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EPSRC & BBSRC Synthetic Biology Centre for Doctoral Training EPSRC & BBSRC Synthetic Biology Centre for Doctoral Training Student Handbook 2015 1 Contents Introduction 3 Programme Background 4 Key Objectives Programme Summary 7 Module Outlines 8 Core Modules; Career Development Skills; DTC Teaching Experience, Graduate Academic Programme Projects 18 The Supervisory Relationship Monitoring and Assessment 20 Student Space, Weblearn, Module Assessment; Module Assessment Submission; Module Questionnaires; Project Assessment; Project Assessment Submission; Academic Integrity; Project Questionnaire; Transition to DPhil; DPhil Assessment; Oxford Digital Theses; Alumni DTC Fourth Year Symposium Student Representatives Internships Resources 34 Libraries; DTC Library; Computing Facilities; Seminar Programmes; Telephone/Email/Mail Staff 39 DTC Staff; SynBioCDT Staff, Affiliated Staff Rex Richards Building 53 Parking; Access and Security; Fire Alarms; Office Etiquette; First Aid University of Oxford, Bristol and Warwick 55 University Card; Careers Service; Medical Care; Student Associations; Student Counselling Service; Sports and Physical Recreation; Support for Student Parents Administrative Matters 61 Programme Management; Position within the University; Timekeeping; Attendance; Absence/Illness; Academic Terms; Finance; Proof of Study, Equality and Diversity Unit; Interruption of Studies; University Health and Safety; Data Protection City of Oxford, Bristol and Warwick 69 Travelling to Information; Maps Appendix 77 MPLS Research Supervision, A Brief Guide 2 Introduction Welcome to the EPSRC & BBSRC Centre for Doctoral Training in Synthetic Biology (SynBioCDT), which is a joint venture between the Universities of Oxford, Bristol and Warwick. SynBioCDT is a 4-year Doctorate Programme in the interdisciplinary field of Synthetic Biology, which has been identified as an emerging discipline with the potential to create new industries and economies in the recent UK Synthetic Biology Roadmap report (http://www.rcuk.ac.uk/publications/reports/syntheticbiologyroadmap/). Our CDT operates in collaboration with three universities (Oxford, Bristol and Warwick) and with departments therein and with a wide range of Industrial, Academic and Public Facing Partners that cover all potential application areas of Synthetic Biology to create a unique training environment. This handbook has been designed to provide information about our policies and procedures and what is involved in studying at the DTC. It will also provide information that should be useful throughout the first year at Oxford. 3 Programme Background The three universities have extensive world-leading research activity at the life/sciences interface, much of which is underpinned by substantial existing funding from the EPSRC, BBSRC and other UK research councils, charitable trusts and HEFCE. The Universities also have a very strong track record in delivering innovative graduate level training in the physical and life sciences, providing skills acquisition and research training within the context of leading research teams in well-established interdisciplinary environments. Close alliance with major interdisciplinary centres gives students access to world leading research in the areas where engineering, mathematical and physical sciences meet the life sciences. In all three universities, students will become part of a growing, vibrant synthetic biology community. For example, the University of Warwick has recently established the Warwick Centre for Integrative Synthetic Biology (WISB) that brings together research groups from engineering, physics, computer science, life sciences and social sciences. WISB also acts as a hub of an international network including research partnerships with the University of Sao Paulo, University Pompeu Fabra, and Boston University. The University of Bristol also has a multi-disciplinary research centre, BrisSynBio, in which chemists, biochemists, biologists, engineers and mathematicians collaborate on synthetic biology projects. Topics comprise: Enzyme cascades and cell factories, Self- assembled systems and minimal cells, Programming complexity in natural systems, Engineering and modelling across scales and Research and Responsible Innovation. International collaborations include University of California at San Diego and MIT. The first year of your training will be at Oxford’s Doctoral Training Centre (DTC). This has become a major focus within Oxford for the training of doctoral researchers at the life sciences interface, helping to change the culture of graduate training in Oxford and in the UK as a whole. The DTC is comprised of six four-year graduate programmes: the Systems Biology (SysBio) DTC, the EPSRC-MRC Systems Approaches to Biomedical Science Centre for Doctoral Training (SABS CDT), the BBSRC Interdisciplinary Biosciences Doctoral Training Partnership (DTP), the EPSRC-MRC Oxford- Nottingham Biomedical Imaging CDT (ONBI), the Synthesis for Biology and Medicine CDT (SBM) and the EPSRC-BBSRC Synthetic Biology (SynBio) programme: The EPSRC-funded SysBio DTC was established at the start of the 2007/8 academic year and provides a comprehensive training programme for graduates from both the physical and life sciences wishing to undertake research careers in the exciting interdisciplinary field of Integrative Systems Biology. The SysBio DTC has its own distinctive research programme whose focus is to develop a systems approach to ‘bridging the gap’ between theoretical and experimental knowledge from the level of individual molecules to the level of the whole cell or organism. The EPSRC-funded SABS CDT (formerly SABS IDC) was established in the 2009/10 academic year. It provides a comprehensive training programme to graduates from both the physical and life sciences who wish to undertake research careers at the industrial interface in this exciting interdisciplinary field. The programme aims to create the next generation of research leaders in drug discovery particularly in the areas of computational and structural therapy discovery, data-driven drug discovery and physiological modelling. 4 The BBSRC-funded DTP began in 2012 and provides a training programme for graduates from biological or physical science backgrounds who wish to conduct leading-edge bioscience research and acquire the knowledge and skills needed to take full advantage of recent technological and theoretical developments in fields such as imaging and image analysis, bioinformatics, quantitative analytical techniques and computational modelling. The main themes of this programme are: Integrative Animal and Plant Biology, Mechanistic Molecular and Cellular Bioscience, Bioscience for Food, Industry and energy, and Exploiting New Ways of Working. The EPSRC and MRC-funded ONBI CDT is a collaborative venture between the Universities of Oxford and Nottingham, designed to provide a unique training in imaging science. The programme combines world-leading expertise in all aspects of cellular and clinical biomedical imaging across both institutions to create the next generation of industrial, healthcare and academic leaders in this vital field of research. The EPSRC SBM CDT provides a programme focused on excellence in synthetic chemistry. The programme offers joint academic-industrial training in all aspects of synthesis coupled with an in-depth appreciation of its application to biology and medicine. Research within the SBM CDT programme is clustered around a number of training and research foci (‘Project Fields’) in which synthesis is the unifying core discipline. The SBM CDT will adopt an 'open access' model to allow completely unfettered exchange of information, know-how and specific expertise between students and supervisors on different projects and across different industrial companies. The EPSRC- and BBSRC-funded Synthetic Biology CDT is an exciting collaboration between the Universities of Oxford, Bristol and Warwick which started in 2014. The programme combines world-leading expertise in engineering and the physical and life sciences across all three Universities to create the next generation of industrial and academic leaders in this important new field. Synthetic Biology provides opportunities for revolutionary advances in fundamental science and industrial technology. The CDT's four-year programme of research and training has strong industrial links and is highly multi-disciplinary, accepting students from a wide range of scientific backgrounds and focusing on the application of engineering principles to the design of biologically based parts, devices, and systems. 5 Key Objectives Provide basic background in biology, biochemistry, experimental techniques and biological physics. Provide practical and theoretical research skills in mathematical modelling, scientific computing, computer programming, and statistical methods. Provide extensive generic career development training in communication, presentation, writing, rhetoric and reading literature across disciplines (throughout the four-year programme). 6 Programme Summary The EPSRC & BBSRC Centre for Doctoral Training in Synthetic Biology (SynBioCDT) is a doctoral training program that combines the fundamental understanding of biological systems with the principles of engineering, so as to create the next generation of industrial and academic leaders in the nascent field of Synthetic Biology. The CDT focuses on the design and engineering of biologically based parts, novel devices and systems as well as the re-design of existing, natural biological systems across all scales from molecules
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