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Bioinformatics

Supervisor: prof. RNDr. Luboš Brim, CSc.

The field is designed for students who want to acquire, in addition to general knowledge of computer science, the latest knowledge in the dynamically developing fields of bioinformatics and computational systems biology. The graduate of the field will be prepared for practical or research work in the informatics-biology tandem. They will be able to work in positions requiring cooperation between teams of experts from these two fields. Specialization is possible within the field of study through the appropriate choice of compulsory elective courses. It is possible to focus either on the processing, storage and analysis of genomic and proteomic data or on the use of formal methods to analyse and predict the behaviour of biological systems.

Requirements

  • Obtain a minimum of 120 credits over the entire period of study and pass a state examination.
  • Obtain 20 credits for the SDIPR course and defend a thesis, see guidelines.
  • Complete all required courses in the major by the highest form of completion.

Required courses

  • IV108 Bioinformatics II (2+2 cr.)
  • PA017 Software Engineering II (2+2 cr.)
  • PA054 Formal Models in Systems Biology (2+2 cr.)
  • PA055 Visualization of Complex Data (2+2 cr.)
  • PA103 Object-Oriented Methods in Information Systems Design (2+2 cr.)
  • PA152 Effective Use of Database Systems (2+2 cr.)
  • PA159 Computer Networks and their Applications I (2+2 cr.)
  • PB051 Computational Methods in Bioinformatics and Systems Biology (2+2 cr.)
  • PřF:M4180 Numerical Methods I (4+2 cr.)

Required electives

  • at least 1 of:
    • PV021 Neural Networks (4+2 cr.)
    • PV056 Machine Learning and Knowledge Mining (3+2 cr.)
  • At least 2 of:
    • MA002 Mathematical Analysis (4+2 cr.)
    • MA007 Mathematical Logic (3+2 cr.)
    • MA009 Algebra II (4+2 cr.)
    • MA010 Graph Theory (3+2 cr.)
    • MA012 Statistics II (4+2 cr.)
    • MA015 Graph Algorithms (3+2 cr.)
    • MV008 Algebra I (4+2 cr.)
    • MV011 Statistics I (4+2 cr.)
    • M7130 Computational geometry (2+2 cr.)
    • PřF:M9100 Numerical Methods for Solving Ordinary Differential Equations (3+2 kr.)
  • at least 3 z:
    • IA006 Selected Chapters in Automata Theory (3+2 cr.)
    • IA008 Computational Logic (4+2 cr.)
    • IA012 Complexity (2+2 cr.)
    • IA014 Advanced Functional Programming (2+2 cr.)
    • IA023 Petri Nets (2+2 cr.)
    • IA046 Computability (2+2 cr.)
    • IV003 Algorithms and Data Structures II (4+2 cr.)
  • At least 15 credits in one of the following groups:
    • Molecular Data Analysis option:
      • IV106 Bioinformatics Seminar (1+1 cr.)
      • IV110 Bioinformatics Project I (2+1 cr.)
      • PA010 Advanced Computer Graphics (2+2 cr.)
      • PA128 Similarity Searching in Multimedia Data (2+2 cr.)
      • PřF:C4660 Fundamentals of Physical Chemistry (2+2 kr.)
      • PřF:C7790 Computational Chemistry and Molecular Modelling I (2+2 kr.)
      • PřF:C7920 Structure and Function of Proteins (2+2 kr.)
    • Systems Biology option:
      • IA159 Formal Verification Methods (2+2 cr.)
      • IV120 Continuous and Hybrid Systems (3+2 cr.)
      • PA183 Systems Biology Project (2+1 cr.)
      • PB172 Seminar in Systems Biology (2+1 cr.)
      • PV027 Optimization (2+2 cr.)
      • PV225 Systems Biology Laboratory (3+1 cr.)

Recommended course of study

Molecular Data Analysis

1st semester

  • IV108 Bioinformatics II (2+2 cr.)
  • PA017 Software Engineering II (2+2 cr.)
  • PA055 Visualization of Complex Data (2+2 cr.)
  • PA159 Computer Networks and their Applications I (2+2 cr.)
  • PřF:C7790 Computational Chemistry and Molecular Modelling I (2+2 cr.)
  • Optional course I (5 cr.)
  • Optional course M (5 kr.)

2nd semester

  • PA103 Object-Oriented Methods of Information Systems Design (2+2 kr.)
  • PB051 Computational Methods in Bioinformatics and Systems Biology (2+2 cr.)
  • PřF:C4660 Fundamentals of Physical Chemistry (2+2 cr.)
  • PřF:M4180 Numerical Methods I (4+2 kr.)
  • Electives I (5 cr.)

3rd semester

  • IV110 Bioinformatics Project I (2+1 cr.)
  • PA010 Advanced Computer Graphics (2+2 kr.)
  • SDIPR Thesis (10 kr.)
  • Elective course I (5 kr.)
  • Optional course M (5 kr.)

4th semester

  • PA054 Formal Models in Systems Biology (2+2 cr.)
  • PA152 Effective Use of Database Systems (2+2 cr.)
  • PV056 Machine Learning and Knowledge Mining (3+2 cr.)
  • SDIPR Thesis (10 cr.)

Systems Biology

1st semester

  • IV108 Bioinformatics II (2+2 cr.)
  • PA017 Software Engineering II (2+2 cr.)
  • PA055 Visualization of Complex Data (2+2 cr.)
  • PA159 Computer Networks and their Applications I (2+2 cr.)
  • Electives I (5 cr.)
  • Optional course M (5 kr.)

2nd semester

  • IV120 Continuous and Hybrid Systems (3+2 kr.)
  • PA103 Object-Oriented Methods of Information Systems Design (2+2 kr.)
  • PB051 Computational Methods in Bioinformatics and Systems Biology (2+2 cr.)
  • PB172 Seminar in Systems Biology (2+1 cr.)
  • PřF:M4180 Numerical Methods I (4+2 cr.)
  • Electives I (5 cr.)

3rd semester

  • PA183 Project in Systems Biology (2+1 cr.)
  • PV225 Systems Biology Laboratory (3+1 cr.)
  • SDIPR Thesis (10 kr.)
  • Electives I (5 cr.)
  • Elective course M (5 kr.)

4th semester

  • PA054 Formal Models in Systems Biology (2+2 cr.)
  • PA152 Effective Use of Database Systems (2+2 cr.)
  • PV056 Machine Learning and Knowledge Mining (3+2 cr.)
  • SDIPR Thesis (10 cr.)