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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.

Contact

Carl Troein
Victor Olariu
Henrik Jönsson

Course evaluations

Spring 2015
Spring 2016
Spring 2017

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
Tue 6/11 10-12
HUB
Introduction
Lecture 1.1 (Carl)
Wed 7/11 10-12
HUB
Lecture 1.2 / Project 1: Deterministic models
Papers: Gardner (bistable switch) & Elowitz (repressilator)
Fri 9/11 10-12
HUB
Project guidance, project 1
Tue 13/11 9-12
HUB
Presentations, project 1
Wed 14/11 15-17
HUB
Lecture (Victor)
Fri 16/11-
Tue 20/11 10-12
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 21/11-
Fri 23/11 10-12
HUB
Project guidance, project 2
Mon 26/11 9-12
HUB
Presentations, project 2
Tue 27/11 10-12
HUB
Lecture (Henrik)
Henrik's notes on modeling
Wed 28/11 10-12
HUB
Project 3: Spatial models
Papers: Peña (Brusselator),
Meinhardt (pattern formation),
Turing (morphogenesis)
Schmoller (dilution of Whi5)
Fri 30/11 10-12
HUB
Project guidance, project 3
Tue 4/12-
Wed 5/12 9-12
HUB
Presentations, project 3
Fri 7/12 10-12
HUB
Lecture (Carl)
Tue 11/12 10-12
HUB
Project 4: Simpson's paradox
Papers: Chuang (Simpson's paradox) & Melke (quorum sensing)
Wed 12/12-
Fri 14/14 10-12
HUB
Project guidance, project 4
Tue 18/12 9-12
HUB
Presentations, project 4
Wed 19/12 10-12
HUB
Lecture (Victor)
Fri 21/12 10-12
HUB
Project 5: Parameter optimization (Carl)
Data for optimization
Tue 8/1 10-12
HUB
Project checkup and guidance, project 5
Wed 9/1-
Fri 11/1-
Tue 15/1 9-12
HUB
Presentations, project 5
Wed 16/1
TBA
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: