1. Computational models of the living cell Ralph Back Dept. of Information Technologies Åbo Akademi Ralph Back Dept. of Information Technologies Åbo Akademi

2. Computational models of the living cell Lecturer: Ralph Back Place: A5059 Time:every second Thursday, 13 - 16 Dates: 31.1, 14.2, 28.2, 13.3, 27.3, 10.4, 24.4, 8.5 and 22.5 Credits: 5 points Working methods: lectures, seminar presentations, hands on training on selected problems Lecturer: Ralph Back Place: A5059 Time:every second Thursday, 13 - 16 Dates: 31.1, 14.2, 28.2, 13.3, 27.3, 10.4, 24.4, 8.5 and 22.5 Credits: 5 points Working methods: lectures, seminar presentations, hands on training on selected problems

3. Purpose of course Give an overview of Systems Biology, from a Computer Science/Mathematics point of view. Show how to model and analyze the different computational mechanisms in the cell. Systems biology is a new and very challenging research area in the intersection of Computer Science, Biology and Mathematics Enormous potential for practical applications in areas such as Medicin, Pharmacology and Nanotechnology. Give an overview of Systems Biology, from a Computer Science/Mathematics point of view. Show how to model and analyze the different computational mechanisms in the cell. Systems biology is a new and very challenging research area in the intersection of Computer Science, Biology and Mathematics Enormous potential for practical applications in areas such as Medicin, Pharmacology and Nanotechnology.

4. Intended audience Students working on their masters or Ph.D. degree in Computer Science, Computer Engineering, Mathematics, or Biology The course serves as a special course in Computer Science (informationsbehandling) Computer Engineering (datateknik) at Abo Akademi. Students working on their masters or Ph.D. degree in Computer Science, Computer Engineering, Mathematics, or Biology The course serves as a special course in Computer Science (informationsbehandling) Computer Engineering (datateknik) at Abo Akademi.

5. Preliminaries No a priori knowledge of biology is assumed. A basic understanding of formal methods and some mathematical maturity is an advantage. No a priori knowledge of biology is assumed. A basic understanding of formal methods and some mathematical maturity is an advantage.

6. Contents Overview of the cell cell biology basic computational mechanisms in a cell Standard approach to modeling cells ordinary differential equations analysis tools stochastic models Petri net based models Basic Petri nets Timed and hybrid Petri nets Overview of the cell cell biology basic computational mechanisms in a cell Standard approach to modeling cells ordinary differential equations analysis tools stochastic models Petri net based models Basic Petri nets Timed and hybrid Petri nets

7. Contents, cont. Process algebra models Pi calculus Stochastic models. Cell network motifs gene regulatory networks Process algebra models Pi calculus Stochastic models. Cell network motifs gene regulatory networks

8. Litterature To be announced