Graduate School of health and Medical Sciences

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Benchmarking of Bioinformatics Tools
Provider: Faculty of Health and Medical Sciences

Activity no.: 3352-25-00-00	There are 12 available seats
	Enrollment deadline: 20/10/2025

Date and time	17.11.2025, at: 10:00 - 12.12.2025, at: 16:00
Regular seats	14
Course fee	3,720.00 kr.
Lecturers	Lars Rønn Olsen
ECTS credits	6.10

Contact person	Lars Rønn Olsen E-mail address: lronn@sund.ku.dk

Enrolment Handling/Course Organiser	PhD administration SUND E-mail address: phdkursus@sund.ku.dk

Enrolment guidelines This is a generic course. This means that the course is reserved for PhD students at the Graduate School of Health and Medical Sciences at UCPH. Anyone can apply for the course, but if you are not a PhD student at the Graduate School, you will be placed on the waiting list until enrollment deadline. After the enrollment deadline, available seats will be allocated to the waiting list. The course is free of charge for PhD students at Danish universities (except Copenhagen Business School), and for PhD students at NorDoc member faculties. All other participants must pay the course fee. Learning objectives A student who has met the objectives of the course will be able to: 1. Explain the principles, challenges, and best practices of benchmarking in bioinformatics. 2. Apply the OmniBenchmark framework to design and execute reproducible benchmarking studies. 3. Critically assess performance metrics and interpret benchmarking outcomes in relation to biological and computational relevance. 4. Conduct a small-scale benchmarking study relevant to their own research or to a provided case study. 5. Communicate benchmarking results effectively through scientific presentations and in the form of a draft manuscript. Content The course in Benchmarking of Bioinformatics Tools introduces participants to the principles and practices of benchmarking in computational biology. Students will be introduced to the conceptual foundations of benchmarking, including motivations, methodological considerations, evaluation metrics, reproducibility, and reporting standards. These elements will provide the theoretical grounding needed to design and critically assess benchmarking studies in bioinformatics. The students will learn to use OmniBenchmark, a flexible framework for carrying out reproducible benchmarking projects. Students will gain hands-on experience setting up and running OmniBenchmark workflows, exploring how to define relevant tasks, select datasets, and evaluate tool performance in a structured and transparent way. Following the introductory module, students will spend three weeks working asynchronously individually or in groups to design and execute a benchmarking study. Students are encouraged to pursue a benchmark relevant to their own research, though suggested case studies will also be available. The group work will be supported by both instructor and peer feedback, ensuring that students engage with one another’s ideas and learn to evaluate benchmarking approaches critically. The course concludes with group presentations and discussions. Each group will present their benchmarking study, receive feedback from both peers and instructors, and submit a draft manuscript based on their work. The manuscript may serve as the foundation for a future publication, providing students with both practical experience and a tangible research output from the course. Participants Seats: 14 The course is aimed at PhD students in bioinformatics, computational biology, biostatistics, and related disciplines. Participants should have: • Basic experience with bioinformatics data analysis (R/Python or similar). • Interest in tool evaluation, reproducibility, and methodological rigor. No prior experience with OmniBenchmark is required. Relevance to graduate programmes The course is relevant to PhD students from the following graduate programmes at the Graduate School of Health and Medical Sciences, UCPH: Biostatistics and Bioinformatics Select graduate programme Select graduate programme Language English Form The course combines lectures, discussions, and hands-on exercises with independent group work. The first two days consist of lectures and practical sessions, where students are introduced to the theoretical foundations of benchmarking and guided through the use of the OmniBenchmark framework. During the following three weeks, students will work asynchronously in groups to conduct their own benchmarking studies, supported by structured peer feedback. The course concludes with a final day dedicated to group presentations and discussions, where students present their results, receive instructor and peer feedback, and hand in a draft manuscript based on their work. Course director Lars Rønn Olsen, Professor, Department of Immunology and Microbiology, University of Copenhagen, Denmark, lronn@sund.ku.dk Teachers Frederik Otzen Bagger, Head of Bioinformatics, Center for Genomic Medicine, Rigshospitalet, frederik.otzen.bagger@regionh.dk Mark Robinson, Professor, Department of Molecular Life Sciences, University of Zürich, Switzerland, mark.robinson@mls.uzh.ch Izaskun Mallona Gonzales, Research Associate, Department of Molecular Life Sciences, University of Zürich, Switzerland, izaskun.mallona@mls.uzh.ch Dates Lectures: 17-18 November 2025, 10.00 – 16.00 Group work: (Asynchronous) 19 November - 10 December 2025 Presentation: 12 December 2025, 10.00 – 15.00 Course location Department of Immunology and Microbiology Blegdamsvej 3B 2200 Copenhagen Registration Please register before 20 October 2025 Expected frequency Annually Seats to PhD students from other Danish universities will be allocated on a first-come, first-served basis and according to the applicable rules. Applications from other participants will be considered after the last day of enrolment. Note: All applicants are asked to submit invoice details in case of no-show, late cancellation or obligation to pay the course fee (typically non-PhD students). If you are a PhD student, your participation in the course must be in agreement with your principal supervisor.

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