Course syllabus

Course-PM

FFR110 / FIM740 Computational biology 1 lp3 VT20 (7.5 hp)

The course is offered by the department of Physics

Teachers

Examiner, lectures: Kristian Gustafsson, Room S3013, tel: +46-700502211 (kristian.gustafsson@physics.gu.se)
Lectures: Bernhard Mehlig, Room S3005
Problem sessions: Anshuman Dubey, Room S3047

Course purpose

The aim of the course is to introduce students to the mathematical modeling of biological systems. The emphasis is on macroscopic phenomena such as population growth, morphogenesis and spreading of infectious diseases. Also microscopic phenomena are introduced, such as biochemical reactions, population genetics, and molecular evolution. A major topic is the role played by chance in the dynamics of biological systems, giving rise to stochastic fluctuations that must be described with statistical methods. The goal is to introduce mathematicians, physicists, and engineers to current important questions in Biology that require quantitative methods to solve.

To read the course it is advantageous but not mandatory with some prior knowledge about continuous dynamical systems, for example Dynamical systems (TIF155/FIM770). The needed concepts from continuous dynamical systems are covered by the course book by Murray, but we will not cover all in the lectures. It could also be helpful to have a look at the following compilation of essential concepts from dynamical systems. The most relevant parts of this document are the classification of fixed points in Sec. 3.2 and linear stability analysis Secs. 2.2 and 4.2 (see also Appendix A in Murray).

Schedule

TimeEdit

Course literature

Lecture notes will be made available.on the schedule on the start page.
Textbook The course partly follows Mathematical Biology, by J. D. Murray (Possible to buy at Cremona)
Other references
The content on pattern formation and morphogenesis follows Chapters 11-12 in Mathematical Biology II, by J. D. Murray.
The introduction to stochastic populations follows Chapter 1 in Diffusion and Ecological Problems: Modern Perspectives, by A. Okubo and S. A. Levin (free to download within the Chalmers domain).
The content on population genetics follows Chapters 5 in Calculating the Secrets of Life, by E. S. Lander and M. S. Waterman (free to download).
The content on time series analysis follows Nonlinear Time Series Analysis, by H. Kantz and T. Schreiber.
A good introduction to dynamical systems is Nonlinear Dynamics and Chaos, by S. Strogatz.

Course design

Teaching The teaching is divided into lectures and problem sessions. In the lectures the course material is introduced and in the problems session example problems are solved and the homework problems are discussed. The course outline is found on the start page. There you will also find the lecture notes as they become available.

Examples Students are encouraged to calculate example problems on their own as this is often a good way to understand the details of the subject. There are some example problems in the course book. There are also the hand-in problems and old exam problems.

Lecture quizzes During lectures ungraded quizzes are given as new material is covered. The aim is for both the students and the teacher to check whether the students have understood the material. The questions will be of varying level, where some are simple questions on definitions and other require heavy thinking and a mature understanding of the subject.

Communication The discussion board is used to ask questions (rather than emailing the teaching staff). You are advised to ask questions about lectures, the course book, example problems, problem sets, old exams and other course material. To encourage students to answer each others questions, the teachers will typically not answer immediately (but we will check that answers given by fellow students are reasonable). You can of course also ask questions directly to the teachers during, or directly after the lectures.

Changes made since the last occasion

Due to the cancellation of Computationally biology 2 some parts of that course is now covered in Computationally biology 1 (two lectures on population genetics have replaced one lecture on spreading of diseases and one lecture on metapopulations).
Migrated the course to Canvas.

Learning objectives

The course follows the study plan on Studieportalen.

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

Examination

The examination of the course consists of three problem sets and a written exam which are all graded to give your final grade. The problem sets are published on the start page when the corresponding content has been covered in the lectures (green dates in the schedule on the start page). For each problem set a problem session is given. The aim of the problem sessions is to answer your accumulated questions, you are supposed to have worked on the problem set before the problem session is given. The problem sets must be handed in before the deadlines (yellow times in the schedule on the start page), otherwise they are not corrected.  The aim of the problem sets is to encourage students to start working by themselves early in the course and to complement the written exam in assessing the learning goals.

For each problem set you hand in written solutions in the lectures, or alternatively in the white mail box on Soliden floor 3 (mounted on the wall to the right from the elevator, not in the shelves to the left).
You also need to mail a pdf copy to kristian.gustafsson.gu@analys.urkund.se
Note special instructions for the urkund email: Subject = [FIM740] (GU) or Subject = [FFR110] (Chalmers), then attach the pdf file with the filename in the format firstname-lastname-hw1.pdf (if you work in pair, only submit one copy with filename firstname1-lastname1_firstname2-lastname2-hw1.pdf )

Format of written solutions In the written solutions you must explain/describe what you have done and clearly state your answers/results to the questions, as well as your conclusions. If appropriate you should discuss possible errors and inaccuracies in your results. If you are asked to plot results/make graphs, you do this in a figure with axis labels. All symbols and lines must be explained in the figure or in a caption. You do not need to include program code in the paper submission. The web submission (urkund) should be identical to the paper submission, with the addition that you append your code, for example using

	\begin{verbatim}
	your code
	\end{verbatim}

in Latex.

Group work You are encouraged to collaborate and you are allowed to hand in the solutions to the problem sets in groups of two persons with the restriction that you must have different partners in each submission (of course it is also fine to submit one to three reports by yourself). If you want collaboraotrs, you can try the course discussion forum.

Format of written examination The exam covers the material in the lecture notes as well as in the homework problems. No books, lecture notes, personal notes, or calculators are allowed. The only allowed material is Mathematics Handbook for Science and Engineering, Lennart Råde and Bertil Westergren (available at Cremona). Any edition of this handbook is allowed.

Grading principles Three problem sets are graded during the course. Each problem set gives a maximum of 6 points, making 18 points the maximum number of points for the problem sets. The number of points for each task/subtask is quoted in the problem formulation. The written exam gives a maximum of 12 points. The total combined score on the four problem sets and the written exam determine the grade according to the scales:

• Chalmers: 3: 15-19.5p, 4: 20-24.5p, 5: 25-30p
• GU: G: 15-22.5p, VG: 23-30p
• ECTS: C: 15-19.5p, B: 20-24.5p, A: 25-30p

In addition, to be able to pass the course, a score of at least 7 points must be achieved on the combined problem sets, and at least 5 points on the written exam.

Late problems Deadlines for the problem sets are sharp. Both electronic version and paper version must be handed in before the time of deadline (usually 23.59). Thus, you might as well turn in what you have at the appointed time. If you are on travel and absolutely cannot turn in a paper copy on time, you can email me your work, pdf only. It must however still be received by deadline.

Course representatives

The following persons are (randomly selected) course representatives:

Marvin Becker	becker.12[_at_]web.de
Thomas Johansen	thomjoh[_at_]student.chalmers.se
David Larsson	davidlarsson97[_at_]gmail.com
Sara Romeo Atance	atance[_at_]student.chalmers.se
Jan Schiffeler	jansch[_at_]student.chalmers.se

Contact them if you have any comments or suggestions about the course. At the end of the course all students need to fill out a course evaluation form.