Title:

Advanced Bioinformatics

Code:

PBI

Ac.Year:

2017/2018

Term:

Winter

Curriculums:

Programme	Field	Year	Duty
IT-MSC-2	MBI	2nd	Compulsory

Language of Instruction:

Czech

Credits:

Completion:

examination (written&verbal)

Type of
instruction:

Hour/sem	Lectures	Seminar Exercises	Laboratory Exercises	Computer Exercises	Other
Hours:	20	0	0	13	6
	Exams	Tests	Exercises	Laboratories	Other
Points:	51	0	0	29	20

Guarantor:

Lexa Matej, Ing., Ph.D. (FI)

Lecturer:

Lexa Matej, Ing., Ph.D. (FI)

Instructor:

Lexa Matej, Ing., Ph.D. (FI)
Puterová Janka, Ing. (DIFS)

Faculty:

Faculty of Information Technology BUT

Department:

Department of Computer Systems FIT BUT

Learning objectives:

To build on the introductory bioinformatics course. Introduce the students to selected, fast-evolving, or otherwise noteworthy areas of bioinformatics. To allow space for creative activities resulting in the creation of a computational tool based on studied principles.

Description:

During the lectures, the students will get acquainted with areas integrating different bioinformatic data-types. They will study possibilities of data integration to solve specific problems or create specific computational tools. Textbook material will be supplemented by recently published scientific papers. Students will work on individual computational modules in the exercises/projects leading to the creation of an integrated whole-class tool suitable for general bioinformatic analysis (functional annotation, structural prediction, molecule visualization).

Subject specific learning outcomes and competences:

Knowledge of less-common algorithm and analysis methods, better ability to design and implement algorithms for bioinformatics.

Generic learning outcomes and competences:

Deeper understanding the role of computers in the analysis and presentation of biological data.

Syllabus of lectures:

Introduction
Primary and derived bioinformatic data
Genomes and genome analysis methods
Uniprot and sequence analysis methods
Statistical, information-theory and linguistic aspect of data
Coding algorithms for biological sequence analysis
PDB and structural data analysis
Gene Ontology and functional data analysis
Integration of data from multiple sources for genomics and proteomics
Tools and libraries for software development (Biopython)
Visualization tools (PyMol)
Bioinformatics and nanotechnology: DNA computing, sequencing by hybridization
Recent trends

Syllabus of computer exercises:

Biological sequence analysis
Genome Browser, Biomart
Biopython a PyMol
R/Bioconductor
Integration of bioinformatic data

Syllabus - others, projects and individual work of students:

Design and implementation of an integrated computational tool for bioinformatics and its presentation on a mini-conference.

Fundamental literature:

Zvelebil M., Baum J.: Understanding bioinformatics. Garland Science, London, 2007 ISBN 978-0815340249
UniProt URL: http://www.expasy.uniprot.org/
Gene Ontology URL: http://www.geneontology.org
Protein Data Bank URL: http://www.pdb.org/

Study literature:

Jones N.C., Pevzner P.: An introduction to algorithms in bioinformatics. MIT Press, 2004, ISBN 978-0262101066

Progress assessment:

Project, computer labs assignments.

Exam prerequisites:

None.

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Advanced Bioinformatics