Clearing and adjustment 2020

Take a look at our vacancies to see if this course, or similar, has spaces available. Join us now and help shape tomorrow.

Search clearing vacancies

MSci Genetics

Year of entry: 2020

Coronavirus information for applicants and offer-holders

For the latest updates on how coronavirus will affect applicants and offer-holders, you can visit our FAQs.

Read our latest coronavirus information

Holding an offer for 2020 entry? Visit our dedicated offer-holders page.

Information for offer-holders

Course unit details:
Computational Approaches to Biology

Unit code BIOL33021
Credit rating 10
Unit level Level 3
Teaching period(s) Semester 1
Offered by School of Biological Sciences
Available as a free choice unit? No

Overview

Computational methods are increasingly used in all areas of biology in order to better understand complex living systems and develop models that generate testable predictions. This unit introduces a range of computational techniques, including differential equations, machine-learning, network and constraint-based analysis, which are used for a wide range of biomedical and biotechnological applications, from understanding how intracellular signalling pathways are disrupted in diseases to redesigning organisms by metabolic engineering.

Pre/co-requisites

Unit title Unit code Requirement type Description
MSci Research Project Proposal BIOL33000 Co-Requisite Compulsory
MSci Bioinformatics Tools and Resources BIOL33011 Co-Requisite Compulsory

A-Level Mathematics required.

 

A limited number of places will be available for BSc students, the following rules apply:

a) The student MUST have A’Level Maths (or its International equivalent - but AS or GCSE Maths are not sufficient).

b) The student cannot join the unit in the 2-week grace period at the start of the semester, they would have to be pre-accepted in early September.

c) The student must first discuss with their PD whether taking the unit is appropriate for them or not.

d) Where demand exceeds capacity, acceptance onto the unit will be based on the student’s Year-2 average mark.

Aims

 

This unit aims to introduce students to a wide range of computational methods and tools required to carry out interdisciplinary research in the biological sciences.

Syllabus

The unit will start with an introduction to essential mathematical concepts used in biological modelling and an introduction to the Python programming language. Students will be introduced to the Jupyter Notebook system, a widely used online application allowing the development of code for data analysis and numerical simulation.

The core of the unit will be structured along three main sections, each covering a particular set of techniques and applications:

Section 1: Dynamic models

·      Introduction to differential equations-based modelling

·      Modelling gene regulatory pathways I: gene transcription

·      Modelling gene regulatory pathways II: cellular signalling pathways

Section 2: Models of large cellular systems

·      Network reconstruction and analysis: protein-protein interaction networks, metrics for network analysis, integration of high-throughput biological data.

 

·      Logical modelling: Boolean models, logical steady state analysis, applications to cancer systems.·      

·    Constraint-based modelling of metabolic networks.

 

Section 3: Dimensionality reduction and clustering

·      Dimensionality reduction: Principal Component Analysis (PCA) and interactive plotting with applications to visualising single-cell expression data

·      Clustering: hierarchical, k-means and mixture model clustering

·      Non-linear dimensionality reduction methods: GPLVM and t-SNE for non-linear dimensionality reduction and visualisation of single-cell data

 

Teaching and learning methods

The unit will be delivered as a succession of lectures (1 hour) and practical sessions (2 hours), where each lecture will introduce the theory behind a method/tool, and students will apply the method/tool to solve a particular biological problem in the practical.

 

Students will be assessed by completing three in-sessional online modules, one for each of the main sections of the unit, taking place during the last practical of the respective section. These modules will consist of a series of multiple choice questions and short questions, some of which will require a short piece of code to be written.

 

Knowledge and understanding

Students should:

·         Understand essential mathematical concepts required for biological research.

·         Understand and apply differential equations and stochastic modelling of intracellular systems.

·         Understand and apply constraint-based modelling of metabolic systems.

·         Understand and apply network analysis and logical modelling of molecular systems.

·         Understand and apply Bayesian inference and machine learning.

·         Understand the applications and limitations of different modelling techniques and tools.

Intellectual skills

Students should: 

Develop problem-solving skills

Construct models and design experiments to test biological hypotheses.

Practical skills

Students should: 

·         Use the Python language and develop models using the Jupyter Notebook system.

·         Construct models of signalling, regulatory, metabolic and environmental systems.

·         Use Bayesian methods to infer computational models from biological data.

Transferable skills and personal qualities

Students should: 

·         Develop computational skills.

·         Develop report writing skills.

·         Learn to communicate computational results.

Employability skills

Analytical skills
Critical appraisal of research papers.
Project management
To be able to work in a group to meet deadlines for written and experimental work.
Problem solving
Planning of modelling strategies to test a specific hypothesis.
Research
Learning computational techniques and applying these to your planned goals.
Written communication
Scientific writing skills preparing a report.

Assessment methods

Three in-sessional online modules (each 33.3%)

Feedback methods

 

Verbal feedback will be communicated during the practical sessions.

Written feedback will be communicated through annotated comments for each online assessment.

Recommended reading

Specific material will be provided with each lecture.

Study hours

Scheduled activity hours
Lectures 12
Practical classes & workshops 24
Independent study hours
Independent study 60

Teaching staff

Staff member Role
Jean Marc Schwartz Unit coordinator

Return to course details