| TDDD74 |
Databases for Bioinformatics, 6 ECTS credits.
/Databaser för bioinformatik/
For:
MED
TB
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OBS! |
The course is not availble for exchange students
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Prel. scheduled
hours: 46
Rec. self-study hours: 114
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Area of Education: Technology
Main field of studies: Computer Engieering
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Advancement level
(G1, G2, A): G2
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Aim:
The aim of this course is to give a thorough introduction to the theoretical and practical issues underlying the design and implementation of modern biological database systems that are used in bioinformatics research.
After the completion of the course you should:
- understand and be able to use important terminology in text-based information management in a correct way.
- be able to design a data model using EER diagrams.
- be able to design and use a relational database.
- understand the theory behind the relational model and how this affects good design of databases.
- understand which file structures in the database management system can be used to implement a database system.
- know the basic principles for indexing a database.
- understand which problems can occur when several users use the database and solutions to this.
- understand how a database can guarantee persistence of data och how this is solved using recovery and back-up.
- understand which problems can occur when a user needs to integrate information from different databases and solutions to this.
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Prerequisites: (valid for students admitted to programmes within which the course is offered)
Basic programming course.
Note: Admission requirements for non-programme students usually also include admission requirements for the programme and threshhold requirements for progression within the programme, or corresponding.
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Supplementary courses:
Advanced Data Models and Databases; data mining
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Organisation:
The course consists of lectures, laboratory work and a project. Some lectures are given in English. Lectures are devoted to theory and techniques. Database design and implementation techniques are practised in the laboratory work. During the project work a number of well-known biological databases are studied and a database system that integrates the information in these sources is implemented.
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Course contents:
Methods for storage of information: text, semi-structured data, data models, rules. Text: basic issues in information retrieval, conceptual models, file models, query mechanisms, ranking. Semi-structured data: conceptual model, query mechanisms. Data models: relational model, object-oriented model. Databases:
General database management systems (DBMS). Methods for data modelling and database design. Physical database. Data structures for databases. Query language. Multiple user issues: transactions, concurrency control and recovery. Integration of biological databases.
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Course literature:
Elmasri, R. and Navathe, S. B. Fundamentals of Database Systems, 3e, 4th, 5th or 6th edition, Addison Wesley.
OBSERVE: The title of the 6th edition is: Database Systems - Models, Languages, Design, and Application Programming.
Article collection 2015.
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Examination: |
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Written examinaton
Laboratory work and project
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3 ECTS
3 ECTS
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Course language is Swedish/English.
Department offering the course: IDA.
Director of Studies: Patrick Lambrix
Examiner: Olaf Hartig
Link to the course homepage at the department
Course Syllabus in Swedish
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