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Description of Course Modules
- Biocomputing I. Programming is an essential skill for bioinformaticians. This module focuses on Perl, 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 Bioperl 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 Management. With the rapid growth in the quantity of biological data, there is a growing need for bioinformaticians to manage data in an efficient and reliable manner. This module explains how to design, create and query relational databases using the Open Source software MySQL, with a strong focus on the challenges of modelling biological data. It also covers other important data-handling topics: The use of XML for data exchange and for handling poorly-structured data (using the Open Source native XML database management system; and the particular challenging involved in handling very large data sets. 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 Maya Topf.
- 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.
- Molecular Structure. The Department of Biological Sciences (formerly the School of Crystallography) at Birkbeck is famed for its research in the field of structural biology. In this module lecturers from the department teach the fundamentals of DNA and protein structure. Module organizer: Dr Jim Pitts.
- Structural Bioinformatics. 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 Mark Williams.
- 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.