Description of Course Modules

Computational/statistical modules

• Biocomputing I. Programming is an essential skill for bioinformaticians. This module focuses on Python, the most widely-used programming language for bioinformatics. The module addresses a range of topics, including: how to write short scripts for handling biological data; how to use Biopython to handle DNA and protein sequence data; and the good programming practices and habits relevant to any programming language. Module organizer: Dr Adrian Shepherd.
• Biocomputing II. Building on the fundamental concepts introduced in Biocomputing I, the aim of this module is to address the practical challenges faced by bioinformaticians tackling larger-scale and collaborative programming tasks. The module includes a range of interactive sessions during which students have the opportunity to discuss various programming topics with professional programmers, post-docs and PhD students. Assessment is via a group project. Module organizer: Dr Andrew Martin.
• Data Science. With the rapid growth in the quantity of biological data, there is a growing need for bioinformaticians to handle data effectively — prepare it, analyze it, and query it. This newly revised module covers a range of important topics: modelling data with UML; creating and querying relational databases (with practical experience using MySQL); data handling in Python (notably using the Pandas library); data visualization (including the Python Seaborn library); and using machine learning (the Python Scikit-learn library) to analyze data. Module organizer: Dr Adrian Shepherd.
• Statistics. Provides a rigorous introduction to the essential statistics that underpin modern bioinformatics. Practical sessions focus on programming in R, which is the most important (free) statistical analysis tool for bioinformatics applications. Module organizer: Dr Mark Williams.

Biological modules

• Molecular Basis of Life. This is a substantially revised module (formerly known as Molecular Structure) running for the first time in 2016. The aim of the module is to tackle fundamental biological topics from a bioinformatics perspective, including: proteins as the principle molecular machines of life; DNA as the information store of life; cell biology and the major domains of life; genetic and infectious disease. Module organizer: Dr Mark Williams.
• Sequence Analysis and Genomics. This module covers classical methods of biological sequence analysis and their applications to the problems of modern biology. It also discusses different aspects of molecular evolution: from sequence to structure and function. Module organizer: Dr Irilenia Nobeli.
• Structural Bioinformatics. The Department of Biological Sciences (formerly the School of Crystallography) at Birkbeck is famed for its research in the field of structural biology. Proteins are the nanoscale machines that carry out the overwhelming majority of the essential processes in living organisms. Understanding how these machines work is an important area of current computational research that finds practical application in structure-based drug design. This module provides an introduction to the quantitative analysis and prediction of protein structure with a particular focus on the analysis of interactions with small molecules. Module organizer: Dr Maya Topf.
• Systems Biology. Systems biology is an emerging and challenging field that involves integrating information at different levels (e.g. molecules, cells, organs) in ways that aid our understanding of how a given biological system functions. In this module we focus on: some key sources of information that underpin systems biology research (microarray and proteomics data); the generic mathematical techniques and simulation software relevant to systems modelling; and various biological systems that are the focus of current systems biology research. This module also addresses the role of bioinformatics in the context of emerging experimental techniques such as Next Generation Sequencing. Module organizer: Dr Irilenia Nobeli.