Master's project in bioinformatics

Prerequisites

To start the master's thesis in bioinformatics you need to have passed 45 ECTS of the master's program including 30 ECTS from the obligatory courses, Intro to Bioinformatics, Comparative Genomics, Molecular Modelling, Protein Physics and Protein Structure prediction of globular and membrane proteins. 

• For other students, 210 ECTS should have been taken, including at least 30 ECTS in relevant subjects.
• The master's project could be 30, 45 or 60 ECTS

Steps to be fulfilled

1. Before you start the thesis project you need to contact the examinator (program coordinator) and present a description of the project, to make sure it fulfills the requirements. It should include Introduction, Methods and Materials, a clear definition of inputs and expected outputs. It should contain a timeline with how you plan to divide the time between different activities, and clearly state what the goals are.
2. For 45 and 60 ECTS projects a "halftime report" should be submitted at the latest 2 month before the end of the project to the examiner. This report should include a background describing how this project relates to the state of the art in the field and also all preliminary results. It should be between two and five pages long and include references to earlier and related work.
3. Time for the oral presentations will be arranged twice each semester. For other occations it is necessary to prearrange a time with the departmental examiner. At the oral presentation the supervisor needs to be present. The presentation should be about 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, overheads etc. The presentation should include an introduction to the research area to make it possible for the other participants in the seminar to understand. The students are also expected to take active part in the discussions following other presentations.
4. The written report should be handed in before or as soon as possible after the seminar, but always within 60 days after the seminar. 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 an evaluation folowing the guidelines described below and email it to the departmental examiner.

Written report guidelines

The format of the report should be as a scientific paper in an international journal and must 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 period during which the project was performed. There should not be any logo!!

• The report should be written in font 12 with 1.5 line spacing and with 2 cm margins.
• The length of the report including figures, tables and references, must not exceed 20 pages for KB9004, 25 for KB9005 and 30 for KB9006.
• 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.
• References should be ordered alphabetically and numbered, and referred to in the text by numbers in [ ]. 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. 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.
  2. Anagnostopoulos, C., and J. Spizizen. 1961. Requirements for transformation in Bacillus subtilis. J. Bacteriol. 81:741–746.

The report should not be written as a tale about the purification of an enzyme, cloning of agene 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.

Information needed from supervisors

At the end of the project your supervisor should write a summary of how the work has proceeded, including an evaluation of (i) the progress of the project, (ii) the quality of the work performed by the student, (iii) the background of the student in relationship to the project, (iv) the ability of the student to work independently including the capacity to solve problems and come up with new ideas (v) the quality of the written report and finally a recomended grade (A-F).

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 http://bioinfo.se/xjobb/

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 assesment program. Based on these results a wll 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.