Postgraduate Course: Computational Systems Biology (INFR11039)
Course Outline
| School | School of Informatics |
College | College of Science and Engineering |
| Course type | Standard |
Availability | Available to all students |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Credits | 10 |
| Home subject area | Informatics |
Other subject area | None |
| Course website |
http://www.inf.ed.ac.uk/teaching/courses/csb |
Taught in Gaelic? | No |
| Course description | Systems Biology is the application of computational modelling and simulation to complex systems in biology. Examples include biochemical pathways, metabolic processes, protein complexes and information processing, genetic networks, self-organising systems, neuronal networks and cell-cell communication. This course will focus on the level of molecular and genetic systems and simulations. |
Entry Requirements (not applicable to Visiting Students)
| Pre-requisites |
Students MUST have passed:
Bioinformatics 1 (INFR11016)
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Co-requisites | It is RECOMMENDED that students also take
Bioinformatics 2 (INFU11058) OR
Models and Languages for Computational Systems Biology (INFR11047)
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| Prohibited Combinations | |
Other requirements | For Informatics PG and final year MInf students only, or by special permission of the School.
Bioinformatics 1 (or strong biological background).
Students are expected to have: - basic biological knowledge (BIO1 course) - basic mathematical knowledge of differential equations and linear algebra - basic programming skills, in any language. |
| Additional Costs | None |
Information for Visiting Students
| Pre-requisites | None |
| Displayed in Visiting Students Prospectus? | Yes |
Course Delivery Information
|
| Delivery period: 2011/12 Semester 2, Available to all students (SV1)
|
WebCT enabled: No |
Quota: None |
| Location |
Activity |
Description |
Weeks |
Monday |
Tuesday |
Wednesday |
Thursday |
Friday |
| Central | Lecture | | 1-11 | | 16:10 - 17:00 | | | | | Central | Lecture | | 1-11 | | | | | 16:10 - 17:00 |
| First Class |
Week 1, Tuesday, 16:10 - 17:00, Zone: Central. DHT 4.18 |
| Exam Information |
| Exam Diet |
Paper Name |
Hours:Minutes |
|
|
| Main Exam Diet S2 (April/May) | | 2:00 | | |
Summary of Intended Learning Outcomes
1 - Discuss the potential benefits and predictive value of systems biology approaches.
2 - Implement a molecular genetic model in an appropriate modelling framework.
3 - Compare and contrast existing models at the biochemical, genetic, proteomic and metabolic levels
4 - Discus the methods used to establish parameters in models and how to test and refine them.
5 - Discuss the mathematical basis for biomolecular simulations.
6 - Describe the limitations of modelling strategies. |
Assessment Information
Written Examination 70
Assessed Assignments 30
Oral Presentations 0
Assessment
A single piece of coursework that may involve implementation of a simulation or the modification and assessment of an existing model.
If delivered in semester 1, this course will have an option for semester 1 only visiting undergraduate students, providing assessment prior to the end of the calendar year. |
Special Arrangements
| None |
Additional Information
| Academic description |
Not entered |
| Syllabus |
Course Delivery
The course will be start with a series of core lectures introducing the main topics and will be complemented by home excersizes on simulations. The later half of the course will focus on exploring existing models, how they were established, their value and their limitations.
Topics covered
* Packages and methods for simulations
* Dynamics and design of cellular reaction networks
* Metabolic pathway analysis
* Network architecture
* Genetic regulatory networks
* Protein complexes
* Self-organisation in cellular systems
* Application of modelling and simulation to drug discovery
* Systems Biology Mark-up Language
Relevant QAA Computing Curriculum Sections: Data Structures and Algorithms, Developing Technologies |
| Transferable skills |
Not entered |
| Reading list |
* Edda Klipp, Systems Biology in Practice, Wiley-VCH, 2005.
* Athel Cornish-Bowden, Enzyme kinetics / Oxford : IRL, 1988.
* David Fell, Understanding the Control of Metabolism: Portland Press, 1997.
* David L. Nelson, Lehninger principles of biochemistry / 4th ed., W.H. Freeman, 2005.
* Basic Mathematics for Biochemists, Athel Cornish-Bowden, Oxford University Press.
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| Study Abroad |
Not entered |
| Study Pattern |
Lectures 20
Tutorials 8
Timetabled Laboratories 0
Non-timetabled assessed assignments 40
Private Study/Other 32
Total 100 |
| Keywords | Not entered |
Contacts
| Course organiser | Dr Michael Rovatsos
Tel: (0131 6)51 3263
Email: mrovatso@inf.ed.ac.uk |
Course secretary | Miss Kate Weston
Tel: (0131 6)50 2701
Email: Kate.Weston@ed.ac.uk |
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© Copyright 2011 The University of Edinburgh - 16 January 2012 6:17 am
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