BIOS-IN9010 – Computational physiology

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

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.

Course participation is limited

20 students can be admitted to BIOS-INF5010 and BIOS-IN9010. The program is designed for early PhD and late MSc students.
Acceptance will be prioritized as follows:

1) PhD candidates 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

Prerequisites

Recommended previous knowledge

Fundamental knowledge of ordinary differential equations and their numerical solution, corresponding to IN1900 – Introduction to Programming with Scientific Applications MAT-INF1100 – Modelling and computations 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

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. PhD students will be examined during the final presentations in San Diego and required to submit a final report detailing this work shortly after the summer school has finished. Travel support is provided by SSRI. For further details and to apply for travel funding.

Examination

- Written project report.

- 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.

Language of examination

The examination text is given in English, and you submit your response in English.

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.

Re-scheduled examinations are not offered to students who withdraw during, or did not pass the original examination.

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: INF9560

Special examination arrangements

Application form, deadline and requirements for special examination arrangements.

Facts about this course

Credits

10

Level

PhD

Teaching

Every summer

Examination

Every autumn

Teaching language

English