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Course Structure

Introductory module: This module will start with an Introduction that will deal with the concepts, history, and future aspirations of systems biology. The module will further comprise three interweaving sub-modules. Sub-modules INT1 and INT2 have lectures that deal with the nature of modern biological science in relation to the concepts, approaches, methods and tools of Systems Biology. Sub-module INT3 is a contextualised mathematical and computer modelling toolkit comprising lectures and classes. This Module will run in the first two weeks of the Michaelmas Term and comprise 26 lectures plus 5 computer-based practical sessions.


Data Acquisition and Handling (DAH): Systems biology relies on the ability to obtain a ‘global’ view of the physiology of a cell by the simultaneous identification and quantification of thousands of different molecules (such as proteins, nucleic acids and metabolites).  This module will present the techniques used to acquire data in the various ‘omics’ approaches (transcriptomics, proteomics and metabolomics), as well as in high-throughput genetics.  Because of their size and experimental limitations, the handling of these datasets presents unique challenges.  Therefore, the module will emphasise the practical aspects of dealing with this type of data.  Large-scale approaches are generally applied to cell populations, and often lack spatial and temporal resolution.  The module will introduce how they are complemented by in vivo analysis of single cells using advanced microscopy, which can provide information on cell-to-cell variation and spatial control.

This Module will run in the Michaelmas Term and consist of 18 lectures plus 6 computer-based practical sessions.


Modelling and Analysis of networks (MAN): The module will focus on mathematical and statistical methods used to evaluate and analyse large-scale data sets and use them for the reconstruction of biological networks. Methods for the analysis of metabolic, gene-regulatory, and large-scale networks will also be introduced.

This Module will run in the Lent Term and comprise 11 lectures plus 11 computer-based practical sessions.


Synthetic and Executable Biology (SEB): This module aims to introduce students to the de novo design of biological systems using the techniques of Synthetic Biology and computational simulation. The theory and practice of Synthetic Biology is introduced  both in the context of designing exemplar biological systems to test our understanding of natural systems and in that of systems design and fabrication to produce novel devices of commercial or medical utility. The design, simulation, and analysis of biological modules using some of the main computational techniques in Executable Biology is then introduced. Finally the two strands of the module are integrated by a design exercise in which students design a system using standard synthetic biology components and test its feasibility by computer simulation.

This Module, consisting of 13 lectures and 5 computer-based practical sessions, will run in the Lent Term.


Seminars: One set of seminars will be in a journal club format, where students will present seminal papers from the field. There will be 10 such seminars, with two students presenting at each. In addition, there will be talks given by invited speakers. The second seminar format will involve small-group teaching sessions led by post-docs to review journal articles and consolidate course material. Overall, there will be a total of two one-hour seminars per week.


Research Project: The project will run for 12 weeks in Michaelmas and Lent Terms, starting in week 4 of Michaelmas Term. It may consist of any (agreed) combination of practical, theoretical or analytical work and will have support from classes or seminars from active researchers. Each project will have a research group leader as overall (senior) supervisor and a day-to-day supervisor (post-doctoral or senior graduate student). Joint projects will be encouraged where pairs of students, one with a biological and one with a mathematical/physical/computational background, collaborate to address a systems problem.  Students will present the results of their project to the group and submit individual project reports.