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