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DEGREE REGULATIONS & PROGRAMMES OF STUDY 2022/2023

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DRPS : Course Catalogue : School of Biological Sciences : Postgraduate

Postgraduate Course: Practical Systems Biology (PGBI11089)

Course Outline
SchoolSchool of Biological Sciences CollegeCollege of Science and Engineering
Credit level (Normal year taken)SCQF Level 11 (Postgraduate) AvailabilityNot available to visiting students
SCQF Credits20 ECTS Credits10
SummaryMolecular biology is being transformed by the recent invention of new technologies, particularly in genome sequencing and single-cell assays, and future research biologists will be expected to be as familiar with the computer as with the pipette. Systems biology is now a generic term to describe such quantitative approaches, particularly in cell and molecular biology. Given that we know the sequence of all the genes in many organisms, the challenge is to understand how these genes interact and, functioning together as a system, produce the remarkable behaviours we associate with life.
Course description Week 1 Lectures 1 & 2: "What is systems biology?"
The general systems approach with examples; why a systems approach is important for molecular and cellular biology.

Weeks 2-3 Lectures 3-6: "Fundamentals of modelling biochemical networks"
Mathematical modelling of biochemical reactions; the law of mass action; and a discussion on ultrasensitivity, cooperativity, and Hill numbers.

Weeks 4-5 Lectures 7-10: "Modelling gene expression"
Modelling the rate of transcription for genes controlled by activators and repressors.

Weeks 6-7 Lectures 11-14: "Positive feedback and genetic switches"
Positive feedback and MAP kinase cascades; bifurcations and hysteresis; cellular memory and bistable genetic networks.

Weeks 8-10 Lectures 15-20: "Negative feedback and oscillations"
Circadian rhythms; the Tyson model of the circadian clock in the fruit fly; relaxation oscillations; and oscillations through positive and negative feedback

Week 11, Lectures 21-22: ┬┐Stochastic simulations and statistical inference┬┐
Stochastic simulations of biochemical systems using the Gillespie algorithm; an introduction to fitting models to time-series data
Entry Requirements (not applicable to Visiting Students)
Pre-requisites Co-requisites
Prohibited Combinations Other requirements None
Course Delivery Information
Academic year 2022/23, Not available to visiting students (SS1) Quota:  50
Course Start Semester 2
Timetable Timetable
Learning and Teaching activities (Further Info) Total Hours: 200 ( Lecture Hours 22, Programme Level Learning and Teaching Hours 4, Directed Learning and Independent Learning Hours 174 )
Assessment (Further Info) Written Exam 0 %, Coursework 100 %, Practical Exam 0 %
Additional Information (Assessment) Two in-course assignments (20% each) and a research project (60%).

The assignments will involve working through a step-by-step computational analysis of a model of a biological system.
Feedback Model answers will be given in class to the first assignment and students will have the opportunity to discuss their solutions one-on-one in a follow up tutorial.
No Exam Information
Learning Outcomes
On completion of this course, the student will be able to:
  1. explain how interactions between genes can generate some of the behaviour we see in cells
  2. predict the different behaviours expected of dynamical systems and know how to biochemically 'code' for some of these behaviours
  3. formulate a mathematical model of a biological system
  4. generate different hypotheses on the function of a biological system
  5. perform basic programming and run computer simulations, and use simulation as a tool to help decide between different biological hypotheses
Reading List
An introduction to Systems Biology, U Alon (Chapman & Hall, 2006)

A Student's Guide to Python for Physical Modelling, JM Kinder & P Nelson (Princeton, 2015)

Primer on Python for Scientific Programming, HP Langtangen (Springer, 2009). Available online.
Additional Information
Graduate Attributes and Skills Not entered
KeywordsPracSystBiol
Contacts
Course organiserProf Peter Swain
Tel: (0131 6)50 5451
Email: peter.swain@ed.ac.uk
Course secretaryMs Karen Sutherland
Tel: (0131 6)51 3404
Email: Karen.Sutherland@ed.ac.uk
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