Undergraduate Course: Making Sense of Disease Pathways (BIME10034)
|Deanery of Biomedical Sciences
|College of Medicine and Veterinary Medicine
|Credit level (Normal year taken)
|SCQF Level 10 (Year 4 Undergraduate)
|Not available to visiting students
|Ever wanted to know a better way of organising your knowledge? This course provides a solution!
Underpinning all biology is a tangled web of interconnected molecular pathways. Biochemical pathways, signalling pathways, and genetic pathways, all interact to dictate biological form and function in health and disease. Over the past few decades, scientists have painstakingly identified many of the molecular components of these pathways and are trying to understand how they work together and what happens when they go wrong. This practical course is designed to show you a simple method by which you can compile network models of complex biological systems and how these models can be used to simulate their activity.
This course has two components:
┐ The first is an overview of modern analytical laboratory techniques. This includes providing a general knowledge and use cases for techniques such as transcriptomics, mass spectrometry and proteomics, recombinant protein expression, gene targeting and transgenesis. These methods provide the cellular and molecular information with which pathways can be defined. This is a taught component of the course. It is designed to provide an overview of current analytical techniques employed in biological research and context to the pathway modelling component but is not examined.
┐ In the second part to the course students will be taught how to synthesise complex ideas and information into informative and accessible pathway models. You will be given a subject area around a given molecular pathway, and asked read the available information about it to build up an integrated picture of events. You will be taught a standard pathway modelling language and software with which to build diagrams that describe your system of interest. For the duration course you will work largely independently to construct a detailed diagram of what is known about your system of interest with support of the course organisers when required. As your model takes shape you will also be shown how it can then be used to predict the behaviour of the biological systems in question, and model what might happen in disease.
Entry Requirements (not applicable to Visiting Students)
Course Delivery Information
|Academic year 2018/19, Not available to visiting students (SS1)
|Learning and Teaching activities (Further Info)
Seminar/Tutorial Hours 15,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
|Assessment (Further Info)
|Additional Information (Assessment)
|Assessment of the course will be based on the quality of a participant┐s pathway model (55%), a 5,000 word essay describing the techniques used to determine how the pathway was discovered (40%) and an end of term presentation to other members of the group about their work (5%).
|No Exam Information
On completion of this course, the student will be able to:
- an understanding of methods used to identify and characterize protein and gene interactions
- an appreciation of how genetically modified animals can be generated and used to study normal and pathological systems
- skills in finding, reading and deriving understanding from the scientific literature, presentation of information in a diagrammatic form communicating clearly using pictures and skills in using new software tools
- an understanding of networks and genome science
- a deep understanding of the molecular machinery that makes up cellular pathways
|A number of pathway diagrams produced during the course of previous years can be found at: http://www.virtuallyimmune.org/
See also: O'Hara L., et al. Modelling the Structure and Dynamics of Biological Pathways. PLoS Biol. 14(8):e1002530 (2016).
Livigni A.,et al. A Graphical and Computational Modelling Platform for Biological Pathways. Nature Protocols in press (2018).
|Graduate Attributes and Skills
|Prof Thomas Freeman
Tel: (0131 6)51 9203
|Miss Mary Cummings
Tel: (0131 6)51 3094