Bachelor study

Lectures are in Czech language only.


Study plan

1. grade

winter semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B101001 General and Inorganic Chemistry I

Annotation

The contents of the subject covers basic topics of general chemistry – atom structure, periodicity in properties, chemical bond theory, stereochemistry of molecules and basic chemical equilibrium. These principles are used for description of reactivity and properties of essential groups of inorganic substances. Systematic part is explained not as chemistry of elements but as chemistry of inorganic phases. Basic discussed categories are molecular gaseous and liquid substances, ions in aqueous solution and their salts, metals and intermetallic phases, solid oxides and inorganic polymers, carbides, nitrides and other solid compounds of metals.

Syllabus

  1. Structure of substances. Structure of atom.
  2. Periodic law and the periodic system of elements.
  3. Chemical bond and chemical reactions.
  4. Elemental non-metals. Chemical bonding, properties and reactivity.
  5. Polyatomic molecules of non-metals - structure, chemical bonding and properties.
  6. Gaseous and liquid molecular compounds of nonmetals.
  7. Monoatomic ions in aqueous solutions and their salts.
  8. Oxoanions in agueous solutions and crystals.
  9. Coordination compounds.
  10. Structure, chemical bonding and properties of metals.
  11. Metals and intermetallic phases - reactivity, extraction and uses.
  12. Solid oxides and inorganic polymers.
  13. Binary solid compounds of metals and non-metals.
 3/3/0 z, Zk 8
B413023 Mathematics for Chemists I

Annotation

This course is designed for undergraduate students to acquire solid background in elementary mathematics. The studied topics are: properties of functions, limits, derivatives of functions of one variable, primitive functions and definite integrals. Students will become familiar with the mathematics needed for applications in the fields of physics and chemistry. The topics covered are also followed by Mathematics for Chemists II.

Syllabus

  1. Limit of a function and basic techniques for its computation. Continuity of a function. Properties of continuous functions.
  2. Derivative of a function and its geometric meaning. Calculation of the derivative. Equation of the tangent. L’Hôpital’s rule. Asymptotes.
  3. Investigation of monotonicity and local extrema of a function using the first derivative. Higher-order derivatives. Convex and concave functions. Inflection points. Analysis of the function's behavior.
  4. Differential of a function. Curves and their parametrization.
  5. Antiderivative. Indefinite integral and its computation using integration by parts and substitution.
  6. Integration of selected types of functions.
  7. Definite integral. Newton (Riemann) integral and its computation.
  8. First-order differential equations. Separable equations and their solution.
  9. Homogeneous linear differential equations of first and second order with constant coefficients and their solution.
 2/3/0 z, Zk 5
B413015 Math Start

Annotation

The course provides beginning bachelor's students with an introductory overview of high school mathematics essential for subsequent mathematics courses, especially Mathematics for Chemists.

Syllabus

  1. A straight line and its expression. Systems of two linear algebraic equations. Vectors and their addition and multiplication by a number, scalar product. Norm and metric.
  2. Linear and quadratic equations and inequalities.
  3. Elementary functions of one variable. Domain, range of values and graph of a function. Composite functions.
  4. Trigonometry. Exponential and logarithm. Complex numbers. Trigonometric form of a complex number. Euler's formula.
 0/2/0 z 2
B143010 Software Application Development

Annotation

The course introduces students to practical software development from initial design through deployment and long‑term maintenance of applications. It focuses on understanding the software life cycle, working with both compiled and interpreted languages, systematic debugging and testing, including unit tests and code coverage measurement. Emphasis is placed on using Git for team-based version control, including branching, working with remote repositories, and basic CI/CD. Students will learn how to design modular project structures, create APIs, write documentation, and apply principles of readable, long-term maintainable code. They will also become familiar with deploying applications using containers (Docker, Apptainer), basics of networking and cybersecurity, the use of artificial intelligence in programming, and the specifics of developing scientific software on HPC infrastructures. In the final team project, they will experience the complete development workflow from design through implementation, version control, testing, and documentation to a demonstration of deployment in practice.

Syllabus

  1. What software is and basic development workflow {Software life cycle from idea through development and deployment to long‑term maintenance. Key concepts: release, version, bugfix, refactoring, etc. Code editing, text editors, integrated development environments (IDEs). Brief introduction to agile software development methodologies.}
  2. Path from source code to binary {Debugging, compilation (build systems), linking and testing. Unit tests and analysis of code coverage. Analysis of typical errors such as linking errors, segmentation faults and memory leaks. Specifics of compiled and interpreted languages. Differences between typed and untyped languages. An example of comparing a typed and an untyped language is C and Python.}
  3. Basics of version control: teamwork and main Git concepts {Basics of working with Git in a local repository. Staging area and commits. The .gitignore file. Viewing project history using the log, blame and diff commands. Merging branches and resolving conflicts. Release tags. Remote repositories for sharing code (GitHub/GitLab). Operations clone, fetch, pull and push. Setting up access via SSH and HTTPS. Basic CI/CD workflow using GitHub Actions. Working with pull requests and merge requests; basic code review.}
  4. Project structure and modular code {A group project will be assigned as part of this block. The group project will focus on developing a larger software system in a team. Students will learn to organize a project into clear directories and modules. Students will find out what an API is and what role it plays in software structure. They will learn to design interfaces between project modules that are stable, extensible and easy to understand. They will work on project documentation and understand its importance. They will become familiar with README files and what they should contain. They will learn to write comment‑based documentation directly in the code. They will try simple documentation generation using tools such as Doxygen or similar systems.}
  5. Artificial intelligence in software development {Students will learn how to work effectively with agent systems and AI‑based tools for code generation. They will learn about the benefits of using artificial intelligence and also about the pitfalls and risks of so‑called “vibe coding”.}
  6. Code readability and coding style {Principles of readable code and their practical application. Students will focus on appropriate naming of variables, functions and modules. Emphasis will be placed on maintaining a consistent style across the project. Students will understand the importance of coding style guidelines in team work. They will learn about options for formatting code manually and with autoformatters.}
  7. Deployment and user interfaces {Students will gain a basic overview of virtualization and its use in application deployment. They will learn to work with Docker and Apptainer containers. Introduction to network communication on the internet (REST APIs). Basic principles of cybersecurity. Brief introduction to container orchestrators such as Kubernetes. Introduction to the concept of graphical user interfaces and to selected GUI frameworks.}
  8. Specifics of scientific software development {FAIR principles for scientific data and software. Overview of HPC infrastructures used in scientific environments. Basics of working on HPC systems for computations. Introduction to job schedulers such as Slurm and PBS.}
  9. Project work and consultations {The last three blocks will be devoted to intensive work on student projects. Students will continuously consult the status of their project with the instructor. They will finalize the implementation of individual parts of the software. Thorough testing and debugging of the final solution will be included. Students will complete the project documentation and prepare its presentation, including a demonstration of its deployment in practice.}
 0/0/3 kz 3
B143003 Programming in shell

Annotation

The course is focused on programming in a shell - a command line of Linux operating system. In a series of practical exercises, students will learn to use basic commands and advanced tools of the shell. They gain skills and techniques of writing scripts for automated and efficient data processing.

Syllabus

  1. Introduction. Command line. Shell control. Working with commands. Manual pages and other documentation.
  2. Manipulation with files and directories. Searching.
  3. Input, output and redirection. Expansion operators.
  4. User permissions.
  5. Regular expressions.
  6. Manipulation with text.
  7. Advanced text transformations.
  8. Structure of shell script. Sequence of commands.
  9. Construction of conditions.
  10. Construction of loops.
  11. Arithmetic and logic operations.
  12. Arrays.
  13. Functions.
  14. Processes. Archivation and compression.
 0/3/0 kz 4
B500001 FIT Programming and Algorithmics 1

Annotation

Students gain the ability to formulate algorithms for solving basic problems and write them in the C language. They understand data types (simple, structured, pointers), expressions, statements, functions, concept of recursion. They learn to analyse simple cases of algorithm complexity. They know fundamental algorithms for searching, sorting, and manipulating with linked lists and trees.

Syllabus

  1. Algorithms, Programs and Basic support of development.
  2. Variables, Input and Output in C language.
  3. Floating point arithmetic. Expressions in C language.
  4. Flow control statements in C language.
  5. Functions in C language.
  6. Arrays and strings in C language.
  7. Structures and Pointers in C language.
  8. Pointers and dynamic memory allocation in C language.
  9. Complexity, Searching and Quadratic sorting.
  10. Linked structures and Trees.
  11. Recursion, MergeSort, QuickSort introduction.
  12. Working with files, Modular programming in C language.
  13. Abstract data types (boolean, complex numbers, queue, stack).
 2/4/0 z, Zk 8

summer semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B110003 Organic Chemistry I

Annotation

The structure - reactivity concept is involved in the modern teaching of organic chemistry of the main groups of hydrocarbons and their monofunctional derivatives: alkanes, alkenes, alkynes, arenes, and their halo derivatives, alcohols and phenols, carbonyl compounds, carboxylic acids and functional derivatives of carboxylic acids.

Syllabus

  1. Introduction to organic chemistry, bond theory, basics of nomenclature.
  2. Stereochemistry – R/S nomenclature, conformation of alkanes and cycloalkanes.
  3. Description of bonds in organic compounds, acid-base properties of organic compounds.
  4. Alkenes – Electrophilic addition, hydrogenation, radical addition, polymerization.
  5. Conjugation, conjugated systems – Electrophilic addition, diene polymers.
  6. Alkynes – acid-base behavior, electrophilic addition, hydrogenation.
  7. Arenes – Aromatic electrophilic substitution, side chain reactions – radical substitution.
  8. Haloalkanes – Nucleophilic substitution, dehydrohalogenation and dehalogenation.
  9. Organometallic compounds – Preparation of organometallic compounds and organometals as nucleophiles.
  10. Alcohols and phenols – Acid-base properties, dehydration and oxidation of alcohols.
  11. Carbonyl compounds – Enolization and nucleophilic addition to the carbonyl group.
  12. Carboxylic acids and their derivatives – Acid-base properties of acids, nucleophilic substitution on the acyl group.
  13. Amines – Structure, acid-base properties, preparation and reactivity of amines.
  14. Chemistry of natural products – Carbohydrates and amino acids, structure, properties and basic reactivity.
 2/2/0 z, Zk 5
B444003 Physics I

Annotation

The course is aimed at understanding the fundamental physical phenomena and the development of technical thinking. The laws of physics and physical principles, that are essential for connecting objects in a bachelor study program, are discussed and explained.

Syllabus

  1. Introduction: Physical quatities, The International System of Units.
  2. Basic concepts of Mechanics I: Force, the Newton's laws, work, power, kinetic and potential energy. Conservation of mechanical energy and linear momentum, elastic and inelastic collisions.
  3. Basic concepts of Mechanics II: Moment of inertia, torque, angular momentum. Work, power and energy in rotational motion. Rolling motion of rigid bodies. Static equilibrium conditions, center of gravity.
  4. Continuum and fluid mechanics: Forces in continuum, deformation, Hooke's law. Hydrostatic presure, Archimedes' law. Bernoulli's equation, real liquid flow.
  5. Oscillations: undamped, damped and forced harmonic oscillations. Composed oscillations.
  6. Waves: Description, propagation velocity, intensity. Huygen's principle, refraction and reflection, Snell's law. Interference, standing waves.
  7. Wave optics: Concept of light, interference, thin film, sigle-slit diffraction, diffraction grating, polarization, optical activity.
  8. Geometric optics: Basic concepts, reflection and refraction, optical instruments: magnifying glass, microscope.
  9. Electrostatic field: Coulomb's law. Electric dipole. Potential, voltage, work. Capacitor, dielectric polarization. Charge motion in an electric field.
  10. Direct current circuits: Ohm's law, Joule's law. Kirchhoff's rules. Current, voltage and resistance measurements.
  11. Magnetic field: Magnetic force. Mass spectrograph, electric measurement instruments, cyclotron, the Hall effect. Biot-Savart law, Ampere's law. Magnetic fields in matter.
  12. Electromagnetic field: Electromagnetic induction, proper and mutual inductance. Electromagnetic waves, energy of electromagnetic field.
  13. Alternating current circuits: Generator. Power. Impedance, phase shift, serial resonance circuit.
  14. Basic concepts of modern physics: Blackbody radiation, Stefan-Boltzmann radiation law, Planck radiation law, absorption, emission, laser. The photoelectric effect, X-rays, X-ray diffraction.
 3/2/0 z, Zk 6
B413024 Mathematics for Chemists II

Annotation

This course is designed for undergraduate students to acquire solid background in elementary mathematics. The studied topics are: properties of functions, limits, derivatives of functions of one variable, primitive functions and definite integrals. Students will become familiar with a number of applications in the field of physics and chemistry. Evaluation is based on the final written exam.

Syllabus

  1. Linear dependence and independence. Homogeneous systems of linear algebraic equations and their solution.
  2. Solution of nonhomogeneous systems of linear algebraic equations. Determinant.
  3. Matrix multiplication. Inverse matrix.
  4. Real functions of several real variables. Vector fields. Partial derivatives. Gradient. Directional derivative.
  5. Divergence, curl and their geometric meaning. Directional derivative. Nabla operator, Laplace operator.
  6. Chain rule. Total differential and tangent plane.
  7. Extrema of functions of several variables. Method of least squares.
  8. Implicitly defined functions of one and several variables and their derivatives.
  9. Double integral. Fubini’s theorem and interchange of the order of integration.
  10. Geometric interpretation of the double integral. Transformation to polar coordinates.
  11. Line integral of a scalar function. Arc length. Line integral of a vector function.
  12. Path-independence of the line integral. Potential of a vector field.
  13. Differential forms and their integration. Green’s theorem.
 2/3/0 z, Zk 5
B834001 Professional English Language A

Annotation

The aim of the course is to develop all language skills, with a special focus on the field of professional language and its specifics. The topics cover the academia, chemistry and other natural sciences, and work in the laboratory.

Syllabus

  1. Introduction to the course. How to prepare a scientific presentation.
  2. Education and academia: The academic world
  3. Education and academia: Life at university
  4. Education and academia: Learning environment
  5. Science: Introduction to chemistry
  6. Science: Elements and compounds
  7. Science: Physics and maths
  8. Science: Biochemistry I
  9. Science: Biochemistry II (Enzymes)
  10. Laboratory and research: Laboratory equipment
  11. Laboratory and research: Laboratory safety rules
  12. Laboratory and research: Research and exepriments
  13. Laboratory and research: Laboratory report and abstract
  14. General revision
 0/2/0 z 1
B500002 FIT Object-oriented Programming in Java

Annotation

Object-oriented Programming in Java introduces the concept of the object-oriented programming and Java programming language to the students.

Syllabus

  1. Introduction to OOP and Java, history, development and Java concepts.
  2. OOP, variables, expressions, primitives, classes and objects.
  3. Classes, objects, inheritance, catching and handling exceptions, try-catch and Autoclosable in Java 7, Run Time Type Identification.
  4. Arrays in Java and java.util.Arrays API, collections and JCF.
  5. Input and Output, files and streams, serialization, java.io and java.nio libraries.
  6. Threads and processes, interaction, synchronization, programming of multi-threaded applications.
  7. Java and Internet, net communication, client-server architecture.
  8. Graphical user interface in Java, AWT, Swing, layout managers, events, containers and components, listeners and adapters.
  9. Swing, applets and images.
  10. Databases, JDBC, interfaces Connection, Statement, PreparedStatement and ResultSet.
  11. Remote Method Invocation, inner and nested classes, local classes.
  12. Differences between Java versions 5 and 7, Enum, generics.
  13. Documentation, JAR, logging, regular expression in Java, JNI.
 2/5/0 z, Zk 7
B143006 Computational systems management

Annotation

The course is based on a series of practical exercises in the field of computational systems management. Students will be acquainted with the architecture and technical equipment of computers. The course provides an overview of the function of computational systems, computer networks and operating systems. Attention is also focused on the importance and principles of software development, its categorization and relation to hardware.

Syllabus

  1. Logic circuits.
  2. Architecture of computational systems.
  3. Hardware. Components of computational systems. Peripherals.
  4. Software. Development methodology. Testing.
  5. Operating systems. Function and structure of resource system manager.
  6. Installation and management of operating system.
  7. File systems. Data backup. External storage.
  8. Cryptography and hashing. Principles and corresponding data structures.
  9. Version control systems.
  10. Computer networks. Models, architecture and infrastructure.
  11. Network communication protocols.
  12. Data communication. Transmission media.
  13. Computational models and remote access.
  14. Virtualization.
 0/3/0 kz 3
B143007 Web Technologies

Annotation

The course should give students overview of the main technologies involved in modern web communication. These comprise of markup languages XML and HTML5, their formal description in schema languages and technologies for their visual and dynamic presentation (CSS, ECMAScript, DOM) and an overview of related technologies (network protocols, server applications).

Syllabus

  1. History and philosophy of web technologies.
  2. The semantics in textual data: XML metalanguage, its structure and validation, namespaces, encoding of text, character entities.
  3. Querying the tree structure: selectors in CSS (plus úvod do CSS), XPath
  4. The object reprezentation of XML: DOM versus SAX, their usage in JavaScript and Python.
  5. HTML5: elements, its DOM representation, visualization via CSS, scripting with JavaScript.
  6. HTTP and other protocols, forms in HTML5, WSGI in Python.
  7. Selected web libraries.
 2/0/0 Zk 3

2. grade

winter semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B403003 Physical Chemistry I

Annotation

The subject covers elementary parts of physical chemistry (i.e. basic ideas and quantities, state behaviour, fundamentals of thermodynamics) which are followed by chapters on phase equlibria and chemical equilibria. Basic principles of behaviour and properties of electrolytes are introduced. The final part is devoted to kinetics of chemical reactions.

Syllabus

  1. Basic terminology, thermodynamic system, thermodynamic process, state properties.
  2. State behaviour of gases, equation of state of ideal gas. Real gas and its behaviour.
  3. 1st law of thermodynamics. Internal energy, heat, work.
  4. Enthalpy, heat of reaction, standard enthalpy of formation. Hess and Kirchhoff's laws.
  5. 2nd law of thermodynamics, entropy. Entropy changes on selected processes.
  6. Helmholtz and Gibbs energy, their significance. 3rd law of thermodynamics.
  7. Thermodymamics of mixtures, chemical potential, activity, standard states.
  8. Material balance of chemical reactions. Equilibrium constant. Equilibria in electrolyte systems. Solubility product.
  9. Equilibrium composition. Reactions in gaseous phase.
  10. Phase equilibria in single-component systems, Clapeyron equation.
  11. Gibbs phase law, vapour-liquid equilibrium in ideal systems, phase diagrams.
  12. Solubility of gases in liquids, equilibria in condensed systems.
  13. Faraday´s law, galvanic cells, Nernst equation.
  14. Basic terms of chemical kinetics, reaction rate, integration of rate equations, catalysis.
 3/2/0 z, Zk 6
B320023 Biochemistry I

Annotation

This course will take you into the world of the chemistry of life - biochemistry, where you will learn about the key principles and processes of life. You will learn to recognize and understand the basic functions and properties of proteins, carbohydrates, nucleic acids, and lipids. Additionally, you will delve into the fundamental metabolic processes that occur in living organisms. What can you expect? You will discover the role proteins play in living organisms and how their structure affects their function. You will find out why carbohydrates are essential for energy acquisition and how they are metabolized. You will understand how genetic information is stored in DNA and RNA and how this information is transferred. You will grasp the importance of lipids for cell membranes and energy reserves. You will learn how living organisms obtain and utilize energy from ingested substances. This course is ideal for anyone who wants to gain basic knowledge of biochemistry and understand how these processes affect the health and functioning of organisms.

Syllabus

  1. Definition of biochemistry and its position in the system of natural sciences, organization of living systems. Amino acids (properties, reactions), peptides. (Definition of what biochemistry deals with. Composition and organization of living systems, molecular recognition. Types of non-covalent interactions. Definition of differences between prokaryotes and eukaryotes and between plant and animal cells. Proteinogenic amino acids – names, formulas, 3-letter codes, properties, titration curves, calculation of isoelectric points. Peptide bond – formula of the polypeptide chain, peptide nomenclature, calculation/estimation of isoelectric points for simple peptides.)
  2. Proteins, classification and general functions of proteins; levels of structure, properties, relationship between structure and function. (Functions of proteins and peptides in living organisms. Description of protein structure levels. Ability to explain denaturation. Common covalent modifications of proteins, namely disulfide bridges, phosphorylation, and glycosylation.)
  3. Methods used for biochemical characterization of living organisms (chromatography, electromigration techniques, immunochemical techniques, mass spectrometry, PCR). (Principle of separation using GC, IEC, affinity chromatography. Electrophoretic methods SDS-PAGE, IEF. Basic types of ELISA, Edman degradation, PCR.)
  4. Enzymes: structure, nomenclature, classification into classes. Explain the principles of enzyme catalysis and comparison with non-enzymatic catalysts. (Specificity of enzymes. Knowing that there are classes of enzymes. Knowing what cofactors are and their relationship to vitamins. Defining the difference between coenzyme and prosthetic group. Defining initial reaction rate. Writing the Michaelis-Menten equation, defining its parameters and their significance. Explaining enzyme inhibition and the use of inhibitors.)
  5. Principles of energy conversion, aerobic and anaerobic respiration, light phase of photosynthesis. (Definition of metabolism. Basics of organism classification in terms of nutrition (trophic). Difference between aerobic and anaerobic organisms. Relationship between autotrophs and heterotrophs. Catabolism, anabolism and their interrelationship. Role of ATP in metabolism and ways of its synthesis. Position of the respiratory chain in metabolism. Principle and significance of respiration. Difference between aerobic and anaerobic respiration. What is proton-motive force, how it arises and what units it has. Coupling of the respiratory chain and ATP synthesis by oxidative phosphorylation. ATP formation by photophosphorylation.)
  6. Citric acid and glyoxylate cycle. (Intracellular localization of TCA. Summary equation. Position in catabolism. Connection to TCA – where reduced cofactors are regenerated. Sources of acetylCoA: connection with β-oxidation of fatty acids, oxidative decarboxylation. Amphibolic aspects of TCA reactions. Importance and position of TCA in metabolism. Summary equation and significance of the glyoxylate cycle.)
  7. Carbohydrates and their metabolism. (Definition of carbohydrates, functions of carbohydrates, structure of the most important mono-, di- and polysaccharides. Catabolism and anabolism of carbohydrates (basics of glycolysis, pentose cycle, glycogenesis, glycogenolysis, gluconeogenesis, Calvin cycle, Cori cycle). Important reactions of glycolysis, energy balance.)
  8. Lipids, biomembranes and basics of membrane transport, lipid metabolism. (Definition of lipids, classification and functions. Structure of membranes and properties. Active and passive transport. Activation of fatty acids. Beta-oxidation and connection to TCA. Ketone bodies, fatty acid synthesis. Shuttles for transport of reduced cofactors.)
  9. Metabolism of nitrogenous substances. (Protein catabolism. Function of proteases, classification of amino acids into glucogenic, ketogenic and glucoketogenic. Elimination of nitrogen from different types of organisms (ureotelic, uricotelic and ammonotelic organisms), Ornithine cycle.)
  10. Regulation of metabolism and its significance. (Basic principles of metabolism regulation at the level of reaction, cycle and endocrine system – examples of hormones. Communication between organisms.)
  11. Nucleic acids and their structure, basics of molecular genetics. (Components of nucleic acids and their role in the organism. Terminology – nucleotide, nucleoside, base. Base pairing. Purine and pyrimidine bases. Recognizing the difference between purine and pyrimidine bases. Structure of prokaryotic and eukaryotic DNA (primary, secondary, tertiary). Structure of RNA (mRNA, rRNA and tRNA).)
  12. Replication, transcription, translation. (Description of transcription and post-transcriptional modifications. Difference between prokaryotes and eukaryotes. What are introns and exons. What is splicing. Explaining what the genetic code is. Describing translation. What is a codon and anticodon. What are ribosomes.)
 2/2/0 z, Zk 5
B834002 Professional English Language B

Annotation

The aim of the course is to develop communication skills with special focus on the specific features of professional language, to enhance the acquired knowledge of grammar and vocabulary. The covered topics include food, drugs, materials, fuels and energy, environmental technology and chemical engineering. One lesson is dedicated to presentation skills.

Syllabus

  1. Presentations
  2. Food Analysis
  3. Food Preservation and Biotechnologies
  4. Administration and Function of Drugs
  5. Drug Discovery and Development
  6. Types and Properties of Materials
  7. Materials of the Future
  8. Energy Sources
  9. Fuels
  10. Water Technology
  11. Waste Technology
  12. What is Chemical Engineering
  13. Chemical Engineering Jobs and Projects
  14. Revision
 0/2/0 z, Zk 3
B101009 Bioinformatics: Specialisation Laboratory I

Annotation

Students will learn about laboratory safety, basic laboratory equipment and experimental procedures used in inorganic and organic chemistry. Preparations and qualitative reactions will complement the theoretical knowledge of properties of elements and inorganic compounds. Working on several simple organic syntheses, students will acquire the requisite skills for the preparation and characterization of organic compounds. Final grade is based not only on the performance in the laboratory, but also on the knowledge of simple calculations (stoichiometry and preparation of solutions) and the chemical principles of procedures carried out.

Syllabus

  1. Laboratory safety, rules, and protocols.
  2. Basic inorganic laboratory equipment.
  3. Basic laboratory procedures - dissolution, filtration, evaporation, precipitation, and decantation.
  4. Basic laboratory operations - crystallization, weighing, determination of density, pH measurement.
  5. Redox reactions - carrying out in solution and solid phase.
  6. Chemistry of nonmetals - reactions of nonmetals and their compounds.
  7. Important qualitative reactions of selected anions, their determination in an unknown sample.
  8. Basic organic laboratory equipment.
  9. Building of reaction apparatuses and basic operations in organic synthesis.
  10. Selected one-step organic syntheses including isolation and identification of products, heating with stirring under a reflux condenser.
  11. Crystallization in organic laboratory.
  12. Extraction.
  13. Distillation under ambient pressure.
  14. Determination of melting point, GLC chromatography of compounds prepared.
 0/0/3 kz 2
B500008 FIT Algorithms and Graphs 1

Annotation

The course covers the basics of efficient algorithm design, data structures, and graph theory, belonging to the core knowledge of every computing curriculum.

Syllabus

  1. Motivation, graph definition, important types of graphs, undirected graphs, graph representation, subgraphs.
  2. Connectivity, connected components, DFS, directed graphs, trees.
  3. Spanning trees, distances in graphs, BFS, topological ordering.
  4. Basic sorting algorithms with the quadratic time complexity. Binary heap as a partially ordered structure, HeapSort.
  5. Extendable array, amortized complexity. Binomial Heaps.
  6. Operations and properties of binary search trees, balancing strategies, and AVL trees.
  7. Randomized algorithms. Introduction to probability theory. Hash tables and strategies of collision resolving.
  8. Recursive algorithms and Divide and Conquer algorithms.
  9. QuickSort. Lower bound of complexity for sorting problem in the comparison model. Special sorting algorithms.
  10. Dynamic programming.
  11. Minimum spanning trees of edge-labelled graphs. Jarníks algorithm and Kruskals algorithm and their implementations.
  12. Shortest paths algorithms on edge-labeled graphs.
 2/2/0 z, Zk 5
B143008 Python Programming

Annotation

In this course students will gain knowledge of programming language Python, its datatype system and accompanying programming constructs. Text and binary data processing together with Python specific approach will be emphasized. Also information about changes between 2.x and 3.x versions of Python language will be discussed.

Syllabus

  1. History and overview of Python.
  2. Basic data structures and control flow tools. Exceptions.
  3. Functions and their special role in Python.
  4. Modules and their usage.
  5. Classes. Magic methods.
  6. Textual and binary input/output. Serialization of data structures.
  7. User input. Subprocess handling. Foreign function interface.
  8. Testing and debugging.
  9. Selected internal and external libraries.
 2/2/0 z, Zk 5
Compulsorily optional courses
B110004 Organic Chemistry II

Annotation

This course is continuation of Organic chemistry I. The course of Organic chemistry II is based on the description of organic reactions according to the mechanistic principles. It also includes chemistry of natural compounds (carbohydrates, amino acids, peptides, nucleic acids) as well as basics of heterocyclic chemistry.

Syllabus

  1. Organic reactions, types, mechanisms, acid-base equilibrium.
  2. Nucleophilic substitution on saturated carbon. Mechanism, stereochemistry, applications.
  3. Elimination E1 and E2. Mechanism, stereochemistry, application.
  4. Nucleophilic addition on unsaturated carbon.
  5. Nucleophilic substitution on unsaturated carbon.
  6. Chemistry of enoles and enolates.
  7. Electrophilic additions on unsaturated systems.
  8. Electrophilic substitution on unsaturated systems.
  9. Nucleophilic substitution on aromatic compounds.
  10. Heterocycles. Basic types of five and six membered heterocycles, synthesis and reactivity.
  11. Radical reactions, halogenation, additions of HBr and thiols.
  12. Oxidation and reduction.
  13. Carbohydrates. Structure, stereochemistry, chemical properties.
  14. Aminoacids, peptides. Structure, chemical properties, synthesis.
 2/2/0 z, Zk 5
B444004 Physics II

Annotation

The subject Physics II builds on the subject Physics I and is dedicated to selected topics in electromagnetic field theory, quantum mechanics, solid state physics, nuclear physics and elementary particle physics. The content of the subject is adjusted to give the students the foundation required to proceed to following courses of the Bachelor study program.

Syllabus

  1. Inertial and non-inertial frames of reference, relativistic dynamics, the principle of equivalence.
  2. Electromagnetic field: Gauss´law, induced electric fields, induced magnetic fields,dielectrics, magnetic materials, Maxwell's equations.
  3. Electromagnetic waves: Traveling, intenzity, energy transport, polarization, optical activity.
  4. Photons and the wave nature of particles: Compton effect, particle-wave duality, de Broglie wavelength, the uncertainty principle.
  5. Roots of the quantum theory: Schrödinger equation,interpretation of the wave function, probability density, operators.
  6. Solution of the Schrödinger equation I: Particle in infinite potential well, energy level diagram.
  7. Solutions of the Schrödinger equation II: Harmonic oscillator, tunneling.
  8. The hydrogen atom I: Bohr theory,energy level diagram, series of spectral lines.
  9. The hydrogen atom II: Quantum solution, hydrogen atom wave functions, energy eigenvalues,radial probality density, quantum numbers.
  10. Atom in magnetic field: The Zeeman effect, electron spin, splitting of the spectral line.
  11. Many - electron atoms: central field approximation, Pauli exclusion principle, electronic configuration, Hund's rules.
  12. Fundamentals of solid state physics I: Band model, Fermi energy, intrinsic and doped semiconductor, PN transition.
  13. Fundamentals of solid state physics II: Contact phenomenon, Seebeck effect, Peltier effect, piezoelectricity, photo diodes.
  14. Fundamentals of nuclear physics: Properties of nuclei, radioactivity, nuclear reactions. Elementary particles: fermions and bosons, quarks and leptons, forces.
 2/2/0 z, Zk 5

summer semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B320024 Biochemistry II

Annotation

The course is a follow-up to the basic course Biochemistry I and should lead students to a broader understanding of biological and biochemical relationships. The individual lecture topics are therefore chosen to bring together knowledge from various areas of biochemistry (metabolic processes, regulation and signaling, molecular genetics, immunology) and explain the possibilities of their practical application (e.g. in clinical biochemistry or the development of new drugs).

Syllabus

  1. Biochemistry and an introduction to the world of ‘omics’
  2. Coordination of metabolic functions in multicellular organisms
  3. Regulatory and signaling mechanisms in different organisms
  4. 200 different posttranslational modifications of proteins
  5. Enzymes - medical and biotechnological aspects of their use
  6. Principles of the immune system and related disorders
  7. The importance of antibodies in medicine and other fields
  8. Principles of molecular genetics
  9. Practical aspects of molecular genetics
  10. Principles of clinical biochemistry
  11. Invited lecture
  12. Discussion of inappropriate or misrepresented biochemical information, selection of appropriate topics for projects
  13. Consultation of projects
  14. Presentation of projects
 2/0/0 Zk 3
B402011 Introduction to Spectral Methods

Annotation

The course introduces the basic overview of spectral methods used for pharmaceutical analysis. It is dedicated to methods of both elemental and molecular analysis. Furthermore, detection, identification and quantification of both active ingredients and excipients by methods of molecular spectroscopy is discussed. The attention is focused on simple data evaluation either from the qualitative point of view using spectral libraries, or to obtain quantitative results using simple regression models.

Syllabus

  1. Classification of spectroscopic methods based on their principles and analytical applications
  2. Spectral methods for elemental pharmaceutical analysis - X-ray fluorescence analysis
  3. Quantitative X-ray fluorescence analysis
  4. Spectral methods for elemental pharmaceutical analysis - optical atomic spectrometry
  5. Spectral methods for elemental pharmaceutical analysis - inorganic mass spectrometry
  6. Methods of molecular spectroscopy - spectrophotometry, luminescence techniques
  7. Identification of active ingredients and excipients - the use of spectral libraries and databases
  8. Detection and identification of active ingredients and excipients - infrared spectrometry
  9. Detection and identification of active ingredients and excipients - Ramanova spectrometry
  10. Spectral methods for identification and quantification - NIR spectrometry
  11. Methods of molecular spectrometry for quantitative pharmaceutical analysis
  12. NMR spectrometry for solution analysis
  13. Quantitative NMR spectrometry
  14. Mass spectrometry for identification of pharmaceutical ingredients
 2/0/0 z, Zk 3
B143002 Essential Bioinformatics

Annotation

This lecture introduces students to the fundamentals of bioinformatics, a multidisciplinary field that combines computer science, statistics, and biology. Bioinformatics focuses on the storage, organization, retrieval, and, in particular, the analysis and interpretation of large biological datasets. These data include, for example, nucleic acid and protein sequences, their structure, function, and interactions. Students will become familiar with the basic concepts of bioinformatics and tools of computational biology. During the practical sessions, the use and details of commonly used online tools and resources will be demonstrated.

Syllabus

  1. Cell biology summary Soubor
  2. DNA recombinant technology, genome maps, Sanger sequencing Soubor
  3. Genome mapping and sequencing, human genome project
  4. Pairwise sequence alignment - homology and similarity, basic principles of alignment
  5. Pairwise sequence alignment - scoring, substitution matrices PAM and BLOSUM, dot plot
  6. Searching in sequence databases, BLAST
  7. Multiple sequence alignment - scoring and creation
  8. Molecular phylogenetic analysis - molecular evolution, phylogenetic trees, models of evolution, methods of phylogenetic trees construction
  9. Structure of biomacromolecules - Protein Databank, protein structure classification - SCOP and CATH
  10. Prediction of the secondary protein structure
  11. Prediction of the tertiary protein structure - homology modeling, threading, ab initio methods, CASP
  12. RNA structure and its prediction
 2/2/0 z, Zk 5
B319001 Biology of the Cell

Annotation

The Biology of the Cell course focuses on deepening knowledge of general and cell biology, with an emphasis on understanding the fundamental principles of key cellular processes and their interconnections. It covers both general mechanisms and specific processes and structures characteristic of selected cell types, including eukaryotic and prokaryotic cells. The course also introduces basic and advanced methods for analyzing individual cells and cell populations.

Syllabus

  1. Introduction to Cell Biology – Organismal and Process Diversity, Model Organisms
  2. Structure of the Prokaryotic Cell – Bacteria, Archaea
  3. Bacteria – Membrane Transport
  4. Bacterial Growth and Cell Division
  5. Bacterial Differentiation and Dormancy, Communication, and Environmental Responses
  6. Animal Eukaryotic Cell: Cellular Compartmentalization and Protein Transport, Exocytosis, Endocytosis
  7. Animal Eukaryotic Cell: Cytoskeleton and Cell Surface Structure
  8. Nuclear Architecture and Transport Across the Nuclear Pore
  9. Intercellular Interactions – Signaling
  10. Structure and Condensation of Eukaryotic Chromatin
  11. Cell Cycle and Its Regulation
  12. Structure of the Plant Cell, Its Growth and Reproduction
  13. Structure and Reproduction of Yeast and Fungal Cells
  14. Tools for Cell Imaging and Population Analysis
 2/0/0 z, Zk 3
B500004 FIT Database Systems

Annotation

Students are introduced to the database engine architecture and typical user roles. They are briefly introduced to various database models. They learn to design small databases (including integrity constraints) using a conceptual model and implement them in a relational database engine. They get a hands-on experience with the SQL language, as well as with its theoretical foundation - the relational database model. They learn the principles of normalizing a relational database schema. They understand the fundamental concepts of transaction processing, controlling parallel user access to a single data source, as well as recovering a database engine from a failure. They are briefly introduced to special ways of storing data in relational databases with respect to speed of access to large quantities of data. This introductory-level course does not cover: Administration of database systems, debugging and optimizing database applications, distributed database systems, data stores.

Syllabus

  1. Basic principles of database systems, architectures of database management systems.
  2. Conceptual, database, and physical level of view of data.
  3. Conceptual data model. Basic constructs, expression of integrity constraints.
  4. Relational data model. Relation, attributes, domains, relational database schema, relational algebra.
  5. Introduction to the SQL language: basics of the SELECT statement, basics of the SQL DDL.
  6. Design of a relational scheme by direct transformation from a conceptual scheme.
  7. The SQL language - advanced querying: aggregation, nested queries, set operations.
  8. The SQL language: parts DCL, DML, TCL.
  9. Transactions, error recovery, parallel access coordination, data protection.
  10. Functional dependencies, normal forms of relations, normalization of a relational scheme by decomposition.
  11. Physical level of view of data. Indexes and their use in relational databases. Basics of SQL query optimization.
  12. Nonrelational database models. Trends in databases.
  13. Access of applications to a (relational) database. Introduction to the concept of software engineering.
 2/3/0 z, Zk 5
B413003 Fundamentals of Statistics

Annotation

The Elementary Course of Statistics is aimed at undergraduate students. Students will learn basic statistical methods and gain insight into basic probability concepts. Data processing will be done using R software which is a programming language designed especially for statistical calculations and graphical outputs. It is a free software with quality help, and thanks to its great popularity in the statistical community, many blogs with tutorials, hints and sample examples can be found.

Syllabus

  1. Random events, probability and its properties, independence of random events, conditional probability
  2. Random variables, their probability distribution and characteristics
  3. Fundamental types of probability distributions (especially normal distribution)
  4. Random vectors and their distributions, correlation and independence of random variables
  5. Sum of large number of random variables — Central Limit Theorem, Law of Large Numbers
  6. Random sample, point estimate of expectation and variance, Maximum Likelihood and Bayesian estimators
  7. Confidence intervals — calculation and interpretation
  8. Testing of statistical hypotheses — basic principle, type I and II errors, interpretation of results (p-value), basic parametric and nonparametric tests
  9. ANOVA
  10. Test of independence of quantitative random variables (correlation test)
  11. Goodness-of-fit testing, test of independence in contingency tables
  12. Fundaments of regression analysis — linear, multiple, nonlinear
 1/2/0 z, Zk 4
B143009 Linear algebra and matrices

Annotation

Methods of liear algebra and matrix operations are key building blocks of various approaches to data analysis and prediction. Their knowledge, therefore, is indispensable in research fields such as multidimensional statistics or machine learning. The course is an introduction to linear algebra and matrix theory. The goal is to present not only practical procedures to solve specific tasks, but also a more general theoretical basis, enabling the students to orient themselves is less standard problems. Theoretical explanations will be supplemented by practical examples illustrating the discussed notions and methods.

Syllabus

  1. Numbers, functions, polynomials
  2. Vector space
  3. Basis, dimension, subspace
  4. Linear transformation
  5. Matrix of a linear transformation
  6. Linear equations, inverse matrices, change of basis
  7. Determinant
  8. Norm and inner product
  9. Method of least squares
  10. Operators on an inner product space
  11. Eigenvalues and eigenvectors
  12. Spectral theorem
  13. Quadratic forms
  14. Factorization of matrices
 2/1/0 z, Zk 4
Compulsorily optional courses
B320006 Bioanalytical Methods

Annotation

The course aims to familiarise students with the principles and applications of analytical approaches utilising specific interactions between biomolecules. The course emphasises methods that provide high specificity (biospecificity), sensitivity and low detection limits, which are essential for analysing complex biological samples. Students will acquire the theoretical foundations and practical knowledge necessary for the use of enzymatic methods, electromigration techniques, immunochemical approaches, genetic methods (especially the polymerase chain reaction and its variants), proteomics methods and other biochemical or microbiological analyses. The course aims to prepare students to select and use appropriate bioanalytical methods independently in research, clinical or diagnostic practice.

Syllabus

  1. Introduction: definition of bioanalytical methods and the basics of the isolation and stability of biological material.
  2. Enzyme methods: enzymes as analytical reagents; determination of substrates and activators; and enzyme methods in clinical and experimental practice.
  3. Immunochemical methods: principles; characterisation of antigen-antibody interactions; preparation and use of antibodies; immunoprecipitation methods and their use in practice; sensitive techniques (e.g. ELISA); methods using radionuclides.
  4. Electrophoretic methods: principles; SDS electrophoresis; isoelectric focusing; blotting techniques; characterisation of analytes after separation by electrophoretic methods; colour and chemiluminescent detection.
  5. Genetic methods: principles, polymerase chain reaction (PCR), detection of specific product sequences in situ and determination of the primary sequence of nucleic acids.
  6. In vitro techniques: use of cell lines in bioanalytical methods; biochemical and microbiological methods in analytical chemistry.
  7. Chromatographic techniques: liquid and gas chromatography; bioaffinity chromatography.
  8. OMICS methods: global characterisation and quantification of biomolecules.
  9. Detection limits and the use of selected bioanalytical methods.
 2/0/0 z, Zk 3
B111011 Trends in Drug Research and Development

Annotation

The subject presents the particular periods of the drug discovery process from searching for active structures to clinical testing. Emphasis is placed on the mutual relationships between biological activity of drugs, their chemical structures and physico-chemical properties.

Syllabus

  1. A historical overview of drug discovery
  2. The drug development process, preclinical and clinical testing
  3. Current trends in drug discovery, biologics, management of drug research and development
  4. Development of generic drugs, relationships between original and generic companies
  5. Modifications of drug structures, structure-activity relationships
  6. The LADME model, pharmacokinetics
  7. Pharmacodynamics, Drug-receptor interactions
  8. Physico-chemical properties of drugs and their parametrization
  9. QSAR and its practical impacts, regression analysis, QSAR descriptors
  10. Interpretation of regression relationships, dependent and independent variables, collinearity of parameters, selection of structure changes
  11. Current QSAR approaches, the CoMFA method, similarity models, lead structures identification, molecular modelling
 2/0/0 z, Zk 3

3. grade

winter semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B320015 Molecular genetics and DNA analysis

Annotation

The subject is focused on understanding heredity principles especially mechanisms and regulation of transfer of genetic information and gene expression in prokaryotic and eukaryotic organisms. Special emphasis will be put on the main regulatory processes mediated by proteins and RNA regulatory molecules. Other focus is on understanding the variability of genetic information due to mutations and recombination. The subject offers information on the most important methods of DNA analysis as PCR, DNA identification by STR analysis and sequencing. The students will learn basic basic principles of pharmacogenomics.

Syllabus

  1. Historic overview and basic genetic laws and terms
  2. Structure and function of nucleic acids, genome organization
  3. Prokaryotic replication, DNA polymerases, replisome complex.
  4. Eukaryotic replication, DNA polymerases, replisome complex
  5. Recombination, gene segregation
  6. Mutations
  7. Repair mechanisms
  8. DNA analysis – PCR, identification of persons, DNA sequencing
  9. Regulation of prokaryotic transcription
  10. Eukaryotic transcription
  11. Posttranscriptional modifications of RNA, regulatory roles of RNA
  12. Translation I
  13. Translation II, post-translational modifications
  14. Fundamentals of pharmacogenomics
 2/0/0 Zk 4
B143004 Bioinformatics seminar I

Annotation

In the course of the seminar, each student gets acquainted with the topic presented in selected scientific articles. The topic and methods should be close to his/her bachelor thesis. Based on the study of the articles, the student then prepares a written presentation. Besides that, he/she prepares and performs an oral presentation followed by discussion.

Syllabus

  1. Assignment of seminar projects
  2. Information resources in bioinformatics
  3. Graphical presentation of scientific data
  4. Publication process - peer review
  5. Publication process - technical details
  6. Presentation of results and rhetorics
  7. Project preparation and presentation
 0/3/0 kz 3
B143001 Chemical Informatics

Annotation

Introductory course aimed at getting basic necessary skills for work with scientific chemistry literature, chemistry and multiple-fields databases. Hands-on training are integral part of the course, ensuring required skills are properly trained.

Syllabus

  1. Introduction, information flow in science
  2. Scholar article - structure, citations
  3. Identifiers of publications - ISBN, ISSN, DOI. Boole algebra, Internet search engines
  4. Citations, citation databases: Web of Science, Scopus
  5. Chemical structures - representation, identifiers, linear notation, connection tables, structure editors
  6. Chemical Abstracts - history, structure of the printed version. SciFinder - introduction, bibliographic searching
  7. Chemical Abstracts - chemical compounds - nomenclature, CAS RN, summary formulas. Bibliographic data for different types of processed documents. SciFinder - structure and reaction searching
  8. Beilstein and Gmelin - history. Reaxys database
  9. Patents - patenting procedure
  10. Standards - standards development, types of standards. ČSN, ISO, CEN
  11. Publishing process - past, present, future. Open access
  12. Copyright
  13. Excursion to joint ICT Prague and NTK library
 1/1/0 kz 2
B320008 Bioinformatics programm Laboratory II

Annotation

The course provides training in the techniques used in routine molecular biology methods producing data, which are often subject to bioinformatics analysis. It aims at methods of isolation and analysis of DNA sequences and electrophoretic separation of target proteins. The course objectives further include: good laboratory practice, the rules of organization of an experiment and appropriate the interpretation of data.

Syllabus

  1. Operational safety in laboratory, good laboratory practice and recording an experiment
  2. Introduction to course organization and the proper use of specific labware and chemicals
  3. Small-scale izolation of plasmid DNA
  4. Restriction digestion of plasmid DNA
  5. Electrophoretic analysis of the fragments of digested plasmid
  6. Polymerase chain reaction (PCR)
  7. Electrophoretic analysis to verify a PCR amplicon correct
  8. DNA sequencing reaction
  9. Analysis of sequencing products and reading the DNA sequence
  10. Preparation of an extract from cells producing a recombinant protein
  11. Electrophoretic separation of cell-free extract and of isolated recombinant protein
  12. Recording and interpretation of the electrophoreogram of separated proteins
  13. Discussion about optional experimental settings and their impact on results
  14. Completion of final report
 0/0/2 kz 1
B500010 FIT Machine Learning I

Annotation

The goal of this course is to introduce students to the basic methods of machine learning. They get theoretical understanding and practical working knowledge of regression and classification models in the supervised learning scenario and clustering models in the unsupervised scenario. Students will be aware of the relationships between model bias and variance, and know the fundamentals of assessing model quality. Moreover, they learn the basic techniques of data preprocessing and multidimensional data visualization. In practical demonstrations, pandas and scikit libraries in Python will be used.

Syllabus

  1. Introduction and basic concepts of Machine Learning
  2. Supervised learning setup, Classification setup, Decision trees
  3. Regression setup, K-nearest neighbors for classification and regression
  4. Linear regression - Ordinary least squares
  5. Linear regression - geometrical interpretation, numerical issues
  6. Ridge regression, bias-variance trade-off
  7. Logistic regression
  8. Ensemble methods (Random forests, Adaboost)
  9. Model evaluation, cross-validation
  10. Feature selection
  11. Unsupervised learning setup, Association rules
  12. Hierarchical clustering, the k-means algorithm
 2/2/0 z, Zk 5
B500005 FIT Automata and Grammars

Annotation

Students are introduced to basic theoretical and implementation principles of the following topics: construction, use and mutual transformations of finite automata, regular expressions, and regular grammars, context-free grammars, construction and use of pushdown automata, and translation grammars and transducers. They know the hierarchy of formal languages and they understand the relationships between formal languages and automata. They are introduced to the Turing machine and complexity classes P and NP.

Syllabus

  1. Basic notions, Chomsky hierarchy.
  2. Deterministic and nondeterministic finite automata.
  3. Operations on automata.
  4. Regular expressions.
  5. Conversions between regular grammars, regular expressions, and finite automata.
  6. Properties of regular languages.
  7. Context-free grammars.
  8. Pushdown automata. Parsing.
  9. Translation grammars and transducers.
  10. Context-sensitive, recursively enumerable and recursive languages. Turing machine.
  11. Time complexity, classes P and NP.
  12. Program and circuit implementation of finite automata.
  13. Finite automaton as a lexical analyzer.
 2/2/0 z, Zk 5
B143011 Applied Bioinformatics and Cheminformatics

Annotation

The course provides students with insight into the practical use of bioinformatics and cheminformatics, teaches them to work with essential software tools required for key tasks in these fields, develops analytical thinking for solving real-world problems in practice, and integrates skills acquired during their studies so far.

Syllabus

  1. Introduction to bioinformatics and cheminformatics. Case studies from literature and practice.
  2. Bioinformatics 1 – content to be supplemented.
  3. Bioinformatics 2 – content to be supplemented.
  4. Bioinformatics 3 – content to be supplemented.
  5. Bioinformatics 4 – content to be supplemented.
  6. Bioinformatics 5 – content to be supplemented.
  7. Basic cheminformatics tools {molecular similarity; structural identifiers (InChI, SMILES); RDKit library}
  8. Virtual screening {preprocessing of chemical structures; searching for similar molecules (using fingerprints and pharmacophore models); visualization of chemical space}
  9. QSAR modeling {ML methods in virtual screening; manifestations of typical ML problems on chemical data; specifics of ML model validation on chemical datasets}
  10. Molecular docking {important protein-ligand interactions; basics of molecular modeling (force fields, scoring functions); applications of docking in virtual screening
  11. Assignment and processing of independent project
  12. Project presentation
 2/2/0 kz 5
Compulsorily optional courses
B403011 Computational Chemistry

Annotation

The course is an excursion to modern computational chemistry. Half of the course is devoted to the necessary theory, the other half are examples and exercises. The course covers the quantum tutorial (program Gaussian), molecular simulation (MACSIMUS), computer biochemistry (PyMOL) and the properties of substances.

Syllabus

  1. Introduction to computational chemistry
  2. From electrons to molecules: potential energy and its calculation by the methods of quantum chemistry
  3. Structure of molecules and molecular complexes
  4. Energetics of chemical reactions in the gas phase and in solution (reaction energy, activation energy)
  5. Calculation of molecular properties (electrical properties, spectroscopic characteristics)
  6. Classical molecular modeling, description of molecules by the force field, structure and the radial distribution function
  7. Pseudoexperiments using Monte Carlo and molecular dynamics
  8. Laboratory of molecular dynamics I: model of NaCl, crystal, melt, melting temperature
  9. Laboratory of molecular dynamics II: solvation and water structure around different ions and non-polar solutes
  10. What is interesting in the world of modern genomics and proteomics
  11. Strukture bioinformatics and structural databases
  12. Visualizing biomolecules in the program PyMol
  13. Database of physico-chemical properties
  14. Seminar: presentation of student work
 2/0/0 Zk 3
B111008 Human Biology

Annotation

The main aim of education in Biology of Man is to obtain the basic information from biology of man and clinical genetics; it means to be able to understand ontogenesis, inheritance laws, molecular and/or genetic nature of processes in organism, individuality of every person (on molecular level, physical and mental level as well as individuality of interaction with environment ...) and consider possibilities in the development of new drugs.

Syllabus

  1. Prokaryote, Eukaryote. Eukaryotic cell; Cell cycle and its regulation; Cell signalization. Tissue; Organism.
  2. J. G. Mendel and his laws of inheritance; Gene, Alleles, Genotype, Phenotype; Monogenic inheritance; Interaction of non-allelic genes; Multifactorial inheritance.
  3. Molecular and biochemical reasons of inherited diseases; Prevention and treatment; Pedigree analysis; Pharmacogenetics.
  4. Cytogenetics; Human karyotype; Chromosome number and structure; techniques of examination; Disorders of the autosomes and sex chromosomes; in vitro cultivation of cells.
  5. Mitosis; Meiosis and its disturbances; Nondisjunction; Examples of syndromes; Gametogenesis.
  6. Genetic linkage; crossing-over; genetic mapping (indirect and physical); Haplotype; Application of genetic linkage - Indirect DNA diagnostics.
  7. Genetics of embryonic development; Sex differentiation and its disturbances; Apoptosis; Ontogenesis; Molecular aspects of Aging.
  8. Molecular genetics; DNA structure and function; Replication; RNA (mRNA, tRNA, rRNA) - structure and function; Transcription and RNA processing; Ribosome; Genetic code; Translation.
  9. Gene structure and function; Nucleic acid polymorphisms; Gene polymorphisms; SNP; Gene mutations - types and effects; Direct and indirect methods of DNA diagnostics. Mutagenic and teratogenic factors of environment.
  10. Multifactorial inheritance; Heritability; Diseases; Prevention and treatment - life style, pharmacotherapy, nutrition.
  11. Population; Castle-Hardy-Weinberg law; Factors affecting C-H-W equilibrium - mutations, selection; Genetic drift and gene flow. Consanguinity; Inbreeding; Evolution of human species - macro- and micro-evolution
  12. Immunogenetics; Immunity - non-specific, specific; Antigenes; Antibodies; Blood groups - genetics and clinical importance; Haemolytic disease of the newborn; B and T lymphocytes; Function of immunocompetent cells; Cytokines; Immunoglobulin -structure and function; Histocompatibility - Major histocompatibility complex - HLA locus of man.
  13. Transplantation; Transplantation antigenes; Transplantation principles; Haplotype; GVHR (transplantation of bone marrow); Immunotolerance; Immunodeficiency; Immunosuppression; Immunity and tumours.
  14. Oncogenetics; Protooncogenes, tumour-suppressor genes, mutator genes; Benign and malignant tumours; Angiogenesis; Metastasis; Cancer families; Cytogenetic analysis of tumour cells; New methods of treatment according to genetic
 2/1/0 z, Zk 4

summer semester

CodeCourse nameP/C/LExaminationCredits
Compulsory courses
B963001 Bachelor Thesis 0/12/0 z 15
B500009 FIT Advanced SQL

Annotation

Module is based on knowledge obtained in BI-DBS. Students become familiar with advanced relational and non- relational features of SQL language. In particular stored program unites, triggers, recursive queries, OLAP support, object-relational constructions. Part of the course is dedicated to practical database optimization from the point of view of specialized database structures like indexes, clusters, index-organized tables, and materialized views. as well as from the point of view query optimization. Execution plan and possibilities of its. changes will be discussed. Lectures will usually discuss SQL standard, but many features will be demonstrated on Oracle DBMS. Seminars are based on Oracle DBMS and partially on PostgreSQL.

Syllabus

  1. Program of seminars, organization, structure and requirements for semester project
  2. SQL review, MERGE, OLAP support
  3. Consultation to semester project, the first check point
  4. PL/SQL exercises
  5. Consultation to semester project, the second check point
  6. SQL query optimization, special tools for SQL query optimization
  7. Structures for fast data access
  8. PostgreSQL - SQL queries optimization basics, pgfounie script
  9. Consultation to semester project
  10. Object relational features, semester project evaluation
 0/3/0 kz 4
B500011 FIT Machine Learning II

Annotation

The goal of this course is to introduce students to the selected advanced methods of machine learning. In the supervised learning scenario, they, in particular, learn kernel methods and neural networks. In the unsupervised learning scenario students learn the principal component analysis and other dimensionality reduction methods. Moreover, students get the basic principles of reinforcement learning and natural language processing.

Syllabus

  1. Linear basis expansion, Kernel regression
  2. Support vector machines for classification
  3. Dimensionality reduction - Principal component analysis
  4. Dimensionality reduction - Linear discriminant analysis, Locally linear embedding
  5. Generative models - Naive Bayes
  6. Neural Networks - Perceptron, multi-layer perceptron, deep learning
  7. Neural Networks - backpropagation, regularization
  8. Neural Networks - convolutional neural networks
  9. Neural networks - recurrent neural networks, modern trends
  10. Reinforcement learning - introduction, multi-armed bandit
  11. Reinforcement learning - Markov decision processes
  12. Natural language processing
 2/2/0 z, Zk 5
B143005 Bioinformatics Seminar II

Annotation

In the Bioinformatics seminar II, students will be given the opportunity to discuss and solve scientific problems emerged during their work on the bachelor thesis. An important part of the seminar is also a "test run" of the bachelor's defense, i.e., the preparation of the presentation and its demonstration in front of the audience.

Syllabus

  1. Presentation of topics of bachelor theses
  2. Identification of problems during bachelor theses solving
  3. Consultations and problem solving
  4. Preparation of the bachelor defense
  5. Presentation of the bachelor thesis and its defense in front of the audience
 0/3/0 kz 3