Models in System Biology, 2 credits

Systembiologisk modellering, 2 hp

TBMT19

Course starting semester

Main field of study

Biotechnology

Course level

First cycle

Course type

Programme course

Examiner

Gunnar Cedersund

Director of studies or equivalent

Marcus Larsson

Education components

Preliminary scheduled hours: 18 h
Recommended self-study hours: 35 h

Possible deviation from course syllabus/programme syllabus

ECV = Elective / Compulsory / Voluntary

Course offered for		Semester	Period	Timetable module	Language	Campus	ECV
6CTBI	Engineering Biology, M Sc in Engineering	6 (Spring 2017)	1	3	English	Linköping, Valla	C

Main field of study

Biotechnology

Course level

First cycle

Advancement level

G2X

Course offered for

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

Basics courses in Chemistry, Biology and Mathematics

Intended learning outcomes

This course will provide experience in mathematical modeling of biological systems. After completing this course, the participant shall be able to:

explain why mathematical modeling is a tool in biological experimentation; explain some of the common mistakes
construct a mathematical model of a class of biological systems
analyzing, structuring and simulating mathematical models based on differential equations
use methods for structured modeling in systems biology
adapt mathematical models to measured data
validate mathematical models to measured data; basic statistical tests
use modern computerized tools for mathematical modeling in systems biology
apply and integrate this with knowledge from previous courses

Course content

Lectures, laboratory work covers:

Systems biology: what it is, methods, issues and opportunities.
Mathematical modeling. Types of models and their properties.
Software for mathematical modeling and simulation in systems biology.
System Identification: adaptation of mathematical models to experimental data.
Validation and use of mathematical models. Troubleshooting and uncertainty analysis

Teaching and working methods

The course consists of lectures and a large laboratory assignment and voluntary pre-assignments. The course is examined by two minor tests together with oral discussions of the laboratory work.
The course runs for the first three weeks during the spring semester.

Examination

UPG1

Tests

2 credits

U, G

Grades are given as ’Fail’ or *Pass’.

Grades

Two-grade scale, U, G

Department

Institutionen för medicinsk teknik

Director of Studies or equivalent

Marcus Larsson

Examiner

Gunnar Cedersund

Education components

Preliminary scheduled hours: 18 h
Recommended self-study hours: 35 h

Course literature

Additional literature

Websites

Gunnar’s Crash Course in Systems Biology. Online-lectures.

Compendia

Code	Name	Scope	Grading scale
UPG1	Tests	2 credits	U, G

Grades are given as ’Fail’ or *Pass’.

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)

Additional literature

Websites

Gunnar’s Crash Course in Systems Biology. Online-lectures.

Compendia

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
1. DISCIPLINARY KNOWLEDGE AND REASONING
	1.1 Knowledge of underlying mathematics and science (G1X level)	X	X	X	UPG1
	1.2 Fundamental engineering knowledge (G1X level)	X	X	X	UPG1
	1.3 Further knowledge, methods, and tools in one or several subjects in engineering or natural science (G2X level)	X	X	X	UPG1
	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	X	UPG1
	2.2 Experimentation, investigation, and knowledge discovery	X	X	X	UPG1
	2.3 System thinking	X	X	X	UPG1
	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			X	UPG1
4. CONCEIVING, DESIGNING, IMPLEMENTING AND OPERATING SYSTEMS IN THE ENTERPRISE, SOCIETAL AND ENVIRONMENTAL CONTEXT
	4.1 External, societal, and environmental context	X
	4.2 Enterprise and business context
	4.3 Conceiving, system engineering and management	X			UPG1
	4.4 Designing
	4.5 Implementing
	4.6 Operating	X			UPG1
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	X
	5.2 Economic conditions for knowledge development	X
	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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