The aim of studying and bibliography

The main aim of study: To obtain knowledge and skills in basic methods and bioinformatics tools

The general information about the module: The module realized in the form lectures (15 h) and laboratory (15 h) exercises.

Teaching materials: Bioinformatyka: materiały na portalu e-learning.prz.edu.pl.

Bibliography required to complete the module

Bibliography used during classes/laboratories/others

1

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Bioinformatyka: materiały na portalu e-learning.prz.edu.pl

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Bibliography to self-study

1	A. D. Baxevanis, B. F. F. Ouellette	Bioinformatyka . Podręcznik do analizy genów i białek	PWN, Warszawa .	2004
2	P. G. Higgs, T. K. Attwood	Bioinformatyka i ewolucja molekularna	PWN Warszawa.	2008
3	J.Xiong	Podstawy bioinformatyki	Wydawnictwa Uniwersytetu Warszawskiego.	2009

Basic requirements in category knowledge/skills/social competences

Formal requirements: Registration for current semester.

Basic requirements in category knowledge: Basic knowledge of organic chemistry and biochemistry.

Basic requirements in category skills: Fluent computer skills and knowledge of the Windows operating system

Basic requirements in category social competences: Ability to work individually and in a team of 2-3 persons.

Module outcomes

MEK	The student who completed the module	Types of classes / teaching methods leading to achieving a given outcome of teaching	Methods of verifying every mentioned outcome of teaching	Relationships with KEK	Relationships with PRK
01	Students can search for and retrieve information from bioinformatics databases	lecture, laboratory	written exam, test, observation of the task performance	K_W14+ K_U01++	P6S_UW P6S_WG
02	Student can visualize 3D models of protein structures.	lecture, laboratory, laboratory at which the student solves the problems.	test, observation of the task performance, report on the project	K_W03+ K_W14+ K_U08+ K_U09+	P6S_UO P6S_UW P6S_WG
03	The student is able to apply dedicated bioinformatic software to solve problems of molecular biology and biotechnology	lecture, laboratory	written exam, test, observation of the task performance, written report,	K_W01+ K_W14+ K_U08+ K_U10++	P6S_UW P6S_WG
04	The students can use the e-learning courses in the process of self-education.	lecture, laboratory	observation of the task performance	K_U02+ K_U06+++ K_K01++	P6S_KK P6S_KR P6S_UK P6S_UU

Attention: Depending on the epidemic situation, verification of the achieved learning outcomes specified in the study program, in particular credits and examinations at the end of specific classes, can be implemented remotely (real-time meetings).

The syllabus of the module

Sem.	TK	The content	realized in	MEK
3	TK01	Introduction to bioinformatics. Basic concepts. Bioinformatics databases: data formats and processing. Sequence alignment. Structural bioinformatics. Biological information retrival and analysis.	W01-W15	MEK01 MEK02 MEK03 MEK04
3	TK02	Practical bioinformatics: data formats, prmary data bases. Search and data analysis in bioinformatics.	L01-L03	MEK01 MEK03 MEK04
3	TK03	3D visualisation and analysis of protein in PDB database.	L04-L05	MEK02 MEK03 MEK04

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 3)		contact hours: 15.00 hours/sem.	complementing/reading through notes: 5.00 hours/sem. Studying the recommended bibliography: 5.00 hours/sem.
Laboratory (sem. 3)	The preparation for a Laboratory: 3.00 hours/sem. The preparation for a test: 5.00 hours/sem.	contact hours: 15.00 hours/sem.	Finishing/Making the report: 5.00 hours/sem.
Advice (sem. 3)
Credit (sem. 3)

The way of giving the component module grades and the final grade

The type of classes	The way of giving the final grade
Lecture	The pass note is granted to students with at least 50% of points from the written test.
Laboratory	Credit is granted for to the students who participated in all exercises, passed all control tests and submitted all required reports.
The final grade	The final note is an derivaticve of all points/partial notes collected from the module activities and precise rages are communicated before the test. The final note is calculated according to equation: K=a*wA+c*wC+l*wL (a-lecture coeff., c-tutorial coeff., l-laboratory/project coeff., w=1,0, w=0,9, w=0,8 receptively for the 1st, 2nd, 3rd attempt). The note is calculated only if all components have been passed. Values of coefficiants are presented to the students during the initial teaching session.

Sample problems

Required during the exam/when receiving the credit
(-)

Realized during classes/laboratories/projects
(-)

Others
(-)

Can a student use any teaching aids during the exam/when receiving the credit : no

The contents of the module are associated with the research profile: yes

1	M. Dżugan; A. Łyskowski; M. Miłek	Assessing the Antimicrobial Properties of Honey Protein Components through In Silico Comparative Peptide Composition and Distribution Analysis	2023
2	V. Csitkovits; K. Gruber; C. Kratky; B. Kräutler; A. Łyskowski	Structure-Based Demystification of Radical Catalysis by a Coenzyme B12 dependent Enzyme – Crystallographic Study of Glutamate Mutase with Cofactor Homologues	2022
3	K. Chen; Ł. Jaremko; M. Jaremko; A. Łyskowski	Genetic and Molecular Factors Determining Grain Weight in Rice	2021
4	D. Antos; M. Kołodziej; A. Łyskowski; W. Piątkowski; I. Poplewska; P. Szałański	Determination of protein crystallization kinetics by a through-flow small-angle X-ray scattering method	2019