MBI - Master's thesis guidelines

Master's thesis guidelines

This page describes general guidelines for the Master's thesis project in the MBI programme.  

Where to get a topic of the thesis?

  • Contact an MBI professor or lecturer (-> people involved with MBI). The following list of research interests and names of MBI associated people serves as a starting point:
    • Algorithmic bioinformatics: Mikko Koivisto, Veli Mäkinen, Esko Ukkonen
    • Biological data fusion: Sampsa Hautaniemi, Samuel Kaski, Hannu Toivonen, Mikko Sillanpää
    • Biological data mining: Sampsa Hautaniemi, Heikki Mannila, Hannu Toivonen
    • Biological sequence analysis: Jukka Corander, Harri Lähdesmäki, Ari Löytynoja, Heikki Mannila, Veli Mäkinen, Esko Ukkonen, Sirkka-Liisa Varvio
    • Biological pattern recognition: Petri Koistinen
    • Functional genomics: Sampsa Hautaniemi, Liisa Holm, Samuel Kaski, Harri Lähdesmäki, Veli Mäkinen, Juho Rousu, Mikko Sillanpää
    • Genetic mapping: Jukka Corander, Heikki Mannila, Mikko Sillanpää, Hannu Toivonen, Esko Ukkonen
    • Machine learning in bioinformatics: Jukka Corander, Sampsa Hautaniemi, Samuel Kaski, Harri Lähdesmäki, Juho Rousu, Mikko Sillanpää
    • Metabolic networks: Juho Rousu, Esko Ukkonen
    • Modeling of molecular evolution: Jukka Corander, Ari Löytynoja, Sirkka-Liisa Varvio
    • Phylogenetic data-analysis, sequence evolution, genetics: Mikko Koivisto, Ari Löytynoja, Sirkka-Liisa Varvio
    • Structured population dynamics, evolution and natural selection, ecological modelling: Mats Gyllenberg
  • Contact a research group or company. Note that you should also in this case contact an MBI professor or lecturer to get your topic approved.


Recommended duration of the project

We recommend that you spend a maximum of six months on your thesis and plan your schedule accordingly.

The necessary steps

  1. Get a thesis topic and at least two supervisors (HY) or one supervisor (TKK).
    • At least one of your supervisors has to be from the Faculty of Science, either from the Department of Computer Science or the Department from Mathematics and Statistics. Note that you graduate from the Faculty of Science (not from Computer Science Department or Mathematics/Statistics Department) and you Major will be Bioinformatics (not computer science or mathematics or statistics).
    • The following describes the process of CS/HY (when your other supervisor is from the Department of Computer Science). For MathStat/HY (when your other supervisor is from the Department of Mathematics and Statistics), consult Sirkka-Liisa Varvio for advise in registering yourself as a thesis-student. MathStat/HY has as a Weboodi-registration system in stead of the CS/HY form-system described below. The new Faculty of Science requirement, since. 1.8.2012: All theses must be submitted here https://radr.hulib.helsinki.fi/handle/10138.1/1875/submit before they are registered to Weboodi as completed. There is an option to make only Abstract public (for example googleable). If your thesis is part of a biomedical project (like most bioinformatic theses are), and planned to be published in a scientific journal, you should seriously discuss with your supervisor whether making only Abstract public during e-archive submission is the only reasonable solution.
  2. CS/HY: Write an application for MSc thesis subject. Use this form for a CS/HY thesis.
    • Include a topic definition (1-2 pages) to the application. Outline the basic ideas of the research hypothesis, approach and methods. Include a couple of central literature references in the definition.
    • Hand in the application form, topic definition and an up-to-date (unofficial) transcript of studies to your supervisors.
  3. CS/HY: Write a research plan
    • Length: Approximately 20 pages (see the document template below)
    • The plan should also contain a list of most important references that you are going to use in the final thesis.
    • Planned table of contents of the final thesis. For each section that you have not written as a part of the research plan, give
      • Tentative contents (briefly)
      • Estimate of section length in pages
      • Deadline for completition
    • Hand in the research plan to your supervisors.
    • Give a presentation on your research plan in the MSc thesis seminar
    • Use the following template to write the research plan (CS/HY only): LaTeX (use engl_malli.tex, you may need the other files as well), Open Office. If possible, use LaTeX: the time spent to learn the system is definitely worth the ease of editing large documents, maintaining a consistent style and handling references.
  4. CS/HY: Write the thesis
    • Length: Most good theses fall within 50-70 pages. Unjustified deviations may affect the grade.
    • Use the above template to write the final thesis.
    • See ACM Computing Classification System for classifying your topic.
    • Give a presentation on the final thesis in the MSc thesis seminar
  5. CS/HY:What to do when you have written your thesis
    • Provide your supervisors with printed copies of your thesis
    • Your supervisors will review the thesis: you may be required to make changes to the thesis. Thesis review typically takes about one month.
    • When the review is complete, your supervisors will write you a review statement that includes a description how your thesis has been graded
    • You need to bring a statement to the department secretary where you confirm, that you have received the review.
    • Department steering committee approves the thesis
    • If you do not accept the grade, first discuss the grading with your supervisors.


Grading of the Master's thesis

At the University of Helsinki, MSc thesis grades are the following, with laudatur being the best and approbatur being the worst passing grade:

  1. laudatur (l)
  2. eximia cum laude approbatur (ecl)
  3. magna cum laude approbatur (mcl)
  4. cum laude approbatur (c)
  5. non sine laude approbatur (nsla)
  6. lubenter approbatur (b)
  7. approbatur (a)

Examples of completed theses

You can browse University of Helsinki E-thesis if you want to access completed Master's theses.


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