Master thesis Project Information

Degree Project (Självständigt arbete) at the Department of

Biochemistry and Biophysics (DBB),

15 hp and 30 hp First cycle (grundnivå). 30 hp, 45 hp, and 60 hp, Second cycle (avancerad nivå)

The Degree project can be done at the Department in one of the research groups, with one of the teachers/scientists as supervisor, or as an external project. The choice of research group is made by the student, prior to the beginning of the project. The best way to do this is to contact the scientists at the Department and discuss possible projects. If the project is performed “outside” DBB, an external supervisor, as well as an internal, must be appointed.


Before the student can be registered in LADOK, the supervisor should submit a project plan (a specific form should be used) to the person in charge of the Degree Project = the examiner (see the end of this document). When the project plan is approved, the person in charge of the Degree Project will inform the supervisor and also see to that the student is registered. The student cannot begin the study until being registered.


To pass the course the student has to present the studies at a seminar and in a written report. Students should also attend and take active part in all degree project seminars, in Biochemistry, Biophysics and Bioinformatics respectively, during the project period. In addition the student has to submit a Reflection document to the Department examiner.

Evaluation form

The evaluation (on a form that will be provided by the Department examiner to the supervisor) should be done by the supervisor, taking the seminar, the written report and the student´s performance in the lab into consideration. The final grade will be decided by the departmental examiner, based on the evaluation, the written report and the oral presentation.


The presentation should be 20 min followed by a 5 min discussion. Great effort should be put into the preparation of the presentation, with respect to both science and form of presentation, i.e. PowerPoint. The presentation should include an introduction to the research area to make it possible for the other participants in the seminar to understand. All students are expected to take active part in the discussions following other presentations, but one student will be appointed for each of the students presenting, to specifically ask questions.

Two weeks before the seminar, at the latest, the title and a half-page abstract should be given to the secretariat (presently to Lotta <>) by those expected to present at the seminar. These students will also get a request for an abstract from Lotta. The abstract will be distributed to those attending the seminar. Those students registered but not presenting will get the abstracts and a reminder to be present

at the seminar.

The seminar should be given in English!!

The seminars are usually held at the end of the second to last week of every 9 week period. Supervisor(s) are expected to be present at the seminar.

Written report

A paper copy (as well as a pdf file) of the written report should be submitted to the Department examiner before the seminar or within 7 days after the seminar, alternatively on the last day of the period, which ever is the later. Before giving the report to the departmental examiner, the report must be approved by the supervisor, with respect both to the science presented and the general layout, language etc. The supervisor should fill out the evaluation form and email it to the departmental examiner.

The format of the report should be as a scientific paper in an international journal and be written according to the following specifications:

• The first page should have the title, the name of the student, the supervisor(s) and Department of Biochemistry and Biophysics, Stockholm University (and for external projects, the name of the institution where the work was done), the year when the seminar was given and the number of credits (hp). You will get a file from the Department examiner that should be used as a template for the first page, do notchange or add anything!

·      It should be written in a font 12 with 1.5 line spacing and with 2 cm margins.

·      The length of the report including figures, tables and references, should be 20-25 A4 pages for 15 hp, 25-30 for 30 hp, 30-35 for 45 hp and 35-40 for 60 hp.

·      The report should be organized in Abstract, Introduction, Materials & Methods, Results, Discussion, References. Results and Discussion may be combined when appropriate.

·      Tables and figures should be included in the text.

·      When needed a more detailed description of the method(s) used, including a

·      background, can be given as an Appendix, not included in the page limits given above.

·      References should be ordered alphabetically in the list, and referred to in the text in ()/[] by numbers or author + year. References should be written in a style that includes the title of the paper referred to. The following is an example (For those of you that use EndNote it is the “J. Bacteriology.” style):

1.    Anagnostopoulos, C., and J. Spizizen. 1961. Requirements for transformation in Bacillus subtilis. J. Bacteriol. 81:741–746.

2.    Berry, L. J., R. N. Moore, K. J. Goodrum, and R. E. Couch, Jr. 1977. Cellular requirements for enzyme inhibition by endotoxin in mice, p.321–325. In D. Schlessinger (ed.), Microbiology—1977. American Society for Microbiology, Washington, D.C.

References should be to publications in international peer-reviewed journals, Wikipedia is not allowed!

The report should not be written as a tale about the purification of an enzyme, cloning of a gene, writing an algorithm etc. You will get a good idea of the format from any scientific paper or if you look in Instructions for Authors, which most journals publish on their home page.

The report should be written by you. If you want to quote a sentence or so, you must put that sentence within quotation marks and give the reference. The use of quotes should however be a minimum. If you copy figures from publications, this should be clearly stated in the figure captions. Using text or figures from any publication without giving the reference is plagiarism, which obviously is not allowed, and can lead to that you are expelled from the university for some time period. The report will be run through specific programs to identify any text from published documents.

Reflection document

This document should be 2 A4 pages in total, written in a font 12 with 1.5 line spacing and with 2 cm margins. The following subsections should be included:

·      What did I learn

·      What did I expect to learn

·      In retrospect, what would/should I have done differently, other methods etc

·      Suggest a next step in the project

·      In what way would the results of your project be beneficial to society, any possible application(s)

·      A 0.5 page popular science description of your project, written in Swedish (for those mastering Swedish) or English.

Grading of the Degree Project will only be done if this document also has been submitted.

Scientific Method

This course is an obligatory part of all Degree Projects at the Basic Level (1st Cycle) and it is up to the student to apply. More information can be found at two web pages;


1.216885) and

Department examiners


1st Cycle (Basic level)

Prof Pia Ädelroth (, phone 08 – 16 4183

2nd Cycle (Advanced level)

Prof Stefan Nordlund (, phone 08 – 16 2932


1st and 2nd Cycle (Basic and Advance levels)

Prof Arne Elofsson (, phone 08 – 524 81531


1st and 2nd Cycle (Basic and Advance levels)

Dr Jakob Dogan (, phone 073 705 7571


The final grades are decided by the department examiner. If the grade is not a pass, the student will have to wait at least 30 days before a new presentation and written report is delivered. A set of diploma work reports can be found at

For grading here are a few examples of 30 ECTS theses that would most likely have got the following grades:

  • Grade E: Magnus Nilsson
    • This thesis was a standard well performed work that included some development of novel methods.
  • Grade D: Jia Mi
    • Within this thesis the development of a novel method was done. Unfortunately the project (by the supervisor) was perhaps not feasible and the performance of the developed predictor was not better than the state of the art methods.
  • Grade C: Kristoffer Hallen
    • A well performed development of a novel machine learning method for a difficult problem.
  • Grade B: Björn Wallner
    • This work resulted in the ProQ model quality assessment program. Based on these results a well cited scientific paper was written.
  • Grade A: Håkan Viklund
    • In addition to the scientific results that resulted in a well cited scientific paper this thesis included a large amount of software development and was very well written.
Degree_project_instructions_150901Project_plan_Degree_Project These instructions are in effect from 150901


First page for the report can be found here.