Applied Bioinformatics MSc

Transcription

1 Applied Bioinformatics MSc Full and part-time Award-winning course First-class bioinformatics facilities Excellent employment prospects Delivered by leading experts

2 Bioinformatics is one of the most exciting fields in modern science. It is defined as the application of IT and computational methods to tackling biological challenges. Since its origins in genomic sequence analysis more than 20 years ago, bioinformatics has spread, not only across the whole of molecular biology, but also to every field of life science. This includes drug discovery, food technology, medicine, agriculture, plant genomics and environmental science. The first of its kind in the UK, Cranfield s established Applied Bioinformatics MSc is highly regarded by employers for its real-world relevance and applied content, and has been recognised by the UK BBSRC (Biotechnology and Biological Sciences Research Council) as providing the necessary skills and experience to contribute to their vision of developing and maintaining world-class UK bioscience. Course aims This course aims to equip graduate scientists with the computational skills and awareness needed to archive, analyse and interpret the vast amounts of biological data now becoming available. On completion of this course, you will be able to apply information technology to the development of new drugs and diagnostic tools. Additionally, you will gain the skills to design and implement new tools and software plugins to fulfill the need of the research community, and will be equipped with a diverse set of knowledge and skills that directly meet the requirements of employers in this sector. Career opportunities A degree from Cranfield will fast track your career, enabling you to go further, quicker. 93% of Cranfield s students are in relevant employment or further study within six months after graduation. Bioinformatics is a fast-growing field that offers progressive career opportunities for forward-thinking people who are ready to grasp the challenge; people who understand both the biological and computing aspects of this science. Our MSc is designed to meet the fast-growing international demand from industries such as pharmaceuticals and biotechnology, for competent staff who are skilled in both biological sciences and information technology. The course is also a route to further qualifications or a career in research. Cranfield places a high emphasis on practical, transferable skills. We realise that your current or future employer will value your ability to put your knowledge and skills into action. Our MSc has allowed our graduates to move into jobs in prestigious institutions including the Sanger Institute, European Bioinformatics Institute, Institut National du Cancer (France) and Centro de Investigación Príncipe Felipe (Spain). While some have entered bioinformatics in companies such as GlaxoSmithKline, PubGene and Tessella, others have chosen to move onto PhDs at top universities. Whichever route you choose, Cranfield s MSc will provide you with the skills you need for a successful career in modern biology.

3 Taught modules Eight taught two-week modules, comprising a mixture of teaching and hands-on sessions. The modules run from the beginning of October until December (modules 1-6) and from January until mid February (modules 7-8). Module 1: Introduction to Bioinformatics using Perl Aim: To provide an overview of bioinformatics, and to introduce the most relevant concepts in IT, as well as providing students with the ability to program in PERL; the most popular programming language in the bioinformatics community. Content: Introduction to bioinformatics, IT and bioinformatics; hardware networks & internet, OS & software, algorithms & programming, Introduction to PERL programming for: data manipulation, file maintenance, pipelining, packaging and interfacing system facilities Module 2: Exploratory Data Analysis and Essential Statistics using R Aim: To provide an overview of important concepts in statistics and exploratory data analysis. The module introduces the main concepts in analysing biological datasets using the R environment, as well as developing bespoke scripts for multivariate analysis such as principal components analysis and hierarchical clustering. Content: Introductory, descriptive and inferential statistics, significance testing, exploratory data analysis (PCA, HCA), introduction to programming using R Module 3: Next Generation Sequencing Informatics Aim: To introduce many core types of NGS projects, including ab-initio and de-novo sequence assembly, RNA-Seq analysis, as well as detailed hands-on practical sessions of our best practice data-analysis workflows. Content: Gene expression analysis using microarray, Introduction to Next Generation Sequencing (NGS) platforms, genome assembly and quality control, transcriptome informatics (i.e. RNA-Seq), Sequence data analysis platforms (e.g. Galaxy), variant calling Module 4: Proteome Informatics Aim: To provide an awareness of the current trends in proteomics and the crucial role that bioinformatics plays within this field. Content: Introduction to practical proteomics (qualitative & quantitative), proteomics repositories (PRIDE, PeptidAtlas, etc.), structural biology, Protein/peptide identification algorithms (Mascot, X!Tandem, OMSSA), tools for quantitative proteomic data (from itraq, SILAC, SRM, etc.) Module 5: Informatics for Metabolomics Aim: To explore the analytical and statistical techniques that are central to the field of metabolomics, and to introduce the emerging technologies that will generate yet more data in the future. Content: Introduction to metabolomics, NMR, LC-MS and GC-MS, advanced topics in R, multivariate classification (PLS-DA, SVMs, ANNs), Multiway analysis (PARAFAC), compound identification (e.g. spectral library searching), phenomics and biomarker discovery

4 Module 6: Programming using Java Aim: To introduce the concepts of object-oriented programming using Java, the preeminent programming language for serious application development on the Internet. The module covers the basic fundamentals of programming in Java, with hands-on practical sessions on implementing programs using calculations, variables, control statements and loops. Content: Fundamental principles of programming, object-oriented programming using Java, variables and calculations, strings, arrays, GUI programming Module 7: Data Integration and Interaction Networks Aim: To introduce systems biology, systems methodologies, the most important bioinformatics software tools, and explain the algorithms that underpin them. Content: Introduction to Systems Biology, data standard protocols, database design and normalisation, designing Web-based interfaces using Java EE, introduction to interaction networks, data integration using Taverna, data visualisation using Cytoscape Module 8: Simulating Biological Systems Aim: To develop the concepts of integrated data towards simulation of systems and to introduce the potential applications of robust simulation. Content: Networks dynamics (e.g. ODE and stochastic algorithms to rule based systems), SBML, modelling systems, i.e. ecell, concept of 3Rs and systems modelling, in silico approaches to toxicity and efficacy testing, GUI programming Dr Jennifer Cham User Experience Analyst EMBL-EBI Wellcome Trust Genome Campus My project, based in Vienna, involved developing methods to evaluate crossspecies gene expression data. Everything was new and exciting: bioinformatics hadn t been used in the project before, I had never been to Austria, the aim was to work out how to determine which genes were expressed in recombinant CHO (hamster) cells using data from mouse and rat. A few months later - I had developed a new bioinformatics tool, learned some Viennese dialect, and contributed to my very first peer-reviewed scientific paper! Julia Feichtinger PhD Student at the North West Cancer Research Fund Institute, Bangor University Living in Cranfield allowed me to connect with people from all over the world and broadened my horizons with social, cultural, and educational programs. Coming from Biochemistry and Biotechnology, this masters degree provided me with the knowledge to change into the field of Bioinformatics, where I always wanted to be.

5 Course structure Eight taught modules (40%) Each module runs for two weeks, the first week is based at Cranfield, consisting of lectures and practical sessions and the second week is reserved for private study and coursework preparation for the module assignment. Group Project: Building Bioinformatics Solutions (20%) Working in project teams is part of everyday working life. It requires not only your individual expertise, but also an appreciation of the skills of the other members of the team. This part of the course gives you the opportunity of working as part of a team, on a group project. This is an invaluable experience that will help you to recognise and implement the differing contributions that colleagues bring to team work, and the different roles that we can choose to play within a team. Individual Research Project (40%) A four-month thesis project carried out either at Cranfield or an external research establishment or commercial organisation within the UK or Europe. This gives you the chance to concentrate on a subject area of particular interest to you, perhaps in collaboration with the type of organisation that you are hoping to find employment. Part-time study This MSc is also available on a part-time basis, that usually takes two years to complete. It offers flexibility which suits individuals who need to balance a career with their studies. Most modules require students to spend only one week on-site and students can continue with coursework and assignments at a convenient time and location. Why Cranfield? Cranfield is the UK s only wholly postgraduate university specialising in science, technology and management. Cranfield offers a mature and professional study environment in which to develop your career. We hold a global reputation for inspirational teaching and research, industrial-scale facilities and superior links with industry and commerce. Students choose Cranfield for: Dedicated facilities as part of a 34 million investment Excellent employment prospects Superb academic support Exciting personal research projects that are carried out in either industry or academia Benefit from our reputation and expertise Cranfield University benefits from the input of a group of world-renowned experts in a range of applied sciences, including bioinformatics. We lead and collaborate in diverse research and consultancy projects, both nationally and internationally. Our collaborators include GlaxoSmithKline, Unilever, Sanofi Aventis, Rothamsted Research, the European Bioinformatics Institute, University of Athens and Cambridge University. The Applied Bioinformatics MSc is overseen by an advisory committee comprising senior representatives from leading employers, so you can be sure that what you learn will be applied, relevant and cutting-edge. Support Cranfield provides great support during and after your time with us. Our course has an excellent staff-to-student ratio ensuring that our academic team are able to provide quality teaching and on-going support throughout your studies. Cranfield s Bioinformatics Group comprises a team of entirely computer-based researchers who have been involved in several multi-million pound national and international projects, mainly funded by the BBSRC, EPSRC, the Wellcome Trust, the European Commision, and several companies including Unilever, Sanofi Aventis and GlaxoSmithKline. Our research activities include Next-Gen sequencing informatics, drug discovery, systems biology, food science and basic biology. This wide range of research activities and collaborations gives us the opportunity to offer a variety of research projects to our MSc students that suit their individual research interests. Our Career Service is also supportive with your career development and is accessible for up to three years after graduation. Course Directors and Supervisors are also extremely helpful and may help to connect you with prospective employers.

6 How to apply Apply online at: We recommend that individuals from overseas submit their application by the end of May. Start dates and duration Applied Bioinformatics MSc starts in October. The full-time MSc is a 12-month course. On a part-time basis it can be completed within two-three years. Life at Cranfield Cranfield University offers a professional study environment in which to advance your career. Our student body is made up of students from over 100 countries offering a culturally diverse environment in which to study. Our Cranfield campus is based between the two vibrant towns of Milton Keynes and Bedford, and acts as a great base to explore the area. Cranfield is also only an hour away by road or rail to Oxford and Cambridge and London, as well as major international airports (Heathrow, London Luton, Stansted and Gatwick). Accommodation We offer a variety of on-campus accommodation facilities including catered and self-catered halls and shared housing. Living on campus means students are conveniently close to lecture rooms and amenities. In addition we provide short-stay accommodation on-campus for our part-time students. Cranfield Student Association Cranfield Student Association is run by a team of elected students. The association organises a wide range of clubs, societies and entertainment for your enjoyment. Examples include an Astronomical Society, a Flying Club, various sporting clubs including badminton, football and squash, and a Horticultural Society. Entry requirements First or Second Class UK honours degree, or equivalent in a life science, or computer-science degree. English Language Testing System (IELTS) score of 6.5 or Test of English as a Foreign Language (TOEFL) score of 92 (if English is not your first language). Course fees and funding Funding may be available. Please contact our Enquiries Office for further information. Other opportunities Short courses For even greater flexibility and for those with a specific interest some MSc modules are available as standalone short courses. Please visit our website for more information. PhD We offer fantastic PhD opportunities in Bioinformatics many of which take place in collaboration with industry giving students the opportunity to interact with industry early on in their careers. Our PhD students become part of a rich research community within our Health and Biosciences Doctoral Training Centre. We welcome enquiries from students wishing to pursue their own research interest who are looking for a suitable supervisor. MSc by Research This is a one-year research programme enabling students to focus on a specific area of interest. Students also have the opportunity to attend modules from our taught programmes. If you would like to study an MSc by Research please contact us so we can discuss your research interest. For more information Please visit our website: Please contact our Enquiries Office for further information: T: +44 (0) E: enquiries@cranfield.ac.uk Join our LinkedIn group Follow us on Twitter for the latest news Join our Facebook group