SGN-9406 Signal Processing Graduate Seminar IV, 4 cr
News:
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.
Topic:
Stochastic Modelling for Systems Biology
Time and Place:
Periods II & III, Wednesdays 10:15-12:00, room TB222
First meeting:
October 15, 2008
Instructor:
Harri Lähdesmäki
email: harri lahdesmaki a tut fi
www: http://www.cs.tut.fi/~harrila/
office: TF412
Description:
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.
Requirements:
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.
Prerequisites:
Basic knowledge of probability, statistics and signal processing is
assumed.
Registration:
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.
Homepage:
http://www.cs.tut.fi/~harrila/teaching/SPGSIV2008/
Notes:
The course is accepted as a postgraduate course but M.Sc. students
can participate as well.
Material:
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 |
|
Schedule:
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]
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