FAQs

Master's Thesis and Program: Frequently Asked Questions

Can I start my thesis project over the summer and continue it into the third semester?

Yes, it is possible to start your Master's thesis project over the summer and continue it into the third semester. The Master's thesis typically has a duration of six months, assuming full-time (100%) dedication. If you plan to work on the project part-time, you need to apply to the course administration before starting the thesis to agree on an extended timeframe. You can begin your Master's thesis once you have been assigned a project and established contact with your supervisor. The start and end dates are recorded on a "Master thesis start form."

When is the thesis submission deadline to graduate in the Fall semester 2025?

To graduate in the Fall semester, you need to submit the corrected and graded thesis, along with the supervisor's confidential evaluation, to the Dean's Office by Friday of week 7 in the year following the Fall semester. For the Fall semester 2025, which officially runs from August 1, 2025, to January 31, 2026, this means the deadline would be Friday of calendar week 7 of 2026. The exact date for Friday of calendar week 7 in 2026 is not provided in the sources.

Does week 1 of the semester calendar count from the official start date of the Fall term?

No, week 1 of the semester calendar for lectures does not count from the official start date of the Fall term. The academic year starts on August 1st, and the Fall semester officially runs from August 1st to January 31st. However, lecture times for all degree programs (except Medicine and Dental Medicine) for the Fall semester typically begin in calendar week 38.

What is the exact submission deadline for both the student and supervisor if I want to graduate in Spring 2025?

To graduate in the Spring semester 2025, the corrected and graded thesis must be submitted by the Master's candidate to the Dean's Office as a PDF by email by Friday of week 37 of the same year (2025). Concurrently, the supervisor must send their confidential evaluation, using the prescribed form, as a PDF to the Dean's Office, with a copy to the course administration. The supervisor is entitled to a maximum of four weeks for correction and grading after you submit the thesis to them. The exact date for Friday of calendar week 37 in 2025 is not provided in the sources.

Do I need to submit a presentation in addition to the thesis PDF?

For the Master's thesis itself, the sources do not explicitly state a requirement for a presentation in addition to the written thesis PDF. However, if you are referring to the Research Project (a separate component of the Master's program, worth 7.5 ECTS), then yes, a presentation is required. The research project is completed with an approximately 20-minute presentation by the student within the supervisor's research group and a report of 10 to 15 pages. The final grade for the research project is comprised of the practical work, the presentation, and the report, each weighted equally (one-third each).

Who serves on the thesis examination board?

A Master's thesis is written under the supervision of one or more empowered persons, who are typically lecturers of the Faculty. These individuals also evaluate the thesis with a grade. The study committee has the authority to designate additional persons from the Faculty or other faculties to conduct assessments and supervise Master's theses. Furthermore, individuals not falling into these categories may be granted permission to supervise theses, provided an empowered person retains overall responsibility. If there are multiple supervisors, they must agree on a single grade for the thesis. After submission, there is an approximate 10-14 day "referendum period" during which the thesis is available for examination by all faculty members.

If I submit my thesis by the end of August, do I still need to register for the Fall semester?

Yes, if you submit your thesis by the end of August, you would still need to be registered for that Fall semester. The Fall semester officially begins on August 1st. The regulations state that you must be registered for the semester in which you submit your thesis and for the semester of your graduation. The provision about not needing to re-register for the following semester applies if the definitive thesis and its evaluation are submitted before specific calendar weeks (e.g., week 38 for Fall semester commencement).

Is re-registration required if the thesis evaluation is submitted before week 38 at UniBE?

No, if the definitive Master's thesis, including its evaluation, is submitted to the Dean's Office's study secretariat before calendar week 38, then re-registration for the following semester is not necessary. Calendar week 38 typically marks the start of lectures for the Fall semester.

How many ECTS is the research project worth now that the Deep Learning module has been added?

The Master's thesis has a scope of 30 ECTS points. The Research Project, which is a separate component and part of the "Elective Courses" module, is worth 7.5 ECTS credits. The addition of the "Deep Learning" module (5 ECTS) to the mandatory "Computer Science" module does not change the ECTS value of the Master's thesis or the Research Project.

Can you clarify how to fulfill the elective credit requirements in the Bioinformatics Master’s program?

The study program includes "Elective Courses" as one of its components. Students need to choose elective courses worth at least 1.5 ECTS in total. These courses are primarily to be chosen from a pre-defined list. If a student wishes to take other courses not on this list, the choice requires the approval of the Study Director (Studienleitung). The aim of elective courses is to round off the educational level of the student.

Is there a list of eligible courses that fulfill the missing 1.5 ECTS in the Informatics module?

The concept of "missing 1.5 ECTS in the Informatics module" does not directly align with the program's structure as described in the sources.

  • The "Informatics module" you might be referring to is either "Module A: Programming/Informatics" (6 ECTS) or the broader "Module Computer Science" (28.5 ECTS), both of which are mandatory for specific student groups or all students, respectively. These modules consist of several fixed courses that must be completed.

  • The 1.5 ECTS requirement applies to the separate "Elective Courses" module, where students must choose at least 1.5 ECTS from a list of various elective courses. This list is provided in the annexes of the study plan and includes courses with varying ECTS values, such as:

    • Research Project (7.5 ECTS)

    • Pattern Recognition (5 ECTS)

    • Programmierung I (5 ECTS)

    • Beyond genetic inheritance (3 ECTS)

    • Structure and Functions of Host-associated Microbiota (3 ECTS)

    • Molecular Genetics of Model Organism development (3 ECTS)

    • Seminar and journal club in Population genetics and Bioinformatics (2 ECTS)

    • Theoretical Ecology and Evolution (2 ECTS)

    • Protein Bioinformatics BioPython (1.5 ECTS)

    • Introduction to Docking of Small Molecules to Large Macromolecules and Molecular Graphics (1.5 ECTS)

    • Introduction to Protein Structure and Protein Homology Modelling (1.5 ECTS)

Are there elective courses available that fit into an already full study schedule without exceeding 1.5 ECTS?

Yes, the list of elective courses includes several options that are exactly 1.5 ECTS, such as "Protein Bioinformatics BioPython," "Introduction to Docking of Small Molecules to Large Macromolecules and Molecular Graphics," and "Introduction to Protein Structure and Protein Homology Modelling." The "Elective Courses" module explicitly states that students need to choose courses worth at least 1.5 ECTS in total. This means you could take one of these 1.5 ECTS courses to fulfill the minimum requirement.

Can biology-background students follow biology program electives as part of the Bioinformatics electives?

The study plan states that elective courses are primarily taken from the listed courses within the Bioinformatics and Computational Biology program. However, it also specifies that "The choice of other courses requires the approval of the Studienleitung." Given the interdisciplinary nature of the program, which integrates students from both biological and quantitative backgrounds, and the fact that the program is jointly offered with the University of Fribourg, it is plausible that biology-related electives from other biology programs could be approved if they align with the student's educational goals and the program's objectives. However, explicit approval from the Study Director is mandatory for any course not on the primary list.

Is the course “Structure and Functions of Host-Associated Microbiota” (SBL.20035) eligible for Bioinformatics students with a biology background?

Yes, the course "Structure and Functions of Host-associated Microbiota" with 3 ECTS is listed as an elective course in the annexes of the study plan for the Master's in Bioinformatics and Computational Biology program. Therefore, it is eligible for all students in the program, including those with a biology background.

Will the course SBL.20035 be offered in Spring 2026 or only in 2027?

The provided class schedules include information for Fall semester 2024, Fall semester 2024 (3rd semester), and Spring semester 2025 (2nd semester). However, there are no provided schedules for Spring 2026 or 2027. Therefore, based on the given sources, it is not possible to determine if the course SBL.20035 will be offered in Spring 2026 or 2027.

As a supervisor from DIN/DBMR, how can I formally supervise a Master's or project thesis?

The supervision of Master's theses in Bioinformatics and Computational Biology is governed by the study regulations of the Faculty of Science (Phil.-nat. Faculty) at the University of Bern.

  • General Eligibility for Supervision: Persons authorized to supervise Master's theses are lecturers of the Faculty of Science, according to Article 49 letters a to e UniV.

  • Additional Persons from Other Faculties (like DBMR): The study committee of the Faculty of Science may designate additional persons from the Faculty and other faculties to supervise Master's theses (referred to as "admitted persons"). Since the Master's program in Bioinformatics and Computational Biology is offered jointly with the University of Fribourg, and the Medical Faculty (to which DBMR belongs) as well as the Vetsuisse Faculty at the University of Bern are involved in the study program and offer courses, it is common for lecturers from these faculties to be able to serve as supervisors.

  • Persons Outside Regular Categories: Furthermore, persons who do not belong to the categories mentioned in paragraphs 1 and 2 may also be granted permission to supervise Master's theses, provided that an authorized person from the Faculty of Science (according to paragraph 1) assumes the overall responsibility.

  • Supervision in the Bioinformatics Master's Program: Master's theses are supervised by the lecturers of this Master's program, and adequate supervision must be ensured from both the biology and the computer science/mathematics/computer science side. A list of possible supervisors, according to Article 21 RSL Phil.-nat. 18, is maintained by the study administration.

  • Research Project Supervision: For research projects, supervisors must be affiliated with the University of Bern or Fribourg and possess appropriate bioinformatics expertise. Students may also propose other supervisors and projects by submitting a request to the study coordination, and the suitability of such projects will be assessed by the Director of Studies.

In summary: As a supervisor from DIN/DBMR, you could either be directly approved by the study committee as an authorized supervisor for Master's theses, or you would need to ensure that a lecturer from the Faculty of Science holds overall responsibility if you do not fall into the first category. For research projects, affiliation with the University of Bern/Fribourg and bioinformatics expertise are key.

What steps and deadlines must I follow as a potential supervisor?

The steps and deadlines for potential supervisors of a Master's thesis are as follows:

  • Master Thesis Start Form: Once a project has been assigned and contact has been made with the student, the "Master thesis start form" must be filled out and signed by the supervisor. A copy of this form must be sent to the Master's program in Bioinformatics study administration (stefan.daniel@unibe.ch) within three weeks after the start of the Master's thesis.

  • Duration and Timeframe: The Master's thesis typically lasts six months for 100% full-time dedication. If the student cannot dedicate 100% of their time to the project (e.g., part-time), an application for an extension must be submitted to the course administration (stefan.daniel@unibe.ch) and a later submission date agreed upon before the start of the thesis. Extensions for valid reasons (e.g., illness) can be approved by the supervisor in consultation with the competent directorate of studies.

  • Prerequisites for the Thesis: If you as a supervisor require specific achievements or courses to be completed before the start of the Master's thesis in your group, you can define these. These prerequisites will be listed in the appendix to the study plan.

  • Correction and Grading Period: As the supervisor, you have a maximum of four weeks for correction and grading after the student submits the thesis to you.

  • Submission of Grade and Evaluation:

    • For graduation in the Fall semester: You must communicate the grade and title of the Master's thesis to the Master Course Office by Tuesday of calendar week 7 of the following year at the latest. The corrected and graded thesis, along with your confidential evaluation (in the prescribed format), must be sent as a PDF via email to the Dean's Office (info.natdek@unibe.ch) by Friday of calendar week 7 of the following year, with a copy to the study administration (Stefan Daniel).

    • For graduation in the Spring semester: The corrected and graded thesis must be submitted by the Master's candidate to the Dean's Office (info.natdek@unibe.ch) as a PDF via email by Friday of calendar week 37 of the same year at the latest. Concurrently, you must send your confidential evaluation in the prescribed format as a PDF to the Dean's Office and copy the study administration.

  • Research Project Specifics: The research project must be completed by January 31st at the latest, and the grade must be entered into the Core System Teaching (CST) four weeks after this date. The final grade of the project is composed of the practical work, the presentation, and the report, with each part weighted one-third. After the completion of the research project, the evaluation form must be sent to the study administration of the Interfaculty Bioinformatics Unit.

Is there a platform like ILIAS for posting Master's thesis offers for Bioinformatics, similar to Biomedical Engineering?

The provided sources primarily mention ILIAS in the context of class schedules and registration for courses and exams. A specific platform like ILIAS for posting Master's thesis offers in Bioinformatics is not explicitly named.

  • However, the Interfaculty Bioinformatics Unit (IBU) does publish information about "New projects - new MSc students" in its "News" section. This could be a place to announce opportunities.

  • The study plan states that a list of possible Master's thesis supervisors, according to Article 21 RSL Phil.-nat. 18, is maintained by the study administration. This suggests an internal management of supervision offers rather than a public posting platform.

Could work outside of the university program potentially be credited toward my Master’s degree? For example, during an internship, one has been working on intrinsically disordered proteins, using in-house Python scripts, AlphaFold, Rosetta, and related tools. Can this experience be recognized, for example, as part of the machine learning coursework?

It is not possible to have this work credited toward regular courses in the master's program. The only option is to have this work recognized as a research practical. However, this is only possible if you:

  1. Remain enrolled.

  2. Fulfill the requirements for the research practical (submit a project description in advance, work on the project full-time for at least 21 days, give a presentation, and write a report).

If I pause my studies for one semester, would it be possible to resume afterwards by taking a reduced course load, for example, a few courses per semester, until I complete the degree requirements?

You can take a semester off and then continue your studies with a reduced workload. However, you must remain within the standard period of study. The standard period of study can only be extended in justified cases (e.g., part-time work).