Bioinformatics Thesis

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Writing your Thesis

Be sure to start writing your thesis early in your project. You should include this in your Project Plan. Do not be afraid to waste time writing things down that you may need to change again afterwards; this is unavoidable and a natural part of the writing process. This means that afer, e.g., background reading you can immediately write most of your introduction, after program design and script writing you can write most of your methods section. If unsure where to start, or what to do next, try writing the Discussion or Conclusions first; this may sound very strange but it helps you to focus on the most important parts and see the 'larger picture'.

Importantly, involve your supervisors (certainly your daily supervisor) in the writing process. Start with only a draft outline to structure the story, and add the sections one by one. Ask for feedback at each step. The best way to understand what is expected of you in a project thesis, is to read finished and graded theses from other students.


There is no official word limit, but you should be concise in your writing; wordiness will be marked down.

The thesis should contain the following sections:

  • Title page
  • Abstract (maximum of 200 words)
  • Background
    • including a motivation: why is your work important?
  • Methods
  • Results
  • Discussion
    • also indicate any difficulties or problems with your approach or the results
    • also compare your results with other published work
  • Conclusions
    • no new facts!
  • References
    • citations in the text as (Author, Year)
    • all items in the reference list must be cited in the main text.

Figures & Tables

  • Your thesis should include at least one table and one figure.
  • All tables and figures must have a number, a caption and must be referred to in the main text.
  • Make sure to give a caption with each figure that ensures you can read the figure independent of the main text.
  • Make sure to give variable names AND (SI) units along the axes of your figures.


Scientific work is never performed in isolation. This means you must acknowledge when and where you have been helped by others, which other work you have been building on, etc.

  • existing programs or code, or help with coding
  • data used
  • help with writing (this help is required!)
  • and other forms of collaboration
  • ( don't forget your supervisor(s) )

Writing Style

The style of your thesis should be similar to that of a scientific paper, see for example articles in PLoS Computational Biology or Bioinformatics. However, your thesis should contain considerably more detail than a general research paper. A good guide line would be that your fellow students should not only be able to understand the work, but should also be able to reproduce the work based on your thesis.


We do not impose strict layout rules, but there are a few guidelines:

  • include a title page with Title, (all) author(s), clearly indicating your daily supervisor(s) and VU/UvA supervisor. You also need to include your student number, credits, duration, course, code the MSc you are enrolled in and your chosen track / specialisation. Also the institute, department and group where the work was carried out should be mentioned on the title page.
  • Be sure to use page numbers!
  • Be consistent, esp. in layout of figures and tables
  • Choose a clear formatting of chapter, section and subsection headings (again, be consistent).
  • deliver the thesis as PDF (any closed document format such as MS Word will not be acceptable).


  • Should be given in an (electronic) appendix
  • Should also be described in the "Methods" sections of your thesis
  • All code should
    • be split into modules
    • contain comments
    • only have easy to understand variable names
  • other students should be able to modify the code without problem


Discuss with your supervisor(s) what should be done with data produced during the project. In general, it should be either archived (i.e., put in an archive file and/or on CD/DVD and submitted as an appendix to your thesis) or cleaned up. This can be a requirement for obtaining your grade.

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