Bi7440 Scientific computing in biology and biomedicine

Faculty of Science
Spring 2012
Extent and Intensity
2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
prof. RNDr. Jiří Hřebíček, CSc. (lecturer)
Guaranteed by
prof. RNDr. Ladislav Dušek, Ph.D.
RECETOX – Faculty of Science
Contact Person: prof. RNDr. Jiří Hřebíček, CSc.
Supplier department: RECETOX – Faculty of Science
Timetable
Mon 10:00–11:50 G2,02003
Prerequisites
Passing courses: - Bi3101 Introduction to mathematical modeling - Bi1011 Application software
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
In this course, students will obtain: - Knowledge of current trends in the field of  scientific computing and computational science - Knowledge using application software Maple, MATLAB and SPSS for scientific computing in biology - Experience in the use of parallel computing and cloud computing for scientific computing - Experience of solving practical case studies
Syllabus
  • Basic terminology (scientific computing, parallel computing, computer simulation, cloud computing, etc.)
  • Scientific computing and computational science (Scientific approach based on observation: Observation Science; Scientific approach based on experiments: Experimental Science; Scientific approach based on the theory: Theoretical Computer Science; Scientific approach based on scientific computing: Computational Science, Two views of computational science and scientific calculations; Computational simulation)
  • A brief history of scientific computing (Development abroad; Development in the Czech Republic)
  • Development and limitations of scientific computing (Computing environment; Graphics in scientific calculations, Errors in scientific computing, Computational complexity)
  • Uncertainty and sensitivity in scientific computing (Uncertainty Analysis, Imaging and local sensitivity analysis, Global sensitivity analysis)
  • Application software for scientific computing (Scientific computing using Maple; Scientific computations using MATLAB, Scientific computing using SPSS)
  • Parallel Computing (Introduction; Parallel computations with Maple; Parallel Computing with MATLAB)
  • Case studies (Modelling pollution dispersion in water; Modelling pollution in the air)
Literature
    required literature
  • HŘEBÍČEK, Jiří, Miroslav KUBÁSEK, Lukáš KOHÚT, Luděk MATYSKA, Lucia TOKÁROVÁ and Jaroslav URBÁNEK. Vědecké výpočty v matematické biologii (Scientific computing in mathematical biology). Brno: Akademické nakladatelství CERM, 2012, 117 pp. ISBN 978-80-7204-781-9. info
    recommended literature
  • GANDER, Walter and Jiří HŘEBÍČEK. Solving Problems in Scientific Computing Using Maple and MATLAB. čtvrté. Heidelberg: Springer, 2004, 476 pp. Mathematics. ISBN 3-540-21127-6. URL info
Teaching methods
Lectures supplemented by homework and students presentations
Assessment methods
Lectures of course are reading weekly. Simple homeworks are requested during semester. Oral exam and project close course.
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, Spring 2011 - only for the accreditation, Autumn 2005, Autumn 2006, Spring 2008, Spring 2009, Spring 2010, Spring 2011, spring 2012 - acreditation, Spring 2013, Spring 2014.
  • Enrolment Statistics (Spring 2012, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2012/Bi7440