Course details

Advanced Bioinformatics

PBI Acad. year 2017/2018 Winter semester 4 credits

Current academic year

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

Lexa Matej, Ing., Ph.D. (DFIT-Dean)

Language of instruction

Czech

Completion

Examination (written+oral)

Time span

  • 20 hrs lectures
  • 13 hrs pc labs
  • 6 hrs projects

Assessment points

  • 51 pts final exam
  • 29 pts labs
  • 20 pts projects

Department

Department of Computer Systems (UPSY)

Subject specific learning outcomes and competences

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

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

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.

Prerequisite knowledge and skills

There are no prerequisites

Study literature

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

Syllabus of lectures

  1. Introduction
  2. Primary and derived bioinformatic data
  3. Genomes and genome analysis methods
  4. Uniprot and sequence analysis methods
  5. Statistical, information-theory and linguistic aspect of data
  6. Coding algorithms for biological sequence analysis
  7. PDB and structural data analysis
  8. Gene Ontology and functional data analysis
  9. Integration of data from multiple sources for genomics and proteomics
  10. Tools and libraries for software development (Biopython)
  11. Visualization tools (PyMol)
  12. Bioinformatics and nanotechnology: DNA computing, sequencing by hybridization
  13. Recent trends

Syllabus of computer exercises

  1. Biological sequence analysis
  2. Genome Browser, Biomart
  3. Biopython a PyMol
  4. R/Bioconductor
  5. Integration of bioinformatic data

Progress assessment

Study evaluation is based on marks obtained for specified items. Minimimum number of marks to pass is 50.

None.

Controlled instruction

Project, computer labs assignments.

Course inclusion in study plans

  • Programme IT-MGR-2, field MBI, 2nd year of study, Compulsory
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