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CENTRE FOR LANGUAGES &

INTERNATIONAL EDUCATION

UCL SUMMER SCHOOL


COMPUTATIONAL SYSTEMS BIOLOGY

Key Information

Module code ISSU1057


Taught during Session One: Monday 2 July - Friday 20 July 2018
Module workload 45 teaching hours plus approximately 100 study hours
Module leader Dr Philip Lewis
Department Division of Biosciences, Faculty of Life Sciences
Credit 15 UCL credits, 7.5 ECTS, 4 US
Level Level 1, first year undergraduate
Pre-requisites Introductory (high school) level calculus
Assessment Practical assessments (70%), Computer based examination (30%)

Module Overview
All biological interactions, whether they take place on a molecular, organism or ecosystem scale, are part of
complex dynamical systems. Understanding the behaviour of these systems lies at the heart of many key
challenges in biological research.

In this module you will have the opportunity to develop and investigate mathematical models of biological
systems. You will learn techniques to construct, implement and analyse interaction networks using the Python
programming language.

Research in the field of Systems Biology is highly interdisciplinary. It often involves biologists working with
colleagues from the fields of physics, engineering, mathematics and computer science. Consequently this
module encourages participation from any interested science or engineering student.

Week One
Why should we model biological systems?
An introduction to Python programming
Plotting data using Python
Using Python to analyse DNA sequences

Week Two
How can we model biological systems?
Using Python to simulate biological systems
Physiological models
Mass action kinetics and enzymatic reactions

Please note that this module description is indicative and may be subject to change.
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Week Three
What can we learn from biological models?
Using Python to investigate models
Population models
Gene regulation circuits

Module Aims
This module will provide a practical introduction to computational systems biology focussing on the techniques
necessary to build, code and investigate mathematical models. Examples will be drawn from across the
biosciences spectrum including molecular biology, cell biology, ecology, neuroscience and synthetic biology.

In the lectures and seminars you will explore a range of topics: why biological models are useful; how they have
been used across the range of biological sciences; the difficulties and problems that arise in model development;
and the future potential of the field including its role in synthetic biology.

Computer lab sessions will provide you with an introduction to the Python programming language starting from
basic concepts through to the use of scientific modules that allow simulation of biological systems. You will learn
how these systems can be expressed mathematically and be introduced to key methods that allow you to
investigate and analyse the resulting computer models.

Teaching Methods
The course will involve a mixture of interactive lectures and seminars held alongside a series of computer room
practical sessions. Expert help will be provided so that students to get to grips with Python coding and develop
their computational modelling skills. Students will be encouraged to work together and participate in the
module forums to collaborate and access support online.

Learning Outcomes
Upon successful completion of this module, students will:
Understand the uses of modelling in biology with reference to examples drawn across the spectrum of
bioscience research.
Be able to understand Python code and write computer programs.
Understand how biological models can be constructed using mass action and enzymatic kinetics.
Be able to use Python libraries to run simulation of biological models.
Have developed skills to investigate and analyse models using parameter scans and investigation of
phase space.

Assessment Methods
Practical assessments (70%)
Computer based examination (30%)

Module Leader
Dr Philip Lewis is an Honorary Reader in the Cell and Developmental Biology department at UCL. His work
focuses on mathematical and computational approaches to biological research. He delivers the Dynamic
Biological Systems module to UCL undergraduates and the SysMIC eLearning course which provides training in
quantitative biology aimed at the postgraduate research community. He is working on a number of projects that
aim to utilise web technologies to aid learning and was the recipient of the UCL Provosts Teaching Award in
2014/2015.

Please note that this module description is indicative and may be subject to change.
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Key Texts
Alon, U. (2006) An Introduction to Systems Biology: Design Principles of Biological Circuits (CRC Press)

Burton, R. (2012) Biology by Numbers (Cambridge University Press)

Downey, A. B. (2012) Think Python: How to Think Like a Computer Scientist (OReilly Media)

Jones, M. (2013) Python for Biologists: A Complete Programming Course for Beginners

Milo, R. & Phillips, R. (2015) Cell Biology by the Numbers (Garland Science)

Stewart, J.M. (2014) Python for Scientists (Cambridge University Press)

Strogatz, S.H. (2000) Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and
Engineering (Westview Press)

Voit, E. (2012) A First Course in Systems Biology (Garland Science)

Please note that this module description is indicative and may be subject to change.
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