Period 1, 2015-2016
This course aims to give an introduction to the broad field of computational and systems biology. The course takes a computer science perspective on the field, focusing on the algorithmic and computational challengens and opportunities in this area. We discuss in the course four main topics:
- Algorithms in computational biology
- Computational modeling techniques
- System-level analysis of biomodels
- Molecular computing and programming
This course is primarily meant for Master and PhD students in computer science, computer engineering, and applied mathematics. Students in biology, biochemistry, bioinformatics, and systems biology are also welcome.
- Elements of molecular biology
- Elements of biotechnology
- Molecular computing, molecular self-assembly, basics of synthetic biology
- Combinatorial pattern matching in biology
- Gene mapping
- Sequence assembly
- Genome rearrangements
- Bioinformatics tools and databases
- Algorithmic protein sequencing
- Basic computational modeling techniques: modeling with ODEs and with CTMCs
- N.C. Jones, P.A. Pevzner. An introduction to bioinformatics algorithms. The MIT Press, 2004.
- U. Alon: An introduction to systems biology. Design principles of biological circuits. Chapman & Hall, CRC, 2007.
- A. Kriete, R. Eils (Eds.): Computational systems biology, Elsevier Academic Press, 2006.
- E. Klipp, R. Herwig, A. Kowald, C. Wierling, H. Lehrach: Systems biology in practice, Wiley, 2006.
- M. Buchanan, G. Caldarelli, P. de los Rios, F. Rao, M. Vendrscolo (Eds.): Networks in cell biology. Cambridge University Press, 2010.
Credits: 5 study points.
Components: 28h lectures, final exam.
Time schedule: August 31 – October 23, 2015. Lectures will be given every Monday and Wednesday 10.15-11.45, in room Catbert B3028, ICT House. Exercises (when needed) are on Mondays 13.30-15.00 in room Catbert (B3028), ICT House.
Prerequisites: Basic courses in algorithmics and data structures.
Lecturer: Ion Petre, Department of Computer Science, Åbo Akademi University, ipetre’AT’abo.fi.
Teaching assistant: Charmi Panchal, Department of Computer Science, Åbo Akademi University, cpanchal’AT’abo.fi.
Course webpage: http://users.abo.fi/ipetre/compsysbio/
Exam: The final exams will take place on October 23 and November 6, 2015. Registration should be done via MinPlan (for ÅA students) or through the lecturer (for non-ÅA students) at least one week before the exam.
Lecture slides (to be updated and files uploaded throughout the course):
- Lecture 1 (31.8.2015): Introduction
- Lecture 2 (2.9.2015): Elements of molecular biology for computer scientists (slides from http://bioalgorithms.info/)
- Lecture 3 (7.9.2015): Elements of biotechnology for computer scientists
- Lecture 4 (9.9.2015): Molecular computing
- Lectures 5-6 (14.9.2015, 16.9.2015): Biological sequence comparison
- Lectures 7-8 (21.9.2015, 23.9.2015): Physical mapping
- Lecture 9 (28.9.2015): Algorithmic sequence assembly
- Lecture 10 (30.9.2015): Genome rearrangements
- Lecture 11 (7.10.2015): Bioinformatics tools and databases (guest lecture by Vladimir Rogojin)
- Lecture 12 (12.10.2015): Building and analyzing a computational biomodel
- Lecture 13 (14.10.2015): Algorithmic self-assembly (guest lecture by Eugen Czeizler)
- Lecture 14 (19.10.2015): Network controlability. Course summary
- Set 1: due September 21, 2015. Solutions can be found here.
- Set 2: due September 28, 2015. Solutions can be found here.
- Set 3: due October 5, 2015. Solutions can be found here.
- Set 4: due October 12, 2015. Solutions can be found here.
Last updated: October 16, 2015