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Computational models of the living cell

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

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Computational models of the living cell

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  1. Computational models of the living cell 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

  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.

  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.

  5. Preliminaries • 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

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

  8. Litterature • To be announced

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