reply

    Wonderful post and great info about the tools and processes of writing a Thesis or Dissertation !!
    Thank you very much …

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