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Models and Languages for Computational Systems Biology (P02013)

? Credit Points : 10 ? SCQF Level : 11 ? Acronym : INF-P-mlcsb

This course first explores a variety of modelling methods for biological pathways, whether metabolic, signalling, regulatory or transcriptional. The methods involved are qualitative, differential and stochastic. They are explained via a single unifying basic concept, that of a Petri net.

The course then considers linguistic formalisms that enable the modular specification of such pathways. One such, CCS, a Calculus for Chemical Systems, enables one to model cellular compartments and modified protein complexes. A variety of other recently proposed such biological process calculi are also covered.

Entry Requirements

? Pre-requisites : Computational Systems Biology (can be taken as a companion course if necessary). For Informatics PG students only, or by special permission of the School. Some logic and probability theory. General computer science education.

? Co-requisites : Computational Systems Biology can be taken as a companion course if necessary.

Subject Areas

Home subject area

Computational Systems Biology, (School of Informatics, Schedule O)

Delivery Information

? Normal year taken : Postgraduate

? Delivery Period : Semester 2 (Blocks 3-4)

? Contact Teaching Time : 2 hour(s) per week for 10 weeks

First Class Information

Date	Start	End	Room	Area	Additional Information
07/01/2008	14:00	14:50			To Be Confirmed

All of the following classes

Type	Day	Start	End	Area
Lecture	Monday	14:00	14:50	Central
Lecture	Thursday	14:00	14:50	Central

Summary of Intended Learning Outcomes

- Be able to demonstrate understanding of the different ways in which cellular pathways can be modelled, and the advantages and disadvantages of each.
- Be able to model simple pathways using a variety of tools.
- Be able to program biological pathways of moderate complexity in a modular way, and to employ current tools for their analysis.
- Be able to demonstrate understanding of the variety of process algebra formalisms proposed for modular modelling and their comparative advantages and disadvantages.
- Be able to read, explore and use the modelling literature in Systems Biology, particularly the computationally-oriented literature.