M9203 Simulation modeling in biology

Faculty of Science
Autumn 2014
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: k (colloquium).
Teacher(s)
doc. Ing. Luděk Berec, Dr. (lecturer)
Guaranteed by
prof. RNDr. Ivanka Horová, CSc.
Department of Mathematics and Statistics – Departments – Faculty of Science
Supplier department: Department of Mathematics and Statistics – Departments – Faculty of Science
Timetable
Thu 12:00–15:50 MP2,01014a
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
The aim of the course is to acquaint students with selected simulation techniques and with application of these techniques for solving problems in a variety of biological disciplines, including ecology and epidemiology. The course also aims to teach students systems thinking inevitable for design of simulation models of complex systems.
Syllabus
  • 1. Introduction to the course, definition of systems and models, basic concepts of simulation, advantages of simulation, basic simulation techniques, basic principles of systems thinking, examples
  • 2. Cellular automata: history, principles, presence, applications in biology, Game of Life
  • 3. Discrete event models: events planning, random processes, generation of random variables, applications in biology
  • 4. System dynamics models: global-level system description, flows and causal relationships, applications in biology
  • 5. Agent-based models: “individual”-level system description, basic principles, applications in biology, software tool NetLogo
  • 6. Networks: basic types and principles of their modeling, epidemic spread on networks of human contacts
  • 7. Tools for processing of outputs of simulation models, sensitivity analysis, combining different simulation techniques
Literature
  • Ross SM (2006) Simulation. Academic Press
  • Railsback SF and Grimm V (2012) Agent-based and individual-based modeling. Princeton University Press
  • Kirkwood CW. System dynamics methods: a quick introduction – http://www.public.asu.edu/~kirkwood/sysdyn/SDIntro/SDIntro.htm
  • Schiff JL (2008) Cellular automata: a discrete view of the world. John Wiley & Sons.
Teaching methods
Classes will consist of presentations prepared by the teacher as well as of a practical part in which presented simulation techniques will be applied on selected biological problems. Classes will also be interactive: students will be encouraged to discuss strengths and weaknesses of various modelling approaches and suggest extensions of the simulated models.
Assessment methods
Students will be assessed based on their activity and knowledge during the final, round-table discussion that will cover all of the presented topics, and on their project.
Language of instruction
Czech
Further comments (probably available only in Czech)
Study Materials
The course is taught only once.
General note: Výuka probíhá jednou za dva týdny po 4 hodinách vždy ve čtvrtek od 12:00.
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