Postgraduate Course: Practical Systems Biology (PGBI11089)
|School||School of Biological Sciences
||College||College of Science and Engineering
||Availability||Not available to visiting students
|Credit level (Normal year taken)||SCQF Level 11 (Postgraduate)
|Home subject area||Postgraduate
||Other subject area||None
||Taught in Gaelic?||No
|Course description||Molecular 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. There, 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.
This course will provide an introduction to systems biology by focusing on the behaviours expected from interactions between only a few genes, taking examples from microbes to mammals. Cells are dynamic systems, and we will build intuition about the types of responses expected from different gene ¿circuits¿ by running, adapting, and analysing computer simulations. Throughout, the course will use such simulations and analysis as research tools to understand biology. After an introduction to motifs and modules, we will focus on the role of feedback in genetic networks and how feedback can sometimes create permanent switches, in, for example, stem cells, or at other times can generate oscillations such as circadian rhythms in neurons. We will show how these behaviours can be undermined when numbers of molecules become low, an effect that cells may exploit or regulate away. Finally, we discuss experimental techniques that allow direct comparison between simulations and real biological systems.
Entry Requirements (not applicable to Visiting Students)
||Other requirements|| None
|Additional Costs|| None
Course Delivery Information
|Delivery period: 2013/14 Semester 1, Not available to visiting students (SS1)
||Learn enabled: Yes
|Course Start Date
|Breakdown of Learning and Teaching activities (Further Info)
Lecture Hours 22,
Programme Level Learning and Teaching Hours 4,
Directed Learning and Independent Learning Hours
|Breakdown of Assessment Methods (Further Info)
|No Exam Information
|On completion of this course, the student will be able to:
1. Students will gain an appreciation of how interactions between genes can explain some of the behaviour we see in cells.
2. Students will gain an understanding of the different behaviours expected in dynamical systems and how to biochemically ¿code¿ for some of these behaviours.
3. Students will develop skills in programming and simulation and learn how to use computers as tools to help decide between different hypotheses.
|Two in-course assignments (25% each) and a research project (50%). |
The assignments will involve working through a step-by-step computational analysis of a model of a biological system.
The aim of the research project is to demonstrate that the students are able to use computer simulation to test biological hypotheses.
Lectures 1 & 2: "What is systems biology?"
Lectures 3 & 4: "Simulating a biomolecular network"
Lectures 5 & 6: "Input-output and ultrasensitivity"
Lecture 7 & 8: "Motifs, modules, and attractors"
Lectures 9 & 10: "Positive feedback and genetic switches"
Lectures 11 & 12: "Negative feedback to reduce response times"
Lectures 13 & 14: "Negative feedback and oscillations"
Lectures 15 & 16: ¿Circadian rhythms¿
Lectures 17 & 18: ¿Stochastic gene expression¿
Lectures 19 & 20: ¿Stochasticity and gene regulation¿
Lecture 21 & 22: ¿Connecting models to experiments¿
||An introduction to systems biology, U Alon (Chapman & Hall, 2006)
Primer on Python for scientific programming, HP Langtangen (Springer, 2009). Available online.
Python programming fundamentals, KD Lee (Springer, 2011). Available online.
|Course organiser||Prof Peter Swain
Tel: (0131 6)50 5451
|Course secretary||Mrs Jennifer Morris
Tel: (0131 6)50 5513
© Copyright 2013 The University of Edinburgh - 13 January 2014 4:48 am