Course detail
Advanced Bioinformatics
FIT-PBIAcad. year: 2020/2021
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).
Guarantor
Department
Learning outcomes of the course unit
Deeper understanding the role of computers in the analysis and presentation of biological data.
Prerequisites
Co-requisites
Recommended optional programme components
Literature
Zvelebil M., Baum J.: Understanding bioinformatics. Garland Science, London, 2007 ISBN 978-0815340249.
Xinkun Wang, Next-Generation Sequencing Data Analysis, ISBN: 978-1482217889, CRC Press, 2016.
UniProt URL: http://www.expasy.uniprot.org/
Gene Ontology URL: http://www.geneontology.org
Protein Data Bank URL: http://www.pdb.org/
Planned learning activities and teaching methods
Assesment methods and criteria linked to learning outcomes
Exam prerequisites:
None.
Language of instruction
Work placements
Aims
Classification of course in study plans
- Programme MITAI Master's
specialization NADE , any year of study, winter semester, 4 credits, elective
specialization NGRI , any year of study, winter semester, 4 credits, elective
specialization NNET , any year of study, winter semester, 4 credits, elective
specialization NVIZ , any year of study, winter semester, 4 credits, elective
specialization NCPS , any year of study, winter semester, 4 credits, elective
specialization NSEC , any year of study, winter semester, 4 credits, elective
specialization NEMB , any year of study, winter semester, 4 credits, elective
specialization NHPC , any year of study, winter semester, 4 credits, elective
specialization NISD , any year of study, winter semester, 4 credits, elective
specialization NIDE , any year of study, winter semester, 4 credits, elective
specialization NISY , any year of study, winter semester, 4 credits, elective
specialization NMAL , any year of study, winter semester, 4 credits, elective
specialization NMAT , any year of study, winter semester, 4 credits, elective
specialization NSEN , any year of study, winter semester, 4 credits, elective
specialization NVER , any year of study, winter semester, 4 credits, elective
specialization NSPE , any year of study, winter semester, 4 credits, elective - Programme IT-MGR-2 Master's
branch MBI , 2. year of study, winter semester, 4 credits, compulsory
- Programme MITAI Master's
specialization NBIO , 2. year of study, winter semester, 4 credits, compulsory
Type of course unit
Lecture
Teacher / Lecturer
Syllabus
- 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
Exercise in computer lab
Teacher / Lecturer
Syllabus
- Biological sequence analysis
- Genome Browser, Biomart
- Biopython a PyMol
- R/Bioconductor
- Integration of bioinformatic data
Project
Teacher / Lecturer
Syllabus