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Computational models of the
living cellRalph Back
Dept. of Information TechnologiesÅbo Akademi
Computational models of the
living cell
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
Purpose of coursePurpose 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.
Intended audienceIntended 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.
PreliminariesPreliminaries
• 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.
ContentsContents
• 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
Contents, cont.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
LitteratureLitterature
• To be announced• To be announced