BIOS-IN5010 – Computational physiology
Course description
Course content
This course provides a thorough introduction to mathematical models of electrophysiologic and mechanical processes in the heart. Particular focus is on developing models extending from protein function through to continuum electroconduction and tissue mechanics. The course also introduces relevant numerical methods and software tools for solving ordinary and partial differential equations. The foundation principles of both the models and the numerical approaches are often used in other physiological disciplines, particularly neuroscience, muscle mechanics, and fluid dynamics. For this reason the course is usually relevant to students broadly engaged in multiscale modelling of physiology. The course includes a mandatory assignment in the form of a small research project, which is conducted in collaboration with the University of California, San Diego.
Learning outcome
Through this course you will:
- gain a fundamental understanding of cardiac physiology
- understand the derivation and common implementation strategies for describing chemical, physical and biological processes with mathematics
- be introduced to both the principles and practice of relevant numerical methods and computational tools for modeling cardiac physiology.
Admission to the course
Course participation is limited
20 students can be admitted to BIOS-IN5010 and BIOS-IN9010. The program is designed for early PhD and late MSc students. Acceptance will be prioritized as follows:
1) PhD students and master students with BIOS-IN5010 or BIOS-IN9010 on their approved study plan
2) Master students having passed at least 30 ECTS from master level with a grade average of B in these courses.
3) Master students having passed at least 30 ECTS from master level.
In each category, qualified applicants will be prioritized by credits and then by lottery.
Interested students are strongly encouraged to familiarize themselves with the course content and requirements, before preparing their application. This information can be found here: https://www.simula.no/education/courses/simula-summer-school-computational-physiology.
All applications should be submitted here: www.simula.no/sscp/application As part of your application, you will be asked to upload the following documents:
- A current résumé or CV
- A cover letter
- A letter of support from a mentor or advisor
- Your university transcripts
Recommended previous knowledge
Fundamental knowledge of ordinary differential equations and their numerical solution, corresponding to IN1900 – Introduction to Programming with Scientific Applications and MAT-INF1100 – Modelling and Computations (discontinued) or equivalent. It is also useful to have a basic knowledge of partial differential equations, corresponding to the introductory parts of MAT3360 – Introduction to Partial Differential Equations, or similar.
Formal coding experience is important and used heavily during the course. We offer an introductory Python workshop the Sunday evening before the course starts, and any student without substantial Python experience should expect to take that workshop.
Overlapping courses
- 10 credits overlap with BIOS-IN9010 – Computational physiology.
- 10 credits overlap with INF5560 – Computational Physiology (continued).
- 10 credits overlap with INF9560.
Teaching
The course is organized as a summer school, in collaboration with the Simula School of Research and Innovation (SSRI) and University of California, San Diego. The first two weeks will be held in Oslo in late June, and consists of approximately 50 hours of theoretical lectures, plus time for self-study and preparations. Students will work in small groups to complete a mandatory project assignment in July, and the course concludes with a week of project presentations and reviews in early August. The August component of the summer school is held at the University of California San Diego campus in La Jolla, California. Over this time the students will be required to do an extensive literature review, and to put the results of their investigation into an international research perspective. Master students will be examined during the presentations in San Diego.
Cost of taking the course
Travel support is provided by SSRI. For further details and to apply for travel funding see https://www.simula.no/sscp
Examination
- Oral presentation of project report
All mandatory assignments must be approved prior to the exam and must be completed and approved in the same semester.
It will also be counted as one of the three attempts to sit the exam for this course, if you sit the exam for one of the following courses:INF5560 – Computational Physiology (continued), INF9560, BIOS-IN9010 – Computational physiology.
Grading scale
Grades are awarded on a pass/fail scale. Read more about the grading system.
Resit an examination
Students who can document a valid reason for absence from the regular examination are offered a postponed examination at the beginning of the next semester. The postponed exam can be taken later when back in Norway. Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.
More about examinations at UiO
- Use of sources and citations
- Special exam arrangements due to individual needs
- Withdrawal from an exam
- Illness at exams / postponed exams
- Explanation of grades and appeals
- Resitting an exam
- Cheating/attempted cheating
You will find further guides and resources at the web page on examinations at UiO.