Master's Thesis FAQ

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Ideally, you should start planning your thesis one term before you actually want to write it.

There are two advantages if you start planning early enough:

  1. Only a limited number of students can be supervised by the same docent. These places are distributed on a first-come, first-served basis. If you are late, you might be unlucky, and all the place are already taken.
  2. You might already know your topic one term in advance and have more time to collect appropriate literature.
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There are several options how to find an appropriate (and interesting) topic for your thesis:

  1. You choose an advertised topic of a project group and contact the indicated docent. The advertised topics are only rough suggestions that can be adjusted to your personal interests or preknowledge.
  2. You approach a member of a thematically compatible project group with your own idea. These own ideas are often developed from work experience (e.g. in an enterprise).
  3. Furthermore, you can find inspiration and meet docents in classes (e.g. software project: project management).

Your own ideas are in any case very welcome! It might take some weeks to develop a topic with together your supervisor. During this time you deal intensively with the topic and should clarify the following questions:

  • Can I do that? (or is the question to difficult or too wide for the limited span of time)
  • Do I want to do that? (a task that does not interest you is going to be a torture for all involved parties and mostly ends unsatisfactorily)
  • Is the chemistry between you and your supervisor right?

The first reading up on your subject also takes place during this phase. Your supervisor might support you with your research.

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That depends on your supervisor. Before deciding to write your thesis in an enterprise, you should first think about the topic of your thesis and consider which docent would thematically be interested and willing to supervise your thesis.

The topic of your choice should meet the university requirements, which means that the task is supposed to demonstrate the absolvent’s skills not only on a technical but also on a conceptional level.

If you have found an appropriate topic, write a short text of about 1-2 pages including the content of your topic (What is it about?) and the suitability (How does it meet the university requirements?) and go to the office hours of the docent.

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Yes. You can either go to a docent’s office hours or send her/him an e-mail. It is advantageous to contact docents who you know from pro-/seminars or lectures. However, it is your decision, who you ask.

In case you want to get an overview of potential topics, you might also approach several docents. But:

If you have found an adequate topic under supervision of one of the docents, tell the other docents!

This is not only a gesture of politeness but also an act of thoughtfulness towards your fellow students who now can write their theses on one of your rejected topics.

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If you have someone in mind whom you would like to be your second assessor, you can, in consultation with your supervisor, contact this person via e-mail or personally. Give a short description of your topic and ask him/her to be the second assessor of your thesis. Please note that he/she must be authorized to examine students. In case you do not have a preference, consult your supervisor for suggestions.

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Before you can register your thesis, you have to complete successfully modules of at least 60 credit points (cf. §4 of the examination regulations 2012 and §4 of the study regulations 2012). If you have questions concerning older study regulations please contact the examination office for Mathematics and Computer Science.

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No, usually, you only hand in a working title when registering your thesis in the examination office. This working title comprises a more broadly defined topic than the actual content of your thesis (in most cases your supervisor pays attention to this when formulating the topic). The title of your thesis can (and often should) be changed when the final content of your thesis matches better with a different title. The working title should solely be recognizable (by keeping 1-2 key words).

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You have to submit your master’s thesis within 23 weeks after the release of your topic by the examination board (cf. study and examination regulations 2012). You can extend the period of writing only with a sufficient reason (e.g. illness) and even then only handing in a verification (e.g. doctor’s certificate) (cf. "Allgemeine Hinweise" of the examination office).

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Every student can independently organize the period in which s/he writes her/his thesis. You can attend modules, if you wish. However, do not underestimate the time needed for weekly exercise sheets. It is recommended to attend no or only few modules while writing your thesis.

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For getting a first overview of the topic and the published materials, “Google Scholar” is a good start. However, the next step should be the library portal Primo where you can search the catalogues of all university libraries in Berlin and possibly also find online resources. (Tip: It’s worth searching also other university’s libraries as they might possess more specific literature.)

The following pages might be useful as well:



Web of Science

You might also ask your supervisor for help with your search for papers. On the one hand, s/he can mention some introductory material to you, on the other hand, s/he might have extended access to resources that are not free accessible for students.

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Yes and No. Of course, the thesis as well as the employed programming codes have to be new but you are not expected to find completely new research results. Your master’s thesis should prove your ability to work independently on an advanced problem from the field of bioinformatics using scientific methods, as well as the ability to represent the obtained results appropriately both orally and in writing. These results are also meant to be documented and evaluated (cf. study/examination regulations 2012).

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The concrete structure of a thesis may vary drastically depending on the choice of topic. However, the following basic elements build a common frame:

  • Introduction: What is the problem? Why is it a problem? How does it refer to other works? What is not a problem? What is not solved with this work?
  • Theoretical state: Comparable papers (scientific literature)
  • Chosen problem-solving approach, consideration of alternatives
  • Description if difficulties and how they were solved or avoided
  • Documentation of the process/implementation and the developed artefacts
  • Evaluation (e.g. small field research) / Results (What did I find out?)
  • Perspective
  • Bibliography

Further requirements:

  • The thesis should be well-structured. Do not repeat yourself but use lists and cross references to make the information easily detectable.
  • There should be a summary (of 0.5 – 1 pages) between the front page and the content list.
  • Every assertion has to be proven (by a reference, a thorough argument or your own empirical data).
  • Language: Use clear and easily understandable language. Master theses are generally written in English.
  • Define important terms!
  • Insert helpful and appropriate references. Therefore, you need to have thorough knowledge of the relevant scientific literature.
  • If you need to include huge masses of information (that are tiring to read) add them to the appendix.

Theses that include programming should feature a process-oriented focus. Therefore, special attention should be paid to the following points:

  • Introduction: short description of the chosen method / problem-solving approach
  • Description if difficulties and how they were solved or avoided (or why not)
  • Results (What did I find out?)

The longer the better is NOT true for theses. On the contrary, shorter often proves to be better: Mention the essential concisely; leave out the non-essential. The examination regulations prescribe a length of up to 80 pages (24 000 words) for a Master’s thesis (§5(4) of the examination regulations 2012).

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Generally, a Master’s thesis should be understood by everyone with a Master’s thesis in Bioinformatics. Important terms that are not part of a common basic knowledge should be defined or briefly explained to enable the reader to follow the argumentation.

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Theses are commonly written in LaTeX for which a free download is available on the Internet. There are several introductory courses and handbooks.

For example, have a look at:

LaTeX-Kurzeinführung (pdf)

LaTeX-Einführung von Andrew Roberts

Additionally, there are crash courses offered regularly by the mentoring program.

Of course, it is not forbidden to typeset your thesis in MS Word or Open Office, but using LaTeX and BibTeX it is a way easier to obtain a professional result.

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There are numerous citation systems. For scientific works, generally, the IEEE-citation system is utilized. Each quote must be supported by a precise reference source.

In the text – reference number: as shown by Brown [4], [5]; as mentioned earlier [2], [4]–[7], [9]; Smith [4] and Brown and Jones [5]; Wood et al. [7]

In addition to the correct citation system, also the bibliography plays an important role. It is located at the end of your thesis. Commonly, it is ordered alphabetically by the authors’ last names.

In the bibliography:

  • Books: [1] J. K. Author, “Title of chapter in the book,” in Title of His Published Book, xth ed. City of Publisher, Country if not USA: Abbrev. of Publisher, year, ch. x, sec. x, pp. xxx–xxx.
  • Technical Reports: [1] J. K. Author, “Title of report,” Abbrev. Name of Co., City of Co., Abbrev. State, Rep. xxx, year.
  • Online Sources: [1] J. K. Author. (year, month day). Title (edition) [Type of medium]. Available: http://www.(URL)

For further information concerning direct and indirect citation can be found in:

ThesisGuidelines by Prof. Dr. Prechelt.

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Generally, you can consult your supervisor with any question regarding content or conception of your thesis. This also includes possible problems of understanding or any stagnation of your working process. However, before asking your supervisor for help, you should try to solve the problem yourself (concerns mainly problems of understanding).

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Yes, provided that your supervisor offers you to do so. In case of doubt, you can ask him/her to have a look at one or the other chapter of your thesis that causes you trouble.


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The “defense” of your thesis is part of your final assessment but it has NO influence on your mark. Structure and length are set as follows:

  • Master’s Thesis (cf. §5(9) examination regulations 2012): The defense of the Master’s Thesis consists of a 15 min presentation of the thesis’ results and a 15 min discussion and is not marked.

These statements are based on the study and examination regulations 2012. If you have questions concerning older study regulations, please contact the examination office for Mathematics and Computer Science.

The presentation should contain a brief description of the content of your thesis but also be self-promotion.

  • What did I do?
  • Why was it difficult?
  • Why deserve my results to be called good? (But also: Where can my work still be improved and why?)

Do not arrange your presentation too similarly to your written thesis. It is impossible to present everything in detail when you have only 15 min. It’s really adding by subtraction. On the other hand, the presentation offers you the chance of pointing out the difficulties of the problem or the ingenuity of your solution. In any case, the following points should be included:

  • The problem and its classification in actual research
  • Your Approach to the topic and the chosen methods
  • Your results
  • Evaluation of your results
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No. Even if such a combination is comprehensible from a practical point of view, it is also contestable on grounds of bias. In consultation with the GK chairmanship, the combination of second assessor and supervisor from the same working group was discussed in the examining board with the result to avoid such combinations.

Therefore it is necessary to pay attention that the supervisor and the second assessor of your bachelor or master thesis don't come from the same working group! Especially the combination of examiners consisting of the leader and a member of the working group should be avoided.

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