Databases for Bioinformatics, 6 credits

Databaser för bioinformatik, 6 hp

TDDD74

Main field of study

Biotechnology Computer Science and Engineering

Course level

First cycle

Course type

Programme course

Examiner

José M Pena

Director of studies or equivalent

Patrick Lambrix

Education components

Preliminary scheduled hours: 46 h
Recommended self-study hours: 114 h

Possible deviation from course syllabus/programme syllabus

ECV = Elective / Compulsory / Voluntary

Course offered for		Semester	Period	Timetable module	Language	Campus	ECV
6CMED		8 (Spring 2017)	2	4	Swedish/English	Linköping, Valla	E
6CMED	(Biomedical Modelling)	8 (Spring 2017)	2	4	Swedish/English	Linköping, Valla	E
6CTBI	Engineering Biology, M Sc in Engineering	4 (Spring 2017)	2	4	Swedish/English	Linköping, Valla	C

Main field of study

Biotechnology, Computer Science and Engineering

Course level

First cycle

Advancement level

G2X

Course offered for

Engineering Biology, M Sc in Engineering

Specific information

The course is not availble for exchange students

Entry requirements

Note: Admission requirements for non-programme students usually also include admission requirements for the programme and threshold requirements for progression within the programme, or corresponding.

Prerequisites

Basic programming course.

Intended learning outcomes

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.

Course content

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.

Teaching and working methods

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.

Examination

LAB1	Laboratory work and project	3 credits	U, G
TEN1	Written examination	3 credits	U, 3, 4, 5

Grades

Four-grade scale, LiU, U, 3, 4, 5

Other information

Supplementary courses: Advanced Data Models and Databases; data mining

Department

Institutionen för datavetenskap

Director of Studies or equivalent

Patrick Lambrix

Examiner

José M Pena

Course website and other links

http://www.ida.liu.se/~TDDD74/

Education components

Preliminary scheduled hours: 46 h
Recommended self-study hours: 114 h

Course literature

Elmasri, R. and Navathe, S. B. Fundamentals of Database Systems, 3e, 4e, 5e eller 6e upplaga, Addison Wesley. OBS: Den 6e upplagans titel är: Database Systems - Models, Languages, Design, and Application Programming. Artikelsamling 2015.

Code	Name	Scope	Grading scale
LAB1	Laboratory work and project	3 credits	U, G
TEN1	Written examination	3 credits	U, 3, 4, 5

Regulations (apply to LiU in its entirety)

The university is a government agency whose operations are regulated by legislation and ordinances, which include the Higher Education Act and the Higher Education Ordinance. In addition to legislation and ordinances, operations are subject to several policy documents. The Linköping University rule book collects currently valid decisions of a regulatory nature taken by the university board, the vice-chancellor and faculty/department boards.

LiU’s rule book for education at first-cycle and second-cycle levels is available at http://styrdokument.liu.se/Regelsamling/Innehall/Utbildning_pa_grund-_och_avancerad_niva.

Student rights and obligations (login required)
Linköping University common rules and regulations (in Swedish)

Course literature is preliminary.

Download

Download course literature list as PDF

Note: The course matrix might contain more information in Swedish.

I = Introduce, U = Teach, A = Utilize

		I	U	A
1. DISCIPLINARY KNOWLEDGE AND REASONING
	1.1 Knowledge of underlying mathematics and science (G1X level)			X
	1.2 Fundamental engineering knowledge (G1X level)		X	X
	1.3 Further knowledge, methods, and tools in one or several subjects in engineering or natural science (G2X level)
	1.4 Advanced knowledge, methods, and tools in one or several subjects in engineering or natural sciences (A1X level)
	1.5 Insight into current research and development work
2. PERSONAL AND PROFESSIONAL SKILLS AND ATTRIBUTES
	2.1 Analytical reasoning and problem solving		X	X
	2.2 Experimentation, investigation, and knowledge discovery		X	X
	2.3 System thinking		X	X
	2.4 Attitudes, thought, and learning		X	X
	2.5 Ethics, equity, and other responsibilities	X
3. INTERPERSONAL SKILLS: TEAMWORK AND COMMUNICATION
	3.1 Teamwork			X
	3.2 Communications
	3.3 Communication in foreign languages
4. CONCEIVING, DESIGNING, IMPLEMENTING AND OPERATING SYSTEMS IN THE ENTERPRISE, SOCIETAL AND ENVIRONMENTAL CONTEXT
	4.1 External, societal, and environmental context
	4.2 Enterprise and business context
	4.3 Conceiving, system engineering and management		X	X
	4.4 Designing		X	X
	4.5 Implementing		X	X
	4.6 Operating
5. PLANNING, EXECUTION AND PRESENTATION OF RESEARCH DEVELOPMENT PROJECTS WITH RESPECT TO SCIENTIFIC AND SOCIETAL NEEDS AND REQUIREMENTS
	5.1 Societal conditions, including economic, social, and ecological aspects of sustainable development for knowledge development
	5.2 Economic conditions for knowledge development
	5.3 Identification of needs, structuring and planning of research or development projects
	5.4 Execution of research or development projects	X
	5.5 Presentation and evaluation of research or development projects	X

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