Course detail

Practics of Bioinformatics

FEKT-APBIAcad. year: 2010/2011

Bioinformatics and links to other research areas. Bioinformatic data, accessible databases, basic operations with data. Genome sequences of organisms. Basic operations with genome sequences. Special functions of the library. Bioinformatics of the programming environment Matlab. Non-linear methods of biosignal processing, method of dynamic time warping, hidden Markov models. Employment of non-linear methods in cluster analysis, classification problems. Statistic evaluation of classification procedures.

Language of instruction

Czech

Number of ECTS credits

4

Mode of study

Not applicable.

Guarantor

doc. Ing. Jana Kolářová, Ph.D.

Department

Department of Biomedical Engineering (UBMI)

Learning outcomes of the course unit

The ability to solve the main problems in the area of bioinformatics. Mastering of the basic analysis of bioinformatic data acquired from accessible databases in the programming environment Matlab using special functions

Prerequisites

Knowledge acquired in the previous semesters.

Co-requisites

Not applicable.

Planned learning activities and teaching methods

Teaching methods depend on the type of course unit as specified in the article 7 of BUT Rules for Studies and Examinations.

Assesment methods and criteria linked to learning outcomes

Requirements are specified by guarantor’s regulation updated for every academic year.

Course curriculum

Basic concepts of bioinformatics. Databases GenBank, OMIM, USDA and other. Sequences, fragments. Comparative and levelling methods, classification methods. Structures of molecules.

Work placements

Not applicable.

Aims

To develop the knowledge of the basic concepts and selected problems of bioinformatics

Specification of controlled education, way of implementation and compensation for absences

Extent and forms are specified by guarantor’s regulation updated for every academic year.

Recommended optional programme components

Not applicable.

Prerequisites and corequisites

Not applicable.

Basic literature

Cvrčková F: Úvod do praktické bioinformatiky, Academia, 2006 (CS)

Recommended reading

Not applicable.

Classification of course in study plans

  • Programme BTBIO-A Bachelor's

    branch A-BTB , 3. year of study, summer semester, optional specialized

  • Programme EEKR-CZV lifelong learning

    branch ET-CZV , 1. year of study, summer semester, optional specialized

Type of course unit

 

Exercise in computer lab

39 hours, compulsory

Teacher / Lecturer

Ing. Denisa Maděránková, Ph.D.

Syllabus

1. Bioinformatic data. Genome sequences of organisms., Databases accessible to the public. Reading, data imaging in Matlab. Basic problems from bioinformatics solved in the programming environment Matlab
2. Processing of geonome sequences according to the principal statistical standards.
3. Comparison of sequences. Levelling of sequences. Coincidence rate.
4. Seeking patterns in sequences
5. Non-linear methods for comparison of samples, method of dynamic time warping
6. Hidden Markov models in resolution methods
7. Seeking patterns by means of non-linear methods for classification problems.
8. Cluster analysis using non-linear comparative approaches
9. Statistical evaluation of classification procedures, volumes of processed data.
10. Expert system as a classifier.
11. Presentation of individual work.
12. Presentation of individual work.
13. Test.

The other activities

13 hours, compulsory

Teacher / Lecturer

doc. Ing. Jana Kolářová, Ph.D.

Syllabus

Practical exercises are focused on processing of bioinformatic data in the programming environment Matlab.. The objective of student work is getting information about the special functions of the library Bioinformatics for use in computer exercises. The second part of the semester is focused on processiong of biosignals by means of non-linear methods and their application for the purposes of recognition and classification. The result will be creating of simple functions for processing of one-dimensional biosignals. At the end of the semester the students will present their papers.