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DEGREE REGULATIONS & PROGRAMMES OF STUDY 2011/2012
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DRPS : Course Catalogue : School of Informatics : Informatics

Postgraduate Course: Information Processing in Biological Cells (INFR11056)

Course Outline
SchoolSchool of Informatics CollegeCollege of Science and Engineering
Course typeStandard AvailabilityNot available to visiting students
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) Credits10
Home subject areaInformatics Other subject areaNone
Course website http://www.inf.ed.ac.uk/teaching/courses/ipbc Taught in Gaelic?No
Course descriptionAll biological cells process information. They integrate signals from their environment, respond and adapt to internal changes and store information in a variety of means from transient to persistent. In this course we will look at the various strategies used by cells to process and store information.
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites Students MUST also take: Bioinformatics 1 (INFR11016)
Prohibited Combinations Other requirements None
Additional Costs None
Course Delivery Information
Not being delivered
Summary of Intended Learning Outcomes
1 - Be able to describe a range of examples of information processing in biological cells.
2 - Compare and contrast biological methods for storing information across different time scales.
3 - Discuss the computational limits of the simplest biological organisms.
4 - Explain with reference to examples how cells integrate information from multiple modalities.
5 - Critically evaluate research literature in the field.
Assessment Information
Written Examination 70
Assessed Assignments 30
Oral Presentations 0

Assessment
There is a written examination accounting for 70% of the course mark. For the remaining 30%, two pieces of in-course assessment will be set comprising a mixture of problem, discussion and short answer questions designed to assess and reinforce the lecture material.

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 * General survey of the flow of information and matter in the cell: anatomy of eukaryotic and prokaryotic cells, building blocks and structural elements, cell as a self-reproducing distributed chemical computer. Main flows of information.
* Proteins as elementary units of cellular computation: modular structure, evolution, allosteric regulation, multistability, post-translational modifications that regulate protein conformation. Operation of proteins within functional complexes, cooperative effects. Protein design.
* Transport processes and propagation of cellular information. Diffusion, its laws and fundamental constraints on the information propagation with diffusion. Molecular crowding, failure of propagation, superdiffusion and subdiffusion.
* Non-diffusive intracellular propagation. Molecular motors, principles of motor-mediated transport and the information flows.
* Acquisition of external information. Sensing of extracellular chemical signals, light, pH, temperature, etc. Principles of mechanosensation and mechanotransduction.
* Principles of signal transduction: protein modifications as signals. Encoding and decoding of spatial and temporal information.
* Abstraction of molecular interactions within a cell. Molecular networks, graphical notations, symbolic representations of interactions. Problems, pitfalls and standards. SBGN and SBML.
* Methods of quantitative description and modeling of biochemical and signal transduction networks. Chemical kinetics, mass-action rate law, particle conservation, reaction fluxes.
* Further abstraction of molecular networks. Graph representation. Stability and instability of networks. Positive and negative feedback as the basis for instability. Closed cycles within reaction networks.
* Dynamical elements of intracellular computer. Memory elements through multiple bistable elements. Oscillations. Response time of biological networks to external stimuli and $¨futile cycles&ę.
* Organizational hierarchy of the cellular hard drive. Storage of genetic information on the DNA, its duplication, maintenance (error protection), extraction and transformations.
* Principles of operation of the nuclear computer. Cis-regulatory elements: $¨Junk&ę DNA, regulatory motifs and signals. Trans-regulatory elements: Transcription factors and their regulation. Combinatorial computer in the nucleus.
* Systemic operation of cellular computer. Examples of bacterial networks of signal transduction and gene regulation: principles of logical design, integration of multiple information sources, decision making.
* Advanced topics of cellular information networks. Stoichiometric networks and matrixes, metabolic control analysis, elementary modes and extreme pathways.

Relevant QAA Computing Curriculum Sections: Data Structures and Algorithms, Developing Technologies
Transferable skills Not entered
Reading list See course web page for reading list.
Study Abroad Not entered
Study Pattern Lectures 20
Tutorials 0
Timetabled Laboratories 0
Non-timetabled assessed assignments 30
Private Study/Other 50
Total 100
KeywordsNot entered
Contacts
Course organiserDr Michael Rovatsos
Tel: (0131 6)51 3263
Email: mrovatso@inf.ed.ac.uk
Course secretaryMiss Gillian Bell
Tel: (0131 6)50 2692
Email: Gillian.Watt@ed.ac.uk
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© Copyright 2011 The University of Edinburgh - 16 January 2012 6:17 am