BIOS-IN5010 ¨C 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 to the course

Admission to BIOS-IN5010 is a twostep process.

1. Students admitted to a master¡¯s program at UiO must?register for the exam for this course?and register as a student at UiO in Studentweb and pay the semester fee before the deadline February 1st.

Nordic citizens and applicants residing in the Nordic countries may?apply to take this course as a single course student before the deadline December 15^th

and register for the exam for this course?and register as a student at UiO in Studentweb and pay the semester fee before the deadline February 1^st.

2. All applicants also have to apply for admission at Simula:?www.simula.no/sscp/application?before the deadline February 14^th.

As part of your application, you will be asked to upload the following documents:

• A current r¨¦sum¨¦ or CV

• A cover letter

• A letter of support from a mentor or advisor

• Your university transcripts

Students will be notified once the admission process is completed in early March.

20 students can be admitted to BIOS-IN5010 and BIOS-IN9010. The program is designed for early PhD and late MSc students.

The courses BIOS-IN5010 and BIOS-IN9010 have joint admission. Applicants are ranked by the following criteria:

1) Academic performance

2) Relevance of study plan/research to the course subject matter

3) Recommendation from advisor (specifying how the course work will be helpful to the research)

4) Cover letter of student (specific reasons why this course will be relevant and interesting to them)

PhD students are generally given preference over MSc students. However, the highest priority is accorded to applicants from the three partner institutions (UiO, Simula, UC San Diego), followed by those from Norwegian institutions seeking academic credits.

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.

Recommended previous knowledge

Fundamental knowledge of ordinary differential equations and their numerical solution, corresponding to IN1900 ¨C Introduction to Programming with Scientific Applications and MAT-INF1100 ¨C 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 ¨C 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 ¨C Computational physiology.
• 10 credits overlap with INF5560 ¨C 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 ¨C Computational Physiology (continued), INF9560, BIOS-IN9010 ¨C 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.