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FYTN12: Systems Biology - Models and Computations

In this course you will learn how tools from mathematics and computational physics can be applied to biological problems. Topics include deterministic and stochastic simulations of biochemical systems, population models, spatial models and parameter optimization.

The fall 2018 (second period) schedule for the course is presented below.

The lectures are based on our slides and lecture notes as well as on papers from the scientific literature. These will be provided to you as we go along.


Carl Troein
Victor Olariu
Henrik Jönsson

Course evaluations

Spring 2015
Spring 2016, response
Spring 2017, response
Fall 2018, response


The introduction meeting and lectures will be in the Hans-Uno Bengtsson room (HUB) at Theoretical Physics (Fysicum, building K).

For students who want guidance on the programming projects, the lecturers will be available in their offices at Theoretical Physics as noted in the schedule. It is also possible to ask questions by email or come and look for the lecturers at other times.

Date / RoomTopic
Tue 6/11 10-12
Lecture 1.1 (Carl)
Wed 7/11 10-12
Lecture 1.2 / Project 1: Deterministic models
Papers: Gardner (bistable switch) & Elowitz (repressilator)
Fri 9/11 10-12
CT's office
Project guidance, project 1
Tue 13/11 9-12
Presentations, project 1
Wed 14/11 15-17
Lecture (Victor)
Fri 16/11-
Tue 20/11 10-12
Project 2 (Victor): Stochastic models
Paper: Olariu et al, plus supplement (stem cells)
Paper: Gillespie (method)
Paper: Shea and Ackers (phage lambda)
Paper: Chickarmane et al (stem cells)
Wed 21/11-
Fri 23/11 10-12
VO's office
Project guidance, project 2
Mon 26/11 9-12
Presentations, project 2
Tue 27/11 10-12
Lecture (Henrik)
Henrik's additional lecture notes
Dagmar Iber: Numerical solution of reaction-diffusion
Wed 28/11 10-12
Project 3: Spatial models
Papers: Peña (Brusselator),
Meinhardt (pattern formation),
Turing (morphogenesis)
Schmoller (dilution of Whi5)
Fri 30/11 10-12
Conf-room K327
Project guidance, project 3
Tue 4/12-
Wed 5/12 9-12
Presentations, project 3
Fri 7/12 10-12
Lecture (Carl)
Tue 11/12 10-12
Project 4: Simpson's paradox
Papers: Chuang (Simpson's paradox) & Melke (quorum sensing)
Wed 12/12-
Fri 14/14 10-12
CT's office
Project guidance, project 4
Tue 18/12 9-12
Presentations, project 4
Wed 19/12 10-12
Lecture (Victor)
Fri 21/12 10-12
Project 5: Parameter optimization (Carl)
Data for optimization
Tue 8/1 10-12
CT's office
Project checkup and guidance, project 5
Wed 9/1-
Fri 11/1-
Tue 15/1 9-12
Presentations, project 5
Wed 16/1
Oral exams
Questions on parts 1-5
Thu 17/1
Fri 18/1

The following is an unofficial translation of parts of the course description.

The course aims to give the student basic knowledge of the most important computational methods in systems biology. The student should gain experience in implementing and applying the methods to relevant biological problems.

Course contents: