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B I O I N F O R M AT I C S

POSTGRADUATE CERTIFICATE/DIPLOMA/MSc ONLINE MODULAR DEGREE PROGRAMME

COURSE

OVERVIEW

Bioinformatics: an online Masters Degree programme, delivered jointly by The University of Leeds and The University of Manchester

This new world-class programme is based on modules from the established MRes Bioinformatics Degree course taught at The University of Leeds and the MSc Bioinformatics Degree taught at The University of Manchester. It draws upon expertise from both institutions. You can be admitted to the Certificate, Diploma or Masters Programme, once you complete at least two core modules and no more than four modules.Alternatively, you may choose to study one or more selected modules of your choice.

Who is this course for?


The programme has been created to meet increasing demand from the pharmaceutical, biomedicine, medical informatics, and biotechnology industries for experts skilled in using computers to manipulate and analyse the growing quantities of genetic information available to these industries. It is designed to meet the needs of two types of students: people with a background in the bio-sciences (including those with joint degrees) who wish to acquire competence in biocomputing; and those with a background in computing and computer science who wish to gain a grounding in molecular biology.

What are the benefits for me??


This course will enable you to: study molecular biology if you have a background in computing study computing and modelling techniques if you have a background in bioscience train in one of the most exciting and fast-moving disciplines in the field of bioscience receive support during your studies from academics actively engaged in bioscience research at the universities of Manchester and Leeds acquire subject-specific skills in bioinformatics, including the ability to use a wide range of bioinformatics software, and the ability to write your own programs and software packages gain a practical and theoretical knowledge of computational molecular biology sufficient to prepare you for a career in biotechnology, or for research work gain the multidisciplinary training which is now seen as essential in the biotechnology industries progress your career within the pharmaceutical (especially relating to drug design and delivery), biotechnology or biosciences industries undertake a meaningful research programme, and apply your knowledge to real biological problems retrain, if you have a first degree in Computing, Maths or IT, and want to change career develop problem-solving skills necessary for work in research and industries carry out computer processing for any organisation involved in handling large amounts of biological data

What are the benefits for my organisation?


In addition to the individual benefits outlined above (which will transfer into the workplace), a sponsoring organisation will gain from: the input of a broad interdisciplinary knowledge of bioinformatics a range of transferable skills being applied in the workplace, including communication, presentation, creativity, and teamwork the flexibility of online learning and a reduction in study time spent away from work

COURSE

STRUCTURE

This course shows the value of collaboration between WUN members. Bioinformatics is one of the most critical areas of development in the biological sciences and I am delighted that WUN can make this contribution to a leading-edge agenda.
Sir Alan Wilson, University of Leeds Vice-Chancellor and Chairman of WUN

The programme was developed jointly by The University of Leeds and The University of Manchester, as members of the Worldwide Universities Network (WUN), which is an international partnership of leading higher education institutions. The course is delivered online, via a virtual learning environment known as the Bodington System.This allows you to navigate and search through course notes, protocols, practicals and references to useful texts and URLs.The course notes are provided as web pages.These provide the necessary background to the course, which is focused on problem-based learning.Throughout the course you will interact with the members of the course team, and with other learners, through course study rooms and 'chat rooms' for online tutorials. 3 The programme consists of modules, each of which has a value of 15 credits, and a literature or research project. Some of the modules described here may change, according to demand and availability.The structure of the programme is as follows: Certificate programme 4 modules = 60 credits Introduction to Bioinformatics One module selected from: C for Bioinformatics, Introduction to Molecular Biology, Java for Bioinformatics, or Theory and Applications in Bioinformatics One module selected from: Biocomputing, or Object-orientated analysis and design with UML One further module selected from the Optional Modules Diploma programme 6 modules plus Literature Project = 120 credits Introduction to Bioinformatics Theory and Applications in Bioinformatics One module selected from: C for Bioinformatics, Introduction to Molecular Biology, or Java One module selected from: Biocomputing, or Object-orientated analysis and design with UML Two further modules selected from the Optional Modules The Literature Project (30 credits) Masters programme 6 modules plus Research Project = 180 credits Introduction to Bioinformatics Theory and Applications in Bioinformatics One module selected from: C for Bioinformatics, Introduction to Molecular Biology, or Java One module selected from: Biocomputing, or Object-orientated analysis and design with UML Two further modules selected from the Optional Modules The Research Project (90 credits)

CORE MODULES
Introduction to Bioinformatics
This is designed to develop the skills now needed by the biotechnology industries. It is divided into six sections: 1. Introduction to Bioinformatics and the Internet 2. Sequence databases 3. Sequence alignment and database searches 4. Protein function prediction 5. Protein structure prediction 6. Sequencing projects and contig analysis

Introduction to Programming for Bioinformatics


This part of the course is designed to develop the skills required to enable you to write programs using the C or Java programming languages. The taught half of the course is divided into 18 workpackages (with the final two being optional). For each workpackage there are a number of modules of a specifically developed Computer Based Training (CBT) package to complete, an example program to understand, compile and run, and an exercise to carry out. For the second part of the course you will work on a mini project divided into three separate parts.

Introduction to Molecular Biology for Computer Scientists


This introductory module aims to provide a good basic understanding of contemporary molecular biology to students with a background in one of the physical sciences and with sufficient knowledge of organic chemistry to be able to recognise the common functional groups and their properties. No previous knowledge of molecular biology is required. Current concepts will be presented and issues of debate will be highlighted. It provides a sound basis for further study of Bioinformatics.

Biocomputing
This is designed to develop the skills required by biotechnology industries. As genome-sequencing projects continue to generate huge volumes of data, a major challenge for biologists is the effective management of these data in order to extract useful information. Computational biology, or Biocomputing, is concerned with the development of these methods for storage and processing of biological data. A large part of the work of computational biologists consists of the management and analysis of strings of characters that may be nucleic acid or protein sequences, or their annotation.

Object-oriented analysis and design with UML


This module covers the use of UML throughout the process of objectoriented analysis and design. It includes: an introduction, including basic object-oriented concepts and an example object-oriented model requirements analysis, including use-case diagrams and scenarios object-oriented analysis object-oriented design UML and implementation languages

Theory and Applications in Bioinformatics


This module is designed to provide a theoretical grounding in the key methods underlying biological sequence analysis applications (as

introduced in the Introduction to Bioinformatics module). The module consists of six parts: 1. Introduction to Probability and Statistics using Matlab 2. Traditional Sequence Alignment and Search

genome. You carry out exercises using authentic data from research laboratories at the University of Leeds and use state-ofthe-art software tools for analysis and interpretation.

Intermediate Java
This module is designed to further develop the skills you will need to write more advanced programs using the Java language. The taught half of the course is divided into eight workpackages. Each has a number of modules of a Computer Based Training (CBT) package to complete; a number of example or demonstration programs to understand, compile and run; and an exercise to carry out. For the second part of the course you undertake three mini-projects.

Monte Carlo simulations; conformational analysis; solvation; calculation of thermodynamic parameters and the module finishes with a section on structure-based drug design and virtual screening of lead compounds for drug development.

3. Introduction to Probabilistic Sequence Models 4. Markov Chains and HMM Applications 5. Phylogenetic Methods 6. Neural Networks (in brief)

LITERATURE PROJECT
This provides Diploma students with experience and training in abstracting and assessing information from a variety of published sources. It is designed to give experience in carrying through a substantive review of developments in Bioinformatics. You will be expected to report and make recommendations on the scientific, resource and investment issues that will inform management decisions. Your project results will need to be presented as a bound dissertation of at least 10,000 words.

OPTIONAL MODULES
Introduction to Microarray Data Analysis
This module focuses on microarray data analysis in the context of post-genome bioinformatics. You will work through practical examples using the maxdview visualisation environment. There are six sections: 1. An overview of biological information 2. Data capture 3. Using the data 4. Data integration 5. Strategies for drug discovery 6. Industrial organisation

The Bioinformatics of Protein Structure


This module introduces you to protein structure and function, including the concepts of protein evolution and the molecular biology underlying it, and the structural databases. You carry out exercises to explore homologies between protein structures, and construct phylogenetic trees. You also explore how the threedimensional structure of proteins and their functions can be predicted, and carry out comparative modelling of protein structures.

RESEARCH PROJECT
The objective of the MSc research project is to give you experience and training in bioinformatics research. The project is normally carried out in your workplace. It aims to help you understand and experience: the technical skills required for efficient bioinformatics research the organisation and implementation of research working to deadlines and as part of a team the skills required to record, report and write-up original scientific research The results of your supervised research project will need to be presented as a bound dissertation (minimum length 20,000 words, maximum length 30,000 words or equivalent scientific data content).

The Science of Proteomics


This module explores methods for studying the proteome the entire complement of proteins expressed by a cell. It introduces the modern separation and analytical methods needed to cope with a dataset that is an order of magnitude more complex than that of the

Molecular Modelling and Structure-Based Drug Design


This module introduces the basic principles and applications of molecular modelling. Topics covered include: molecular mechanics; energy minimization techniques; molecular dynamics and

Entry requirements
For admission to the programme you must have a first or upper second class degree or equivalent qualification in a relevant science subject some relevant knowledge or experience of bioscience and/or computer science and/or mathematics relevant to informatics access to a PC running a recent version of Microsoft Windows (preferably Windows XP or Windows 2000), with a screen resolution of 1024 x 768 during the course you will be required to download and install programs and plug-ins which only run under Windows, so no other operating system will be supported the recommended textbooks will be supplied in an online form which will require Microsoft Internet Explorer version 5.5 or above; no other browser is currently recommended you will need to download and install the following plug-ins: Adobe SVG Viewer, MDL Chemscape Chime, and Sun Java plug-in (version depends on Windows version) proficiency in written English you should be able to produce well-structured work, summarise key points clearly and discuss issues in writing from different points of view a willingness to spend some time in discussion and working online with others in your tutor group, sharing your professional experience and learning from them commitment, determination, enthusiasm and the ability to be organised and work independently an average of 7-8 hours a week per module available for your studies.You will need to log on several times a week To progress to registration for an award you will need to demonstrate satisfactory performance in two core modules.

W H AT

IS

ONLINE

S T U DY ?

Online study, sometimes known as eLearning, means that rather than studying and attending lectures at a higher education establishment, the student uses the Internet to access course information and transmit completed assignments for marking. This enables a person from anywhere in the world to take a world-class course at a leading UK university without attending the university in person.

How does online study work?


This course has been purpose-built for online delivery. Substantial investment was made to design and develop the course, and it was thoroughly tested using a rigorous quality assurance process before receiving approval for student use. The Bodington System online learning platform used for this course is highly advanced. It was developed to make it as easy as possible for you to study and navigate through the rich set of learning materials and other features of this course.

materials provided online and you will often need to undertake independent research to find additional reading matter or information. Group activities will be timetabled and will last for a number of days to let you participate at times that suit you personally. A typical small group study might involve a task or exercise linked to a particular theme. A group discussion will bring students together in a larger group to discuss or debate set questions. Your tutor will provide full guidance and support. When you complete the course, depending on your choice of modules and the nature of your research project, you will receive an award from either the University of Leeds or the University of Manchester. This has exactly the same internationally recognised status as the equivalent programme studied at the University.

A broad mix of study resources


A variety of online learning media support the course. Throughout your studies you will be a member of a tutor group of fellow students. You will work with this group throughout your course discussing the programme materials, collaborating on group tasks, participating in group exercises and generally supporting one another. In effect, you will be part of a learning community that shares your goals and aspirations.

The course includes tutor-marked assignments and written assessments. You will be taught and assessed through a combination of media, computer conferencing and the Internet. Your work will be marked and returned to you with detailed comments and advice. You will find this comprehensive personal feedback one of the most valuable aspects of your study.

Programme
You will take part in a range of activities. Private study will include reading

Full support
One or more tutors who specialise in the theory and practice of Bioinformatics will support you and your group. They will act as mentors and provide you with personal guidance as you progress, advising you how to make the most of the course and helping you to overcome any obstacles you encounter. The Universities also provide a comprehensive range of administrative and general support services throughout your course.

What are the benefits of studying online?


You can: study at any time of the day or night that suits you study anywhere you wish, using a computer connected to the Internet: from your home, office, hotel or even while travelling use the Bodington System online learning platform, which is one of the most advanced systems currently available benefit from online tutor support whenever you need help, advice or encouragement take part in online discussion groups and work in collaboration with fellow course participants enjoy access whenever you wish to the online resources at Leeds and Manchester Universities, including journals, reference databases and downloadable reading matter save money by gaining an internationally recognised university qualification without incurring any costs for accommodation or travel

WHO

PROVIDES THIS

COURSE?

Manchester and Leeds Universities deliver the course jointly. Manchesters campus-based Bioinformatics course was among the first anywhere, while the Faculty of Biological Sciences at Leeds is one of the largest life-science research centres in the UK.

The Universities of Leeds and Manchester have worked in close partnership to design, develop and provide this course.

To apply or find out more...


To obtain more information: Please email Heather Vincent Heather.Vincent@man.ac.uk mentioning any specific queries you may have.

The University of Leeds was established as a University in 1904. Internationally acknowledged as a centre of excellence in a wide range of academic and professional disciplines, it is one of the largest and most popular universities in the UK, and rates among the top ten for research.

If you are interested in applying for a place on the course, you can apply online or request more details at: http://www.cs.man.ac.uk/biomed/applications.html

The University of Manchester is a truly international institution with a worldclass reputation for high quality research. In the most recent (2001) Research Assessment Exercise, the University received the top 5* rating, denoting international excellence, in both Biology and Computer Science, for teaching and research.

The Worldwide Universities Network (WUN) is a grouping of research-led institutions of international standing who have come together to create a worldwide research and graduate education partnership.
Please note: This prospectus may contain some details that have subsequently changed. Up-to-date information is available from Heather.Vincent@man.ac.uk or write to: Heather Vincent Room 2.89 Department of Computer Science University of Manchester Oxford Road Manchester M13 9PL UK