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Graduate courses

Departments' graduate courses for PhD-students.

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Syllabus for

Academic year
FFR110 - Computational biology 1  
Beräkningsbiologi 1
 
Syllabus adopted 2019-02-14 by Head of Programme (or corresponding)
Owner: MPCAS
7,5 Credits
Grading: TH - Five, Four, Three, Fail
Education cycle: Second-cycle
Major subject: Bioengineering, Chemical Engineering, Engineering Physics
Department: 16 - PHYSICS


Teaching language: English
Application code: 11122
Open for exchange students: Yes
Block schedule: C

Module   Credit distribution   Examination dates
Sp1 Sp2 Sp3 Sp4 Summer course No Sp
0199 Examination 7,5 c Grading: TH   7,5 c   19 Mar 2020 pm H   10 Jun 2020 am J,  26 Aug 2020 am J

In programs

MPCAS COMPLEX ADAPTIVE SYSTEMS, MSC PROGR, Year 1 (compulsory)
MPENM ENGINEERING MATHEMATICS AND COMPUTATIONAL SCIENCE, MSC PROGR, Year 2 (elective)
MPENM ENGINEERING MATHEMATICS AND COMPUTATIONAL SCIENCE, MSC PROGR, Year 1 (compulsory elective)
MPHPC HIGH-PERFORMANCE COMPUTER SYSTEMS, MSC PROGR, Year 1 (elective)

Examiner:

Kristian Gustafsson

  Go to Course Homepage


Eligibility:


In order to be eligible for a second cycle course the applicant needs to fulfil the general and specific entry requirements of the programme that owns the course. (If the second cycle course is owned by a first cycle programme, second cycle entry requirements apply.)
Exemption from the eligibility requirement: Applicants enrolled in a programme at Chalmers where the course is included in the study programme are exempted from fulfilling these requirements.

Course specific prerequisites

Sufficient knowledge of Mathematics (analysis in one real variable, linear algebra), basic programming skills.

Aim

The aim of the course is to introduce students to mathematical modeling of biological systems. The emphasis of this course is on macroscopic phenomena such as population growth, morphogenesis, and ecological problems. The modeling and computer-simulation techniques discussed are essential tools for understanding ecosystems, with applications, for example, to bioconservation. Microscopic phenomena, on the molecular level, are the subject of Computational Biology B (FFR 115).

Learning outcomes (after completion of the course the student should be able to)

After successfully completing this course the students shall be able to

explain what can be, and what cannot be expected of mathematical models of biological systems;
decide whether deterministic or stochastic models are required in a given context;
efficiently simulate deterministic and stochastic models for population dynamics on a computer, and understand and describe the implications of the results;
analyze models of biological systems using linear stability analysis;
efficiently simulate the partial differential equations describing advection-reaction-diffusion systems on a computer;
apply non-linear time-series analysis to real data;
understand the purpose and predictive power of models of evolution;
write well-structured technical reports in English presenting and explaining analytical calculations and numerical results;
communicate results and conclusions in a clear and logical fashion.

Content

- Continuous and discrete population dynamics: growth models, delay models, linear stability analysis, ecological implications.
- Interacting species: Lotka-Volterra systems, phase-plane analysis, realistic predator-prey models.
- Enzyme reaction kinetics: Michaelis-Menthen approximation, autocatalysis.
- Pattern formation: Belousov-Zhabotinsky reaction, deterministic & stochastic approaches, reaction diffusion systems, traveling waves, spiral waves, morphogenesis.
- Time-series analysis: noise in deterministic systems, linear time-series analysis, non-linear time-series analysis.
- Oscillators: synchronization, phase resetting, surface-of-section.

Organisation

Lectures, set of homework problems, examples classes, and written exam.

Course home page:
http://fy.chalmers.se/~f99krgu/CompBioA/

Literature

Lecture notes will be made available.

Recommended additional material:
J. D. Murray, Mathematical Biology, Springer, Berlin (1993).

A. Okubo, Diffusion and Ecological Problems: Mathematical Models, Springer, Berlin (1980) 

as well as original research papers.

Examination including compulsory elements

The final grade is based on homework assignments as well as on a written examination.


Page manager Published: Thu 04 Feb 2021.