Courses list

Wersja polska

Course code: BIS10017o14
Semester: 2014/2015 summer
Name: Databases
Major: Bioinformatics
Study Type: first cycle
Course type: compulsory
Study Semester: 3
ECTS points: 5
Hours (Lectures / Tutorials / Other): 15 / 30 / 0
Lecturer: dr Wojciech Jakubowski
Language of instruction: Polish
The course exclusively in Polish, with a possibility of support in English

Learning outcomes: Knowledge: - knows thestructure of a relational database, can provide database normalization and formulate a simple queries in SQL language. [BI_W10, BI_W11, BI_W12, BI_W14]; - mastered the method of processing data bases of nucleic and protein sequences, is able to determine the fitting of two sequences – understands the importance of the penalty function, he can write a script that searches for sequences containing the answer patterns. [BI_W10, BI_W11, BI_W12, BI_W14]. Skills: - mastered the structure of relational databases, understands the importance of normalization of the database, he can write a SQL statement for editing and searching the existing relational database. [BI_U01, BI_U04, BI_U06, BI_U09]; - knows the databases structure of nucleic and protein sequences, can in Python read alphanumerical sequences, understands and knows the algorithms for matching two sequences – can use the various functions of punishment, knowns sequential algorithms for searching databases. [BI_U01, BI_U04, BI_U06, BI_U09]. Personal and social competences (attitudes and behaviors): - isprepared to work with different database systems used in bioinformatics, can interact and work in a group, sees the need for constant updating of skills. [BI_K02, BI_K08].

Competences: Completing the course will allow students the efficient use of existing databases, creating meaningful bases for personal use and the free use of the information collected from the databases.

Prerequisites: mathematics, information technology

Course content: Match words with the pattern, regular expressions. Metrics. Measures of similarity between words and objects. String matching algorithms. Database storage structures. Database classification. Flat file database and relational database model. Database management systems. Database normalization. SQL - Structured Query Language. An object database - information. Importance of databases in bioinformatics.

Recommended literature: 1. Date C. J.: Relacyjne bazy danych dla praktyków, Helion 2006; 2. Hernandez M. J.: Bazy danych dla zwykłych śmiertelników. Mikom 2004; 3. Higgs, P. G., Attwood T. K.: Bioinformatyka i ewolucja molekularna. PWN 2008; 4. http://wazniak.mimuw.edu.pl/index.php?title=Bazy_danych 5. Dokumentacja wybranych baz bioinformatycznych (Fasta, Prosite, GenBank) 6. Dokumentacja wybranych systemów zarządzania relacyjnymi bazami danych (MySQL, PostgreSQL)

Assessment methods: Completion of laboratory training, 3 tests and individual project Minimum 60% of knowledge to pass

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