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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 tentative schedule for the course is presented below.

The lectures will be 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


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
Mon 16/1 13-15
Lecture 1.1 (Carl)
Tue 17/1 13-15
Lecture 1.2 / Project 1: Deterministic models
Papers: Gardner (bistable switch) & Elowitz (repressilator)
Fri 20/1 13-15
CT's office
Project guidance, project 1
Tue 24/1 13-16
Presentations, project 1
Thu 26/1 13-15
Lecture (Victor)
Mon 30/1 13-15
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 1/2 13-15
VO's office
Project guidance, project 2
Mon 6/2 13-16
Presentations, project 2
Tue 7/2 13-15
Lecture (Henrik)
Henrik's notes on modeling
Wed 8/2 13-15
Project 3: Spatial models
Papers: Peña (Brusselator),
Meinhardt (pattern formation),
Turing (morphogenesis)
Schmoller (dilution of Whi5)
Mon 13/2 13-15
CT's office
Project guidance, project 3
Thu 16/2 13-16
Presentations, project 3
Mon 20/2 13-15
Lecture (Carl)
Tue 21/2 13-15
Project 4: Simpson's paradox
Papers: Chuang (Simpson's paradox) & Melke (quorum sensing)
Mon 27/2 13-16
Presentations, project 4
Tue 28/2 13-15
Lecture (Victor)
Thu 2/3 13-15
Project 5: Parameter optimization (Carl)
Data for optimization
Tue 7/3 13-15
Project checkup and guidance, project 5
Mon 13/3 13-16
Presentations, project 5
Wed 15/3
Oral exams
Questions on parts 1-5
Thu 16/3
Fri 17/3

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: