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Advanced Bioinformatics, 6 credits

Avancerad bioinformatik, 6 hp

TFTB46

Course starting semester

Main field of study

Engineering Biology Chemical Biology

Course level

Second cycle

Course type

Programme course

Examiner

Björn Wallner

Director of studies or equivalent

Magdalena Svensson

Education components

Preliminary scheduled hours: 48 h
Recommended self-study hours: 112 h

Possible deviation from course syllabus/programme syllabus

ECV = Elective / Compulsory / Voluntary

Course offered for		Semester	Period	Timetable module	Language	Campus	ECV
6CKEB	Chemical Biology (Industrial Biotechnology and Production)	9 (Autumn 2017)	1	2	English	Linköping, Valla	E
6CKEB	Chemical Biology (Protein Science and Technology)	9 (Autumn 2017)	1	2	English	Linköping, Valla	C
6CTBI	Engineering Biology, M Sc in Engineering (Devices and Materials in Biomedicine)	9 (Autumn 2017)	1	2	English	Linköping, Valla	E
6CTBI	Engineering Biology, M Sc in Engineering (Industrial Biotechnology and Production)	9 (Autumn 2017)	1	2	English	Linköping, Valla	E

Main field of study

Engineering Biology, Chemical Biology

Course level

Second cycle

Advancement level

A1X

Course offered for

Chemical Biology
Engineering Biology, M Sc in Engineering

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

Biochemistry, Cellbiology, Microbiology, Gene technology and molecular genetics, Bioinformatics.

Intended learning outcomes

In molecular biology, bioinformatics has become an important tool to manage and take advantage of the large amounts of valuable data produced. Computerized analysis has a role as both a support for laboratory projects and a way to extract knowledge from existing data sets. The rapidly growing amount of information, however, there are new requirements to automate and make large-scale analyzes. This course aims to introduce technologies to meet this challenge. The topics covered by the course has many applications, but we select examples from bioinformatics.

After the course you should be able to:

Working in Unix
Structuring information for effective computer processing
Use a scripting language to solve bioinformatics problems.
Use code libraries in the area to facilitate programming
Create automated pipelines for various applications.

Course content

Working in Unix, introduction to Python, Good practice for scientific programming. Important code libraries for scientific programming, terminology in bioinformatics, databases and important software / methods.

Teaching and working methods

The teaching consists of lectures and practical exercises. Lectures presents underlying theory and applications. The practical laboratory work aims to exemplify and deepen knowledge on realistic problems and issues.

Examination

LAB1	Laboratory work	3 credits	U, G
UPG1	Written examination	3 credits	U, G

Grades

Two-grade scale, U, G

Department

Institutionen för fysik, kemi och biologi

Director of Studies or equivalent

Magdalena Svensson

Examiner

Björn Wallner

Education components

Preliminary scheduled hours: 48 h
Recommended self-study hours: 112 h

Course literature

Practical computing for biologists, Steven H.D. Haddock Vetenskapliga artiklar / Scientific articles

Code	Name	Scope	Grading scale
LAB1	Laboratory work	3 credits	U, G
UPG1	Written examination	3 credits	U, G

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.

Practical computing for biologists, Steven H.D. Haddock Vetenskapliga artiklar / Scientific articles

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	Modules	Comment
1. DISCIPLINARY KNOWLEDGE AND REASONING
	1.1 Knowledge of underlying mathematics and science (G1X level)
	1.2 Fundamental engineering knowledge (G1X level)
	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
	2.2 Experimentation, investigation, and knowledge discovery
	2.3 System thinking
	2.4 Attitudes, thought, and learning
	2.5 Ethics, equity, and other responsibilities
3. INTERPERSONAL SKILLS: TEAMWORK AND COMMUNICATION
	3.1 Teamwork
	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
	4.4 Designing
	4.5 Implementing
	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
	5.5 Presentation and evaluation of research or development projects

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