The aim of studying and bibliography

The main aim of study: Gain knowledge and skills in computer-aided research in biotechnology

The general information about the module: The module is realized in the form of lectures (15h) and problem exercises in computer laboratory (15 h)

Teaching materials: Materiały dydaktyczne dostepne on-line w portalu ZICh PRz oraz www.e-chemia.pl

Bibliography required to complete the module

Bibliography used during lectures

1	T. Stubblebine	Wyrażenia regularne. Leksykon kieszonkowy	Helion.	2008
2	R. L. Schwartz, T. Phoenix, B. d foy	Perl. Wprowadzenie	Helion.	2006
3	B.Dębska, G.Fic	Konspekty do wykładów opublikowane na stronie Zakładu Informatyki Chemicznej	ZICh PRz.	2012

Bibliography used during classes/laboratories/others

1

B. Dębska, G. Fic

Bioinformatyka II. Instrukcje do ćwiczeń laboratoryjnych

ZICh PRz.

2012

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:

Basic requirements in category knowledge: basic knowledge of biochemistry, molecular biology

Basic requirements in category skills: computer skills - Windows, search for information in the biological and chemical databases

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	can test and modify computer programs in Perl to solve simple problems in molecular biology and biotechnology	lecture, laboratory	test, observation of the task performance, project report,	K_W02++ K_W06+ K_U07++	P7S_UW P7S_WG
02	knows the basics of programming in Perl	lecture, laboratory	test, observation of the task performance, project report	K_W02++ K_U07++	P7S_UW P7S_WG
03	is able to use specialized computer programs for searching and for analysis of sequential information.	laboratory	test, observation of the task performance, project report	K_W02++ K_W06++ K_U01+ K_U07++	P7S_UW P7S_WG
04	can use the selected artificial intelligence methods to support engineering tasks and scientific research in the field of molecular biology and biotechnology	lecture, laboratory	test, written report	K_W02+++ K_W06+ K_U07++	P7S_UW P7S_WG

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
2	TK01	Artificial intelligence techniques in bioinformatics. Artificial neural networks	W01	MEK04
2	TK02	Graph theory and decision trees. Methods of presentation and interpretation of decision trees. Methods for generating phylogenetic trees	W02	MEK03 MEK04
2	TK03	Sequence similarity searching. Sequence matching algorithms	W03-W04	MEK03
2	TK04	Beginner’s introduction to PERL Programming Language. Perl in bioinformatics	W05-W06	MEK01 MEK02
2	TK05	Regular expression and their application in bioinformatics	W07	MEK01 MEK02
2	TK06	Sequence similarity searching.	L01	MEK03
2	TK07	PERL programming language in molecular biology	L03-L05	MEK01 MEK02
2	TK08	Genetic and physical maps	L02	MEK03

The student's effort

The type of classes	The work before classes	The participation in classes	The work after classes
Lecture (sem. 2)		contact hours: 15.00 hours/sem.	complementing/reading through notes: 2.00 hours/sem. Studying the recommended bibliography: 2.00 hours/sem.
Laboratory (sem. 2)	The preparation for a Laboratory: 5.00 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. 2)		The participation in Advice: 2.00 hours/sem.
Credit (sem. 2)	The preparation for a Credit: 3.00 hours/sem.	The written credit: 2.00 hours/sem.

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

The type of classes	The way of giving the final grade
Lecture
Laboratory	Credit all the laboratory (test, execution of exercises, report)
The final grade	Final grade (K): K= 0.5w L +0.5wW, L- positive evaluation of the lab; W - positive evaluation of the lecture, w - factor related to the time of credit, w= 1,0 first term, w = 0,9 second term , w = 0,8 third term.

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	J. Buczkowicz; T. Drzazga; G. Fic; M. Jaromin; P. Krajewski; P. Matysik; R. Mazur; P. Milczarski; T. Sikora; M. Szeliga; D. Tyrka; M. Tyrka; E. Witkowski	Selekcja genomowa pszenicy ozimej	2021
2	B. Dębska; B. Dębska; L. Lichołai	Evaluation of the Utility of Using Classification Algorithms when Designing New Polymer Composites	2019
3	B. Dębska; J. Duliban; K. Hęclik; J. Lubczak	Analysis of the Possibility and Conditions of Application of Methylene Blue to Determine the Activity of Radicals in Model System with Preaccelerated Cross-Linking of Polyester Resins	2019
4	B. Dębska; L. Dobrowolski; M. Inger; M. Jaromin; M. Wilk	Komputerowo-wspomagane obliczanie bilansu masowego i cieplnego instalacji chemicznej	2019