Postgraduate Course: Models and Languages for Computational Systems Biology (INFR11047)
Course Outline
| School | School of Informatics |
College | College of Science and Engineering |
| Credit level (Normal year taken) | SCQF Level 11 (Postgraduate) |
Availability | Available to all students |
| SCQF Credits | 10 |
ECTS Credits | 5 |
| Summary | In this course we explore a range of modelling methods for pathways in molecular biology: whether metabolic, signalling, regulatory or transcriptional. These models draw on a rich existing theory of concurrent computational systems, with Petri nets as a unifying basic concept. Techniques range over qualitative and quantitative, discrete and continuous, differential and stochastic models. Working with these models, we look at logics for specifying and characterizing systems' behaviour. Finally, we investigate language-based approaches to modular description and analysis of systems, studying some computationally-inspired biological process calculi. |
| Course description |
* Petri nets: static and dynamic specification; matrix invariants; quantitative variants; biological interpretation and applications.
* Temporal logic: analysis of behavioural properties for biological networks; linear and branching-time logics; model-checking; discrete, stochastic and continuous variants.
* Markov systems: probabilities, discrete and continuous; Poisson and exponential distributions; Markov processes; continuous-time Markov chains; master equation and links between differential and stochastic approaches.
* Stochastic simulation: Gillespie algorithm; modifications; precision/cost trade-offs; relevant tools.
* Language-based approaches: biologically-inspired process calculi; modularity and scaling; computational tools.
Relevant QAA Computing Curriculum Sections: Data Structures and Algorithms, Developing Technologies
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Entry Requirements (not applicable to Visiting Students)
| Pre-requisites |
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Co-requisites | It is RECOMMENDED that students also take
Computational Systems Biology (INFR11039)
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| Prohibited Combinations | |
Other requirements | For Informatics PG and final year MInf students only, or by special permission of the School. Some logic and probability theory. General computer science education. |
Information for Visiting Students
| Pre-requisites | None |
Course Delivery Information
| Not being delivered |
Learning Outcomes
1 - Describe different ways in which cellular pathways can be modelled, and explain advantages and disadvantages of each.
2 - Model simple pathways using a variety of methods.
3 - Program biological pathways of moderate complexity in a modular way, and employ current tools for their analysis.
4 - Describe process algebra formalisms proposed for modular biological modelling and their comparative advantages and disadvantages.
5 - Read, explore and use the literature on computational modelling in Systems Biology.
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Reading List
| Not yet available |
Contacts
| Course organiser | Dr Iain Murray
Tel: (0131 6)51 9078
Email: I.Murray@ed.ac.uk |
Course secretary | Miss Kate Weston
Tel: (0131 6)50 2692
Email: Kate.Weston@ed.ac.uk |
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