Postgraduate Course: Information Processing in Biological Cells (INFR11056)
Course Outline
| School | School of Informatics |
College | College of Science and Engineering |
| Course type | Standard |
Availability | Not available to visiting 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/ipbc |
Taught in Gaelic? | No |
| Course description | All 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 |
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Co-requisites | Students MUST also take:
Bioinformatics 1 (INFR11016)
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| 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'.
* 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' 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 |
| Keywords | Not entered |
Contacts
| Course organiser | Dr Michael Rovatsos
Tel: (0131 6)51 3263
Email: mrovatso@inf.ed.ac.uk |
Course secretary | Miss Gillian Bell
Tel: (0131 6)50 2692
Email: Gillian.Bell@ed.ac.uk |
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