BMB519: Biosimulation (5 ECTS)

STADS: 01001901

Level
Bachelor course

Teaching period
The course is offered in the spring semester.
4th quarter.

Teacher responsible
Email: lfo@bmb.sdu.dk

Timetable
There is no timetable available for the chosen semester.

Comment:
AFLYST F2012.

Prerequisites:
None

Academic preconditions:
Students are admitted after completion of the first two years of education.
Students who has passed BK/BKP41 cannot participate in this course.

Course introduction
The course will give the students a thorough introduction to different methods in computer simulations of biological processes. In recent years biosimulation has developed to a level where it is possible to simulate and predict the course of even very complex biological processes. In some cases computer simulations have obviated – at least partly – the use of costly and complex experimental procedures. The course will give the student an introduction to the basic theory of biosimulation and the special methods, which are needed in the study of biological problems. The topics of the course will constitute the foundation for later work on biosimulation of biotechnological, physiological and cell biological processes.

Qualifications
The student will acquire basic insights into the various methods used for the formulation of mathematical models of biological processes and methods to simulate these on a computer, including
• To employ methods from systems dynamics and systems biology to formulate such models
• To construct causal loop diagrams and flow diagrams of biological processes
• To simulate enzyme catalyzed processes and membrane transport processes
• To set up differential equations of these processes and solve them using different numerical methods
• To know different tools for biosimulations
• Have knowledge about the possibilities of dynamical behaviour of complex biological processes.

Expected learning outcome
After the course has finished the student is expected to be able to

• Use systems dynamics to construct flow-diagrams of mathematical models of a biological system and translate the diagram into differential equations.
• Use simulation programs to perform numerical integration of non-linear first-order differential equations.
• Explain Systems Biology Markup Language (SMBL)
• Describe how to find fixed points and to do stability analysis and phase plane analysis of differential equations with two variables.
• Describe the following dynamical behaviours: steady-state, oscillations and chaos.

Subject overview
The following topics will be presented and discussed:
1. Systems dynamics – causal loop diagrams and flow diagrams.
2. Systems Biology Markup Language (SBML).
3. Introduction to various tools for biosimulation, e.g. Berkeley Madonna, COPASI etc.
4. Linear stability analysis and phase plane analysis.
5. Dynamical behaviours: steady state, oscillation, chaos.
6. Formulation of models of enzyme catalyzed processes and networks.
7. Formulation of models of membrane transport processes.
8. Predator-prey models.
9. Models of the spreading of infectious diseases.
10. Case 1: Models of glycolysis.
11. Case 2: Models of bioreactors.
12. Case 3: models of childhood epidemics (measles, etc.)
13. Case 4: models of the cell cycle.

At the end of the course the students will work on a small project simulating a model of their own choice according to the topics taught.

Literature

• Kompendium. .

Website
This course uses e-learn (blackboard).

Prerequisites for participating in the exam
None

Assessment and marking:
Project repport. External evaluation. Marks according to the Danish 7-scale.

Expected working hours
The teaching method is based on three phase model.

Forelæsninger (20 timer), eksaminatorier (10 timer) og laboratorieøvelser (20 timer).
Educational activities

Language
This course is taught in Danish.

Course enrollment
See deadline of enrolment.

Tuition fees for single courses
See fees for single courses.