Education

The laboratory participates in the education activities related to the study field “Bioinformatics” at the Faculty of Informatics. The laboratory members are also involved in the extension and innovation of this program by courses covering the area of “Computational Systems Biology”.

This field of study targets students who would like to obtain basic knowledge in the area of computer science and at the same time learn how to apply this knowledge to the benefit of molecular biology, genetics, medicine and other recently established disciplines, such as bioinformatics, proteomics, genomics, and systems biology. The progress in these disciplines is often hindered by difficulties in communication between people with technical and biological education. However, the ever-growing biological data can not be dealt with without the use of modern algorithms and detailed knowledge of computer science.

The main goal of teaching Bioinformatics and Systems Biology at the Faculty of Informatics is to introduce this attractive interdisciplinary field of study to interested students, provide them with knowledge needed to understand existing problems and equip them with skills needed to solve many of them effectively. Areas currently using bioinformatics and systems biology include biology, modern biotechnology, medicine, pharmacy, and forensic science. A number of companies, especially abroad, develop software and hardware for scientific and practical needs. The potential for future development in this area is very good.

More details can be found in the Information System of Masaryk University by clicking on the course code below. The list presents courses taught by members of SYBILA that form the core of the study field. We also refer to SYBILA czech pages for additional information.

List of courses

PA052 - Introduction to Systems Biology

Syllabus

Course description: This is a bachelor-level course devoted to application of computer-scientific methods and tools in the emerging field of Systems Biology. The course is focused on functional aspects of mechanisms that drive living organisms. The main goal of this course is to show students that abstract computer-scientific and mathematical methods can be effectively employed for in silico modeling and analysis of living organisms. Moreover, to enhance practical skills, students have to apply some of the techniques and software tools to analysis of a small in silico model of some primitive organism in the range of a semestral project.

IV105 - Bioinformatics seminar

Syllabus

Course description: This seminar will lead the students into the fascinating world of molecules, genes and proteins by study of new methods presented in scientific papers. The Fall Term seminar (P series) will be titled “Prediction of protein function and structure from sequence”. The course will convene for 1hr weekly. The student will chose, study and present an appropriate papers chosen in cooperation with the lecturer.

IV107 - Bioinformatics I

Syllabus

Course description: Currently, bioinformatics is going through a period of unusual growth. Abilities to think and act as a bioinformatician (to work with large biological data-sets using modern computer science methods) are needed in many areas of science and applied disciplines, especially biology, medicine and chemistry. The first part of the course will be dedicated to basics of biology necessary for someone who has not studied biology to enter the field of bioinformatics. In the second part, important biological problems that can be best tackled by computers will be studied. Lectures will be given once a week (2hrs). Written examination will be given at the end of the semester.

IV108 - Bioinformatics II

Syllabus

Course description: Advanced bioinformatics course with explanations of the inner workings of selected algorithms, their advantages and disadvantages. Recent alternatives to common practices will be presented. The students should learn to evaluate or design methods for solving current problems in bioinformatics. Includes writing own code in the practical part of the course.

PB051 - Computational methods in Bioinformatics and Systems Biology

Syllabus

Course description: At the end of the course the student should be able to: select appropriate methods for a given problem; obtain and prepare necessary data; analyze the data (using their own program or publicly available solutions)

PA055 - Visualizing Complex Data

Syllabus

Course description: Students will get aquainted with complex data in bioinformatics and selected other disciplines and their visualization, using examples in R and PROCESSING languages or scientific literature.

IV114 Bioinformatics and Systems Biology Project

Syllabus

Course description: The students will be given a family of problems at the beginning of the semester. After discussion in class and with the lecturer, they will choose a problem to solve using computational approach. Results of their work will be presented towards the end of the semester in a student mini-conference using posters or a lecture/demo format. At the end of this course the students will be able to locate and analyze molecular data independently.

PA183 - Project in Systems Biology

Syllabus

Course description: At the end of the course students should be able to: search in public databases of biological knowledge; create an in silico model of a biological system; apply methods of computational systems biology to model analysis; predict hypotheses regarding emergent properties of the modeled biological system.

PB050 - Modelling and Prediction in Systems Biology

Syllabus

Course description: This course is devoted to applications of computer-scientific methods and tools in the emerging field of Systems Biology. The course is focused on functional aspects of mechanisms that drive living organisms. The main goal of this course is to show students that abstract computer-scientific and mathematical methods can be effectively employed for in silico modeling and analysis of living organisms. Moreover, to enhance practicle skills, students have to apply some of the techniques and software tools to analysis of a small in silico model of some primitive organism in the range of a semestral project.

PA054 - Formal Methods in Systems Biology

Syllabus

Course description: This is a course for master students focused on application of formal methods to system-level study of living organisms in terms of in silico models. The course refines the knowledge presented in PA052 Introduction to Systems Biology. The main goal is to offer students an opportunity to get knowledge necessary for efficient application of computer-scientific and mathematical skills in the applied research of Systems Biology. In the theoretical part, main principles of formal modeling and analysis of living organism functionality are explained. In the practical part, a choice of software tools is demonstrated, including the tools developed at Faculty of Informatics. Requirements for successful finishing of the course include ability to choose and apply suitable tools to solve a given biological problem.

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