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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.

Contact

Carl Troein
Victor Olariu
Henrik Jönsson

Course evaluations

Spring 2015
Spring 2016

Schedule

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
HUB
Introduction
Lecture 1.1 (Carl)
Tue 17/1 13-15
HUB
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
HUB
Presentations, project 1
Thu 26/1 13-15
HUB
Lecture (Victor)
Mon 30/1 13-15
HUB
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
HUB
Presentations, project 2
Tue 7/2 13-15
HUB
Lecture (Henrik)
Henrik's notes on modeling
Wed 8/2 13-15
HUB
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
HUB
Presentations, project 3
Mon 20/2 13-15
HUB
Lecture (Carl)
Tue 21/2 13-15
HUB
Project 4: Simpson's paradox
Papers: Chuang (Simpson's paradox) & Melke (quorum sensing)
Mon 27/2 13-16
HUB
Presentations, project 4
Tue 28/2 13-15
HUB
Lecture (Victor)
Thu 2/3 13-15
HUB
Project 5: Parameter optimization (Carl)
Data for optimization
Tue 7/3 13-15
HUB
Project checkup and guidance, project 5
Mon 13/3 13-16
HUB
Presentations, project 5
Wed 15/3
TBA
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: