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DRPS : Course Catalogue : Deanery of Biomedical Sciences : Biomedical Sciences

Undergraduate Course: Making Sense of Disease Pathways (BIME10034)

Course Outline
SchoolDeanery of Biomedical Sciences CollegeCollege of Medicine and Veterinary Medicine
Credit level (Normal year taken)SCQF Level 10 (Year 4 Undergraduate) AvailabilityNot available to visiting students
SCQF Credits20 ECTS Credits10
SummaryEver 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.
Course description 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)
Pre-requisites Co-requisites
Prohibited Combinations Other requirements None
Course Delivery Information
Academic year 2018/19, Not available to visiting students (SS1) Quota:  25
Course Start Semester 1
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 200 ( Seminar/Tutorial Hours 15, Programme Level Learning and Teaching Hours 4, Directed Learning and Independent Learning Hours 181 )
Assessment (Further Info) Written Exam 0 %, Coursework 100 %, Practical Exam 0 %
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%).
Feedback Not entered
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. an understanding of methods used to identify and characterize protein and gene interactions
  2. an appreciation of how genetically modified animals can be generated and used to study normal and pathological systems
  3. 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
  4. an understanding of networks and genome science
  5. a deep understanding of the molecular machinery that makes up cellular pathways
Reading List
A number of pathway diagrams produced during the course of previous years can be found at:

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).
Additional Information
Graduate Attributes and Skills Not entered
Course organiserProf Thomas Freeman
Tel: (0131 6)51 9203
Course secretaryMiss Mary Cummings
Tel: (0131 6)51 3094
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