Bilogical and medical databases
0800-BIOMBD
The aim of the course is to familiarize students with issues related to searching and combining information from online biological and medical databases, such as databases of genomic and protein sequences, a database of protein structures, a database of diseases and drugs. During the course, students will learn not only how a typical database is built, but also learn about the mechanisms of searching for sequential databases, and in the case of applied computer science students will learn to program tools for searching databases. Students will learn how to combine information from different databases to draw the right conclusions
Total student workload
Hours carried out with the participation of teachers (35 hours):
- participation in lectures -15 hours
- participation in classes - 15 hours
- consultation with the academic teacher - 5 hour
Time devoted to individual work of a student (40 hours):
- preparation for exercises - 15 hours
- writing works, projects - 15 hours
- reading literature - 10 hours
Total: 75 hours (3 ECTS)
Learning outcomes - knowledge
W1 - has knowledge in the field of chemistry, computer science and biology necessary to search for information in databases, can independently build and search a simple database (Informatics K_W01; physics K_W01; technical physics K_W01)
W2 - knows the basic laws of biology, molecular biology, chemistry; can describe the basic components of living matter, and look for information about it in databases. Can find information about medicines (Informatics K_W05, physics K_W05, technical physics K_W02)
W3 - understands the role of IT experiment in scientific research methodology; is aware of the technical and technological limitations of the software in searching databases (Informatics K_W06, physics K_W02, technical physics K_W03)
W4 - knows the basic databases related to biology and medicine, knows advanced tools to search for information important in the biology of chemistry and medicine (Informatics K_W01, technical physics K_W07)
W5 - has the knowledge to work in a secondary way independently and in a group, performing various types of professional roles (Informatics K_W04)
W6 - has detailed knowledge related to the specialty studied (Informatics, Technical Physics K_W06)
W7 - has in-depth knowledge of mathematics useful for advanced aspects of bioinformatics (Informatics and technical physics K_W01)
Learning outcomes - skills
U1 - effectively knows how to search for the necessary information to solve IT problems, has the ability to independently search for and use information in the field of computer science and related fields (e.g., bioinformatics, biological and mega databases) (Informatics, technical physics K_U01)
U2 - has expanded skills of independent work, is able to determine the necessary scope of knowledge that needs to be acquired to implement a specific IT project, has the ability to acquire knowledge / learn, develop his knowledge, uses a variety of information access techniques (Informatics KU_04 and K_U05 , Technical Physics K_U09)
U3 - can design extensions or improvements to IT projects, increase efficiency by using more advanced algorithms, or change the technologies of IT infrastructure devices (Informatics K_U07)
U4 - has the ability to use programming resources and databases related to the study of specialties (Informatics K_U09)
U5 - is able to assess, at a basic level, the usefulness of routine IT methods and tools, and choose and apply the right method and tools for typical IT tasks related to the creation and use of biological and medical databases (Informatics K_U11)
U6 - Can present in written or oral form the results obtained from database searches, is able to debate with specialists. (Technical physics K_U07)
Learning outcomes - social competencies
K1 - understands the need for continuous training caused by the emergence of new achievements, new technologies, etc. understands the need to exchange information in groups of people involved in computer science, understands the possibilities offered by academic education, can critically assess knowledge (Informatics K_K01, physics K_K01, technical physics K_K01)
K2 - is aware of the effects of malfunctioning IT systems such as databases built by the student and search tools in databases, which can lead to moral and financial losses, and even loss of health or life threat (Informatics K_K02)
K3 - is able to demonstrate effectiveness in the implementation of projects of a social, scientific and research nature in the field of analysis of biological and medical databases, entering the study program or implemented outside the studies (Informatics K_K05, physics K_K03)
K4 - is able to convey information on the achievements of computer science and various aspects of the profession of computer science in a universally understandable way (Informatics K_U06)
K5 - understands the need to popularize information about biological and medical databases. (technical physics K_K03)
Expository teaching methods
- participatory lecture
- informative (conventional) lecture
- description
Exploratory teaching methods
- practical
- laboratory
Prerequisites
Elementary knowledge (high school level) in physics, chemistry and biology. Basics of Linux system usage
Course coordinators
Assessment criteria
Completion of classes (for assessment) will take place on the basis of attendance and completion projects verifying knowledge and skills developed in groups or individually. (W1, W2, W3, W4, W5, W6, W7 ,U1, U2, U3, U4, U5, U6, U7, U8, K2, K3, K4).
Bibliography
"Blast" I. Korf, M. Yandell J. Bedell, O'Reilly Media, Inc. 2003
"Bioinformatics" A. Baxevanisa B. Ouellette'a Wiley 2003 or newer
"Bioinformatics and molecular evolution" P. Higgs, T. Attwood, Wiley-Blackwell 2005 or newer
Additional information
Additional information (registration calendar, class conductors,
localization and schedules of classes), might be available in the USOSweb system: