SGN-9406 Signal Processing Graduate Seminar IV, 4 cr

Note: next presentations on Wednesday 14.01.2009.

Lecture on Wednesday 05.11.2008 will start at about 10:25.
Lecture on Monday 27.10.2008 at 13:15 o'clock in TB222.
Presentation topics/pages added (and updated).
Web page open.


Stochastic Modelling for Systems Biology

Time and Place:
Periods II & III, Wednesdays 10:15-12:00, room TB222

First meeting:

October 15, 2008

Harri Lähdesmäki
email: harri lahdesmaki a tut fi
office: TF412

This seminar course provides an introduction to stochastic modeling methods in systems biology. The course is motivated by careful modeling of various biological phenomena using stochastic kinetic models. Topics to be covered include some necessary background in statistics, the theory of stochastic modeling and simulation methods,
discrete and continuous-time Markov processes, ordinary differential equations, Gillespie algorithms and their extensions, parameter estimation and model identification.

Active participation in the lectures
and seminar presentations (at least 70%) and one oral presentation. A small project work, and a written course report. There will be no final exam.

Practical implementation:
The first lectures are given by the instructor. The rest of the seminar consists of student presentations.

Basic knowledge of probability, statistics and signal processing is assumed.

Via email to the course instructor or at the first meeting. If you are unable to attend the first meeting, please email the course instructor.


The course is accepted as a postgraduate course but M.Sc. students can participate as well.

Darren J. Wilkinson
Stochastic Modelling for Systems Biology
Chapman & Hall/CRC, 2006.
Amazon, Google books

Course covers part of the book. The book can be borrowed from the course instructor. The material will be supplemented by recent articles.

Additional reading:

Sections of the course book for student presentations:
Chapter 1 done pages 1-18
Chapter 2 done with or without the SBML part: pages 19-31 (or 19-43)
Chapter 3 reserved: Ali pages 45-89
Chapter 4 reserved: Chenghao pages 91-108
Chapter 5: Sections 5.1-5.3 reserved: Lingjia pages 109-121
Chapter 5: Sections 5.4-5.7 reserved: Henrik pages 121-137
Chapter 6 reserved: Tarmo pages 139-161
Chapter 7 reserved: Eeva pages 163-179
Chapter 8 reserved: Jukka pages 181-196
Chapter 9 open
Chapter 10 open

15.10.2008  Introduction to biological modeling: Chapter 1 [pdf]
22.10.2008  No meeting.
27.10.2008  Representations of biochemical networks: Chapter 2 [pdf]
05.11.2008  Sections 3.1-3.6: Ali
12.11.2008  Sections 3.7->: Ali [pdf]
19.11.2008  Chapter 4: Chenghao [pdf]
26.11.2008  Exam week -- no presentation.
03.12.2008  Sections 5.1-5.3: Lingjia [pdf]
10.12.2008  Sections: 5.4-5.7: Henrik [pdf]
18.12.2008  Chapter 6: Tarmo [pdf]
                      Chapter 7: Eeva [pdf]
14.01.2009  Chapter 8: Jukka [pdf]