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Modelling of Biological Systems

Title
Modelling of Biological Systems
Semester
E2022
Master programme in
Mathematical Bioscience
Type of activity

Course

Teaching language
English
Study regulation

Read about the Master Programme and find the Study Regulations at ruc.dk

Læs mere om uddannelsen og find din studieordning på ruc.dk

REGISTRATION AND STUDY ADMINISTRATIVE
Registration

Sign up for study activities at stads selvbetjening within the announced registration period, as you can see on the Studyadministration homepage.

When signing up for study activities, please be aware of potential conflicts between study activities or exam dates.

The planning of activities at Roskilde University is based on the recommended study programs which do not overlap. However, if you choose optional courses and/or study plans that goes beyond the recommended study programs, an overlap of lectures or exam dates may occur depending on which courses you choose.

Number of participants
ECTS
10
Responsible for the activity
Johnny T. Ottesen (johnny@ruc.dk)
Morten Andersen (moan@ruc.dk)
Louise Torp Dalgaard (ltd@ruc.dk)
Head of study
Jesper Schmidt Hansen (jschmidt@ruc.dk)
Teachers
Study administration
INM Studieadministration (inm-studieadministration@ruc.dk)
Exam code(s)
U60161
ACADEMIC CONTENT
Overall objective

The overall objective of the course is to give the student a fundamental understanding of and experience with modelling biological systems using mathematics and what is achieved by this.

Detailed description of content

During the course, the student will explore examples of mechanism-based mathematical models of biological systems. This can include population dynamics, epidemics, disease spreading in the human body, and resource competition.

The exploration includes mathematical and numerical analysis, validation through biological data, and the models' limitations and possible extensions are discussed.

The course seeks to give the student an integrated understanding of the modelling process. This can, for example, be supported by guest lectures with different scientific backgrounds and research focus areas.

Course material and Reading list

The course syllabus is composed of teacher's notes, selected book chapters, possible relevant scientific papers, etc.

During the course computer code will also be available; this code is not necessarily complete and the students must be able to extent and modify the code for specific purposes.

The material will be made available to the students before and during the semester, depending on the nature of the material.

Overall plan and expected work effort

The teaching format is based on a scientific dialogue between the students and the course teacher, working with exercises, student presentations, etc. The teacher will, of course, highlight relevant points.

For the dialogue to be fruitful, the student must prepare for each class; this includes careful reading the text material, finish exercises, and other home work suggested by the teacher. As a rule of thumb, the student should use 1-2 hours of preparation for every hour in class.

- Total (minimum): 280 hours

  • In class: 80-90 hours

  • Preparation for class: 160-180 hours

  • Preparation for exam: 35-50 hours

  • Exam: 4 hours

Format
Evaluation and feedback

The course includes formative evaluation based on dialogue between the students and the teacher(s).

Students are expected to provide constructive critique, feedback and viewpoints during the course if it is needed for the course to have better quality. Every other year at the end of the course, there will also be an evaluation through a questionnaire in SurveyXact. The Study Board will handle all evaluations along with any comments from the course responsible teacher.

Furthermore, students can, in accordance with RUCs ‘feel free to state your views’ strategy through their representatives at the study board, send evaluations, comments or insights form the course to the study board during or after the course.

Programme

Depending on the specific topic, the teacher, and the student group, the students will engage in a dialogue with the teacher and from this do exercises in groups or individually.

The exercises will be based on pure mathematical analysis, computer-aided analysis, discussion in groups, with teacher, and so forth.

ASSESSMENT
Overall learning outcomes

After the course the student will be able to

  • discuss and apply classic mechanism-based mathematical models of selected areas within biology, for example, populations, epidemics, disease spreading in the human body, and competition.

  • apply the modelling cycle in order to develop mathematical models of biological systems from experimental data.

  • reflect on and argue how modelling is used to gain fundamental new biological insight through model analysis.

  • reflect on and argue how the models can be used to predict and control biological systems and processes.

  • critically and analytically explore the limitations and validity of different models.

  • perform numerical explorations of the mathematical models using relevant programme language(s) like e.g. Python

Form of examination
Individual written invigilated exam.

The duration of the exam is 4 hours.

Permitted support and preparation materials for the exam: All.


Assessment: 7-point grading scale.
Moderation: External examiner.
Form of Re-examination
Individual oral exam with time for preparation.

Time for preparation including time to pick a question by drawing lots: 45 minutes.
Time allowed for exam including time used for assessment: 45 minutes.

Permitted support and preparation materials: Course material and own notes.

Assessment: 7-point grading scale.
Moderation: External examiner.
Type of examination in special cases
Examination and assessment criteria

Individual written invigilated exam; duration of the exam is 4 hours.

The evaluation is based on the student's skill to apply and analyze mechanistic models for biological data. This skill is founded in knowledge and understanding of previous models, their limitations and extensions through the modelling cycle.

In the model analyses it is evaluated whether the student can derive novel biological insight from the model output, which can be on the form of mathematical expressions, graphs, numerical data, and so forth.

Exam code(s)
Exam code(s) : U60161
Last changed 16/05/2022

lecture list:

Show lessons for Subclass: 1 Find calendar (1) PDF for print (1)

Monday 05-09-2022 14:15 - 05-09-2022 16:00 in week 36
Modelling of Biological Systems (MATHBIO)

Friday 09-09-2022 08:15 - 09-09-2022 12:00 in week 36
Modelling of Biological Systems (MATHBIO)

Monday 12-09-2022 14:15 - 12-09-2022 16:00 in week 37
Modelling of Biological Systems (MATHBIO)

Friday 16-09-2022 08:15 - 16-09-2022 12:00 in week 37
Modelling of Biological Systems (MATHBIO)

Monday 19-09-2022 14:15 - 19-09-2022 16:00 in week 38
Modelling of Biological Systems (MATHBIO)

Friday 23-09-2022 08:15 - 23-09-2022 12:00 in week 38
Modelling of Biological Systems (MATHBIO)

Monday 26-09-2022 14:15 - 26-09-2022 16:00 in week 39
Modelling of Biological Systems (MATHBIO)

Friday 30-09-2022 08:15 - 30-09-2022 12:00 in week 39
Modelling of Biological Systems (MATHBIO)

Monday 03-10-2022 14:15 - 03-10-2022 16:00 in week 40
Modelling of Biological Systems (MATHBIO)

Friday 07-10-2022 08:15 - 07-10-2022 12:00 in week 40
Modelling of Biological Systems (MATHBIO)

Monday 10-10-2022 14:15 - 10-10-2022 16:00 in week 41
Modelling of Biological Systems (MATHBIO)

Friday 14-10-2022 08:15 - 14-10-2022 12:00 in week 41
Modelling of Biological Systems (MATHBIO)

Monday 17-10-2022 14:15 - 17-10-2022 16:00 in week 42
Modelling of Biological Systems (MATHBIO)

Friday 21-10-2022 08:15 - 21-10-2022 12:00 in week 42
Modelling of Biological Systems (MATHBIO)

Monday 24-10-2022 14:15 - 24-10-2022 16:00 in week 43
Modelling of Biological Systems (MATHBIO)

Friday 28-10-2022 08:15 - 28-10-2022 12:00 in week 43
Modelling of Biological Systems (MATHBIO)

Monday 31-10-2022 14:15 - 31-10-2022 16:00 in week 44
Modelling of Biological Systems (MATHBIO)

Friday 04-11-2022 08:15 - 04-11-2022 12:00 in week 44
Modelling of Biological Systems (MATHBIO)

Monday 07-11-2022 14:15 - 07-11-2022 16:00 in week 45
Modelling of Biological Systems (MATHBIO)

Friday 11-11-2022 08:15 - 11-11-2022 12:00 in week 45
Modelling of Biological Systems (MATHBIO)

Monday 14-11-2022 14:15 - 14-11-2022 16:00 in week 46
Modelling of Biological Systems (MATHBIO)

Friday 18-11-2022 08:15 - 18-11-2022 12:00 in week 46
Modelling of Biological Systems (MATHBIO)

Monday 21-11-2022 14:15 - 21-11-2022 16:00 in week 47
Modelling of Biological Systems (MATHBIO)

Friday 25-11-2022 08:15 - 25-11-2022 12:00 in week 47
Modelling of Biological Systems (MATHBIO)

Monday 28-11-2022 14:15 - 28-11-2022 16:00 in week 48
Modelling of Biological Systems (MATHBIO)

Friday 02-12-2022 08:15 - 02-12-2022 12:00 in week 48
Modelling of Biological Systems (MATHBIO)

Monday 05-12-2022 14:15 - 05-12-2022 16:00 in week 49
Modelling of Biological Systems (MATHBIO)

Friday 09-12-2022 08:15 - 09-12-2022 12:00 in week 49
Modelling of Biological Systems (MATHBIO)

Monday 12-12-2022 14:15 - 12-12-2022 16:00 in week 50
Modelling of Biological Systems (MATHBIO)

Friday 16-12-2022 08:15 - 16-12-2022 12:00 in week 50
Modelling of Biological Systems (MATHBIO)

Monday 19-12-2022 14:15 - 19-12-2022 16:00 in week 51
Modelling of Biological Systems (MATHBIO)

Tuesday 03-01-2023 10:00 - 03-01-2023 14:00 in week 01
Modelling of Biological Systems - Exam (MATHBIO)

Wednesday 22-02-2023 08:15 - 22-02-2023 16:00 in week 08
Modelling of Biological Systems - Reexam (MATHBIO)