# Systems Biology

Systems Biology
SB5005 - Introductory Mathematics and Modelling
Credit Points
15
Course Coordinator
Dr Carmen Romano

### Pre-requisites

A BSc Hons at class 2.2 or above in a science subject.

### Overview

This course covers the fundamental mathematical concepts required for the description of biological systems e.g. ordinary differential equations and their numerical integration. Students will also use analytical methods based on CAS (Computer Algebra Systems e.g. Maple) to address typical modelling problems.
Some of the concepts from analysis and algebra which will be introduced are: functions, series, derivatives, integrals, systems of equations, eigenvalues & eigenvectors, ordinary differential equations, stochastic equations (Langevin Equations), and basic partial differential equations.

### Structure

2 one-hour lectures and one-hour tutorial (to be arranged).

### Assessment

1st attempt: 1 two-hour written examination (40%); continuous assessment (60%).
Resit: Two-hour written exam (100%).

SB5007 - Regulation in MicrobialBiochemistry
Credit Points
15
Course Coordinator
Dr Ian Stansfield

### Pre-requisites

A BSc Hons at class 2.2 or above in a science subject.

### Overview

This course will consider the mechanisms and complexity of biochemical regulation. Beginning with basic descriptions of enzyme kinetics, it will introduce concepts of inhibition of enzyme systems, including allosteric regulation, and feedback control of whole enzyme systems. The course will end with the introduction of the concept of Metabolic Control Analysis (MCA), and the use of flux control coefficients to describe the steady-state control behaviour of multi-enzyme pathways.

### Structure

16 one-hour lectures, 2 three-hour computer practical, and 2 one-hour tutorials.

### Assessment

1st attempt: 1 two-hour written examination (70%), continuous assessment (30%).
Resit: Two-hour exam (100%).

SB5505 - Biological Modelling Principles and Practice
Credit Points
15
Course Coordinator
Dr Mamen Romano

### Pre-requisites

A BSc Hons at class 2.2 or above in a science subject.

### Overview

Selected mathematical models from the literature will be discussed. For the course, simplified versions will be developed. These models will be theoretically analysed in lectures and the practical implementation in modelling software will be performed in computer tutorials.

### Structure

2 one-hour lectures and 1 two-hour computer practical per week.

### Assessment

1st attempt: Continuous assessment (50%), oral exam (50%).
Resit: Oral exam (100%).

SB5506 - Research Tutorials and Systems Data Manipulation
Credit Points
15
Course Coordinator
Dr Ian Stansfield

### Pre-requisites

A BSc Hons 2.2 class or above in a science subject.

### Overview

This course focuses on intensive study of the primary literature to learn from published examples of systems biology and the application of mathematics in biology. A series of published systems biology papers will form case studies as the basis of this course. Supported by tutorials, the students will study in detail 6 key papers in systems biology, developing presentations on this material and other linked papers to support their learning. In parallel, students will also carry out a series of quantitative analyses of biological systems in computer workshops, providing the students with skills needed for model parameterisation. The course will also contain significant statistical analysis content, taught through the computer workshops. Assessment will be by essay exam.

### Structure

6 two-hour tutorials supported by 3 one-hour presentation sessions. 3 three-hour computer data analysis workshops.

### Assessment

1st attempt: Essay exam (100%).
Resit: Essay exam (100%).

SB5507 - Research Project Model Development
Credit Points
15
Course Coordinator
Dr Ian Stansfield

### Pre-requisites

A BSc Hons 2.2 class or above in a science subject.

### Overview

This course involves the student working in teams with other students on the course, and with their project supervisor, to develop a mathematical model of the biological systems that will form the basis of their summer research project. Supported by a series of 'advice surgeries' and workshops, the student will design a model representation of their systems, develop and code the model, before finally parameterising it and moving to first steps in model validation. The model development exercise will be written up in the form of a paper, and a presentation given of the research undertaken. Assessment will be undertaken of the presentation, and of the manuscript describing the research.

### Structure

4 one-hour tutorials and 3 three-hour workshops to support model development.

### Assessment

1st attempt: Scientific paper assessment (80%) and viva examination of presentation (20%).
Resit: Oral exam of revised scientific paper (100%).

SB5508 - Synthetic biology model development
Credit Points
15
Course Coordinator
Professor Ian Stansfield

### Pre-requisites

A BSc Hons 2.2 class or above in a science subject.
For students on MSci programmes offered by the School of Medical Sciences within the medical sciences subject area, there is a pre-requisite of either MB4050, IM4005, BM4005, SR4005 or BM4004

### Overview

This course involves the student working in teams with other students on the course, and with their project supervisor, to design and develop a mathematical model of a synthetic biological system that will endow an organism with new function. The final synthetic circuit design will be assessed by presentations, both oral and poster.

They will also work with their supervisor to develop a mathematical model of the biological system that will form the basis of their summer research project. Supported by a series of 'advice surgeries' and workshops, the student will design a model representation of their system, develop and code the model, before finally parameterising it and moving to first steps in model validation. The model development exercise will be written up in the form of a paper, and a presentation given of the research undertaken. Assessment will be undertaken of the presentation, and of the manuscript describing the research.

### Structure

Four 1 hour lectures, five 1 hour tutorials and four 3 hour workshops to support model development and sythetic circuit design.

### Assessment

Scientific paper assessment (50%) and viva examination of presentation (20%), presentation of synthetic circuit design (20%) and assessment of a poster presention (10%).