Department of Biochemistry GRADUATE COURSE HANDBOOK (2017-2018) CONTENTS INTRODUCTION Page 3

Graduate Course Handbook 2017-2018

Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom Tel: 01865 613200 Fax: 01865 613201

UNIVERSITY OF OXFORD Department of Biochemistry GRADUATE COURSE HANDBOOK (2017-2018) CONTENTS INTRODUCTION page 3

STUDENT RESPONSIBILITIES ON THE GRADUATE COURSE page 4

A. GRADUATE INDUCTION COURSE Timetable page 7 Topics covered in the Induction Course Postgraduate Research Supervision Supervisors page 8 Secondary Supervisors page 8 Thesis Committee page 8 Graduate Advisors page 9 Director of Graduate Studies page 9 College Advisors page 9 Skills Training Graduate Skills Workshop (VITAE) page 10 Record of Training and Achievement page 10 D.Phil. Symposium page 10 Departmental Facilities page 11 Data Handling and Keeping a Laboratory Notebook page 11 Departmental Safety page 11 Fire Safety page 12 Computing and IT Facilities page 12 Introduction to the Radcliffe Science Library page 13

B. STRUCTURE AND CONTENT OF THE GRADUATE COURSE

POSTGRADUATE WEBLEARN page 15

YOUR RIGHTS AND RESPONSIBILITIES page 15 First Year Probationer Status page 16 Graduate Induction Course page 16 Presentation Skills Course page 16 Preparing PowerPoint Presentations page 16 Effective Scientific Writing Skills Course page 16 Undergraduate Lectures (Master of Biochemistry Course) page 16 Research Seminars page 17 Assignments page 17 Transfer of Status Transfer to M.Sc. (Research) Status page 18 Transfer to D.Phil. Status page 19 Transfer of Status Process Outline page 19 Second Year Public Understanding of Science & Intellectual Property Rights page 22 Preparation for D.Phil. Symposium page 22

Third Year D.Phil. Symposium page 22 Confirmation of Status page 22 Poster Presentation page 23 Thesis Submission page 23 1

C. GENERAL POINTS Research Interests in the Department page 24 New Biochemistry page 24 Departmental Organisation page 24 Membership of Societies page 24 Oxford University Biochemical Society (OUBS) page 25 Teaching and Demonstrating by Graduates page 25 Attendance at Conferences page 26 English Language Courses page 26 Sickness Leave page 27 Holiday Allocation for Graduate Students page 27 Career Options After Your Degree page 27 The University Counselling Service page 27 Living in Oxford page 28 What to do in the event of an attack page 28

Appendix 1 List of new postgraduate students (October 2017) page 29 Appendix 2 List of Departmental Graduate Advisors page 30 Appendix 3 List of 2nd year postgraduate students page 31 Appendix 4 List of 3rd year postgraduate students and email addresses page 32 Appendix 5 List of 4th year postgraduate students and email addresses page 33 Appendix 6 Academic integrity: good practice in citation, and the avoidance of plagiarism page 34 Appendix 7 General Transferable Skills page 35 Graduate Skills Checklists page 36

INTRODUCTION

Welcome to the Department of Biochemistry in Oxford. It is the aim of this Department to be a leading centre of high quality research and scholarship in which postgraduate students make an important and valued contribution. This is one of the largest Departments of Biochemistry in Europe with a total of more than 100 postgraduate research students. Teaching and research in Biochemistry reflect the current growth and importance of the subject.

Research in the Department is broadly based and interdisciplinary, with more than 40 research groups split between five Research Themes: Cell Biology, Development and Genetics; Chromosomal and RNA Biology; Infection and Disease Processes; Microbiology and Systems Biology; and Structural Biology and Molecular Biophysics.

Research activities extend far beyond these premises, by collaboration with other biomedical departments in Oxford and the surrounding area (e.g. the Departments of Pathology, Physiology, Human Anatomy & Genetics, Chemistry and Physics, the Institute of Molecular Medicine, the MRC Genetics Unit at Harwell, and the Wellcome Trust Centre for Human Genetics), other universities, research institutes and industry in the UK and abroad. Some graduate research projects involve such collaborations and some of you will have the opportunity to train at other locations as well as in this department. All these collaborative links provide a rich intellectual environment, opportunities for training and access to other research facilities. We hope you benefit as fully as possible from your time here. Although large, the Department has a friendly atmosphere, and a busy scientific and social calendar.

In addition to providing fundamental training in biochemical research, which is transferable to a variety of disciplines in the biomedical and biological sciences, the graduate course also offers the opportunity for training in analytical and creative thinking, and in project management and personal development. These skills are highly valued in many spheres of employment, Higher Education, Academic and Industrial Research, Business and Commerce. There are workshops and lectures designed to equip you with a broad range of skills that should help you get the most out of your research during your time as a postgraduate student, and in your future career. The activities in which you are required to participate as part of your training are summarised on pages 4 and 5 of this Handbook.

We look forward to working with you.

Graduate Advisors The Director of Graduate Studies

STUDENT RESPONSIBILITIES ON THE GRADUATE COURSE

All Years Attend Research Skills and other Courses and Research Seminars. E.g. M.Biochem courses, Part II Options to fill in any required background, and advertised Postgraduate Programme Courses as required

Arrange and hold regular meetings with Supervisor(s) Submit a report on your progress each term via the Graduate Supervision System (GSS) Arrange and hold meetings with Thesis Committee (biannually)

1st Year All Programmes Michaelmas Term Attend Graduate Induction Course & Annual Postgraduate Symposium

Take the online Research Integrity Course: Biomedical Sciences (in particular module 4, which covers issues such as plagiarism). Access via https://www.admin.ox.ac.uk/researchsupport/integrity. You will need to create a user account before taking an online course Submit a Seminar Report to Graduate Advisors Complete Training Needs Analysis (TNA) form with your supervisor and submit it together with your termly progress report via GSS Towards the end of the term meet with the Director of Graduate Studies (meetings will be arranged by the Graduate Studies Administrator) (not applicable to students on Wellcome Trust D.Phil. programmes)

Hilary Term At the start of Hilary Term arrange and hold first meeting with Thesis Committee Attend Effective Writing Skills Course and prepare a critical review of one scientific paper and submit to Graduate Advisors for discussion *Part II & other courses, as required

Trinity Term Attend Department of Biochemistry Recess Attend Postgraduate Poster Symposium Meeting with Graduate Advisors to practice Presentation Skills and Prepare a Poster Arrange and hold second meeting with Thesis Committee Prepare Transfer of Status Report & Submit an Application for Transfer of Status using Form GSO.2 MSD by Friday of 10th week (except MSDTC & MPLS DTC 2nd Year students who must submit their report by Friday of 8th week Trinity Term)

All Programmes 2nd Year Arrange and hold at least two meetings with Thesis committee

Attend annual Postgraduate Symposium Attend vitae or similar course Attend and participate in Research Seminars Attend Department of Biochemistry Recess Attend annual Postgraduate Poster Symposium *Attend courses & events for generic, transferable skills as required, in areas detailed at https://www.medsci.ox.ac.uk/study/skillstraining *Attend seminars on Learning and Teaching, Ethics, Media, Public understanding of science, Social Context of Science as advertised Prepare an oral presentation for the Postgraduate Symposium and for any additional Programme presentation events that you are notified about.

3 and 4-year Programmes 3rd Year Arrange and hold at least two meetings with Thesis committee Give a presentation on your work to your “Research Laboratory” Attend Annual Postgraduate Symposium and give presentation if selected by your “Research Laboratory” Attend and participate in Research Seminars Present poster at the Annual Postgraduate Poster Symposium Apply for Confirmation of D.Phil. Status in 8th Term (form GSO.14MSD) (students on 4-year programmes, who do rotation projects in their first year, can delay Confirmation of Status until their 9th or 10th term) Attend Department of Biochemistry Recess

*Attend courses & events for generic, transferable skills as required, in areas detailed at https://www.medsci.ox.ac.uk/study/skillstraining Submission of M.Sc. Thesis no later than the end of Trinity Term of 3rd year

Submission of D.Phil. Thesis no later than the end of Trinity Term of 4th year 4th Year

All responsibilities, except those indicated with an asterisk (*) are absolutely required of all students. The seminars on Teaching and Learning are open to graduates in all years, except Year 1. They will be advertised on the web and by email, and require prior consultation with Supervisors and pre-registration.

GRADUATE INDUCTION COURSE

The Induction Course aims to:  Welcome you to graduate study in Oxford  Introduce you to new and current students on the same or related programmes  Introduce local research areas, facilities, support and safety systems  Highlight the importance of graduate skills and training opportunities

Attendance is a course requirement for all programmes. Please arrive at all sessions on time, as a register will be taken at the start of each session.

If your programme requires you to meet your supervisor or potential rotation supervisors or members of their research groups at this time, please arrange meeting time(s) with your supervisors at mutually convenient times. There is some time set aside within the Induction Course programme for meeting should you wish to use this time.

Key venues and people in the Department  New Biochemistry Reception, South-west end of New Biochemistry, Ground Floor  Biochemistry computer accounts: Dr John Elder, New Biochemistry Room 00-070, Tel (6)13333  Proximity cards: Mr Erol Canpunar, New Biochemistry Room 20-018, Tel (6)13210  Biological safety forms: Mr Steve Curnock, New Biochemistry Room 10-017, Tel (6)13275  Scholarships administered by Biochemistry: Mr Chris Manning New Biochemistry Room 50-006, Tel (6)13208

DEPARTMENT OF BIOCHEMISTRY GRADUATE INDUCTION COURSE 2017

Thursday 28th – Friday 29th September 2017 New Biochemistry Seminar Room (NBS)

28th September Time Venue

8:45- 9:15 Registration & Introduction Graduate Advisors & DGS NBS

9:15- 9:25 Welcome from the Head of Department Prof Mark Sansom

9:25- 10:10 Overview of the Graduate Induction & Skills courses Graduate Provisions and Processes Prof Matthew Whitby NBS

10:10-10:40 Keeping a Lab Notebook & electronic record keeping Prof Phil Biggin NBS

10:40-11:00 Refreshments

11:00-12:00 Health & Safety Jonathan Barker NBS

12:00-12:15 Departmental Computing Mr Julian Jordan NBS

12:15-12:35 Overview of services provided by IT Services Ms Pamela Stanworth NBS

12:35-13:15 Introduction of Departmental advisors Graduate Advisors NBS

Sandwich lunch (provided)

13:15-13:25 Graduate Group Photograph Dr Jeremy Rowntree NB

13:25-13:40 Research Facilities in Biochemistry Dr David Staunton NBS

13:40-14:10 Group A visit to Research Facilities Dr David Staunton NB

14:10-14:40 Group B visit to Research Facilities Dr David Staunton NB

14:40-15:10 Introduction to library facilities Ms Karine Barker NBS

15:10- Fire Safety Mr Steve Emery & Abbot NBS &University Parks

29th September Time Venue

9:30-12:30 Meetings with Supervisors or Lab groups at time to be arranged by students as required

13:30- 17:00 D.Phil. Symposium with presentations from Heads of Research Labs NBS

17:00- Drinks reception

A. TOPICS COVERED IN THE INDUCTION COURSE

POSTGRADUATE RESEARCH SUPERVISION –SUPPORT SYSTEMS

The Supervisor(s) together with two other members of staff who are independent research group leaders will monitor a student’s progress from admission to completion of their thesis, thus constituting a student’s Thesis Committee. Close guidance and research skills training and direction will be provided by the Supervisor(s) and their research group, while generic/transferable skills training and pastoral care and advice will be provided by Graduate Advisors, a College Advisor and the Director of Graduate Studies (DGS), all of whom are known as the Supervision Team.

SUPERVISORS

Your supervisor(s) is responsible for your academic guidance. It is most important that students communicate honestly and effectively with their supervisor(s) and their research group(s). It is very important that students communicate to their supervisor(s), without delay, any concerns or difficulties that may negatively impact on their progress. In the first instance, issues should be referred to the supervisor(s). If a student is uncertain whether the supervisor(s) should be informed, Graduate Advisors or the DGS can advise in confidence. Students should meet their Graduate Advisors and the DGS during the Induction Course or shortly after. If you have a problem with your supervision, or any other issue that is affecting your studies, you can discuss it with the DGS in strict confidence. If you are unhappy with the arrangements for your supervision, particularly if you want to change your supervisor, you should first try to discuss the situation with your present supervisor. If, for any reason, you do not wish to do this, then you should contact the Director of Graduate Studies for your department. It is the responsibility of the Director of Graduate Studies to approve a change of supervisor.

Formal Meetings with Supervisors

You are advised to meet regularly with your supervisor(s). In addition to informal meetings you should have at least 2-3 formal meetings each year, and keep a written record of agreed action points. Initially, students will consider possible research topics with their supervisor(s), decide which to attempt, and identify any training requirements. Students will take ownership of their research by reading critically the literature in their field and related areas, learning how to formulate and choose answerable research questions and pursuing these efficiently.

SECONDARY SUPERVISORS

In addition to the main supervisor each student is assigned one other named person who can provide academic advice. This “secondary supervisor” may be a formal co-supervisor, a member of your Thesis Committee or a senior Post-doc from the student’s research group. Unless the secondary supervisor is a formal co-supervisor, he/she does not have the responsibility to submit reports on your progress via the Graduate Supervision System (GSS) or guide your research.

Note that if your secondary supervisor is a member of your Thesis Committee then he/she is disqualified from acting as a Transfer of Status Assessor (see p.19) or Thesis examiner (see p.23).

THESIS COMMITTEE

Students reading for a D.Phil. or M.Sc. by Research in the Department of Biochemistry are assigned a Thesis Committee, which includes their supervisor(s) and two other members of staff. The Committee will have responsibility for following the student’s research progress.

Thesis committees must meet twice a year, for a short time (15 – 60 minutes), preferably in 9th week of Term, or at other times (e.g. you may invite the members of your committee to attend a presentation that you are giving and talk with them afterwards). In the 1st year a meeting is recommended in January and, if Thesis Committee members are not nominated assessors for the Transfer of Status viva, the second meeting should take place before the start of the second academic year. Students may discuss the membership of their committee with their supervisor(s) and the DGS.

Responsibilities of the Student

1. Organise and attend Thesis Committee meetings: Students must contact committee members and arrange a date/time/place for the meeting. Students will be responsible for following up their request and ensuring that meetings do take place.

2. Students must complete Part I of the Meeting Form take it to the meeting for completion and signature, and post it to the Director of Graduate Studies pigeonhole at the reception. The form will be retained in the student’s file to inform the Transfer of Status process.

3. The Thesis Committee may request students to write a report ahead of the meeting or prepare a presentation; otherwise no written reports or formal presentations will be required.

4. If the meeting is to follow a student’s presentation to their Research Theme, the student must invite their committee to the presentation as soon as the presentation is scheduled (well in advance). If neither committee member can attend, another meeting should be scheduled.

GRADUATE ADVISORS Graduate Advisors are a group of senior research staff responsible for monitoring and contributing to the graduate course (see Appendix 2). They are closely involved in the pastoral mentoring of graduate students. In the first year Graduate Advisors monitor students’ scientific writing and presentation skills. Each graduate student will be assigned to a group consisting of two Graduate Advisors and about five- eight students. Advisors will be happy to discuss in confidence any issues or difficulties that you may encounter during your course.

DIRECTOR OF GRADUATE STUDIES The Director of Graduate Studies (DGS) is responsible, among other things, for the departmental/programme administration of your course, for monitoring progression through course milestones and for advising as required (email: [email protected]). If you have a problem with your supervision, or any other issue that is affecting your studies, you can discuss it with the DGS in strict confidence. If you are unhappy with the arrangements for your supervision, particularly if you want to change your supervisor, you should first try to discuss the situation with your present supervisor. If, for any reason, you do not wish to do this, then you should contact the Director of Graduate Studies.

COLLEGE ADVISORS In addition to your supervisor(s) you will have an independent advisor appointed by your College. Their role is to monitor your academic progress and offer additional and independent guidance and support if you encounter problems or difficulties.

SKILLS TRAINING

As a graduate student you are expected to spend the equivalent of 10 days each year receiving formal training in research and transferable skills. Apart from a small number of events which are considered compulsory, and about which you will be notified by email, we encourage flexibility in training so that you can fit it around your other commitments such as laboratory research. It is very important that students liaise with their supervisors when considering whether to take a course, especially when this will require an absence from the laboratory for one or more days.

D.Phil./M.Sc. students in their 1st term are required to complete the Training Needs Analysis (TNA) form with their supervisor and upload the form on the Graduate Supervision System (GSS) along with their report. The form is available to download from the Medical Sciences Division Graduate School Weblearn site and is also available at the Progression forms site. You are encouraged to give examples of any training and/or experience that you have had in each skills area when completing the TNA form.

Students are expected to keep a record of all their training and report on their training in their termly online reports on GSS. Failure to keep a record of training could lead to a failure to transfer to M.Sc./D.Phil. status or failure to have D.Phil. status confirmed.

Details about training opportunities and how to book places for them can be obtained at the Divisional Skills Portal (https://www.medsci.ox.ac.uk/study/skillstraining).

There is a listing of all courses offered across the University on WEBLEARN.

A comprehensive online course on Research Integrity is available (https://weblearn.ox.ac.uk/portal/site/:skills:ricourses:biomed). We require that all students complete this course.

GRADUATE SKILLS WORKSHOPS - VITAE (Year 2) As a Research Scientist you are likely to devote much of your time to your own project and it is important to be able to work independently. However, good teamwork and co-operation between members of a lab is vital, for example where safety is concerned, and to facilitate learning and research. You may need to develop new skills in order to succeed in your D.Phil./M.Sc. and future career. The workshop will raise awareness about the importance of skills such as communication, teamwork, personal effectiveness, leadership, networking and others (see Appendix 7 for Graduate Skills). During your first year you will identify skills that you may need to develop, or your supervisor(s) may raise your awareness of skills you need to develop in order to work/study more effectively. You should then seek and take opportunities to do so.

RECORD OF TRAINING AND ACHIEVEMENT Record keeping will help you report formally to the Board when applying for transfer and confirmation of your D.Phil. student status. You may keep a record of your training using ASPIRE, Oxford's online personal development planning system. It encourages you to reflect on the skills you have acquired through your research and other activities and helps you to identify areas for further development. See https://www.medsci.ox.ac.uk/study/skillstraining You are also strongly advised to record and keep track of your training by self-reporting through the Graduate Supervision System, which informs your supervisors, DGS, and College advisor.

POSTGRADUATE SYMPOSIUM The Postgraduate Symposium is an annual event, forming part of the graduate training programme, at which graduate students entering their third or fourth year, depending on programme, present their work to the 10

Department. In 2010, the Department of Biochemistry was organised into Research Themes, which consist of Research Groups working in related scientific areas. The Research Themes provide a supportive intellectual and research environment for researchers and graduate students, e.g. through participation in seminars attended by researchers from related fields. Advisors organise an annual series of Research Student Presentations (Postgraduate Symposia), to which 3rd or 4th year D.Phil. and 1st year M.Sc. students are required to present their research. Each Research Theme selects 1-2 students to deliver their presentations again during the Graduate Induction week to the new students and the department.

The Heads of the five Research Themes will present an overview of their Theme’s research, followed by 1-2 student presentations. New Graduate students are strongly encouraged to participate by asking questions. There are prizes for the best student presentations and questions.  Chromosomal & RNA Biology (head: Professor Neil Brockdorff)  Cell Biology, Development & Genetics (head: TBC)  Structural Biology & Molecular Biophysics (head: Professor Mark Sansom)  Microbiology & Systems Biology (head: TBC)  Infection & Disease Processes (head: Professor Nicole Zitzmann) The Postgraduate Symposia are unique events at which a large volume of research done by graduate students associated with the Department of Biochemistry is presented. They form a very important part of graduate training in the areas of presenting and discussing research.

DEPARTMENTAL FACILITIES Information on core facilities will be provided to you in the coming weeks and at the Induction Course by Dr David Staunton. Facilities exist for mass spectrometry, micropscopy, NMR, X-ray analysis and crystallography, and a variety of biophysical techniques. DNA sequencing is available from Source Biosciences (https://www.sourcebioscience.com). Training will be provided for the use of equipment. Information about accessing core facilities is provided on the website: http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=services

DATA HANDLING & KEEPING A LABORATORY NOTEBOOK

This session is designed to outline the methods and importance of keeping a laboratory notebook and, in particular, how to record data clearly, precisely and in a secure manner. It will also outline the role of statistics in the analysis and presentation of biochemical data, with particular emphasis on the handling of experimental errors. An appreciation of how to represent various types of data in a quantitative way will be given and simple statistical principles will be explained, emphasising the use of confidence limits, least square analysis and non-parametric analysis. Common pitfalls will be discussed.

DEPARTMENTAL SAFETY

Mr Steve Curnock in the Biochemistry, Deputy Departmental Safety Officer, New Biochemistry, 20-061, [email protected]

Consult your Deputy Departmental Safety Officer if you are studying in additional or alternative Departments, and find out about local rules. All work carried out within the Department of Biochemistry must be in accordance with the University’s Safety Policy, which is in three parts:- (i) The Statement of Safety Policy: a brief document that sets out the general safety principles by which the University operates http://www.admin.ox.ac.uk/safety/hs-mgement- policy/univpolicy/; 11

(ii) Individual Safety Policy Statements: these provide detailed information and advice on specific subjects http://www.admin.ox.ac.uk/safety/policy-statements/

(iii) The Departmental Statement of Safety Organisation: this explains the roles of people who are responsible for various aspects of safety management in Biochemistry https://safety.dpag.ox.ac.uk/dept-specific-info/biochemistry/statement-of-safety- organisation/view

There is a copy of the Safety Policy in the Departmental Safety Office (20-061 New Biochemistry building)

Please note that Biochemistry Safety Pages are currently only able to be read from computers with a Biochemistry IP address.

A two-part Safety Induction needs to be completed by all workers in Biochemistry during their first day or two on the premises. This should be arranged with Mr. Curnock in conjunction with your supervisor. Before undertaking any experimental work you should make sure: that you have adequate supervision; that you have any necessary authorisation, e.g. a Home Office licence for animal work, or registration as a radiation worker; that you have been vaccinated against Hepatitis B if you are working with human blood products or cells; that the lab where you are working is of the appropriate category; and that you will be able to properly dispose of any waste produced. Your lab safety file should include a copy of the Departmental Statement of Health and Safety Organisation. This file should also contain risk assessments for any hazardous work carried out in the lab, including COSHH assessments that describe safe handling and disposal procedures for chemical reagents and micro-organisms. Whenever you are working in the lab it is your responsibility to follow the correct procedures, so as to minimise any risks to yourself and to those working around you. FIRE SAFETY University Safety Office This session will comprise a lecture on the action that should be taken in the event of a fire.

COMPUTING & IT FACILITIES IT FACILITIES

Please read the University IT rules and Biochemistry IT policies: http://www.bioch.ox.ac.uk/networkpolicy http://www.bioch.ox.ac.uk/itpolicies

You will be assigned a Nexus email account by Oxford University IT Services when your University Card becomes active. Information on the University email service is available at http://help.it.ox.ac.uk/email/index

IT Services run many training courses covering both introductory and specialised uses. Further information can be obtained from http://courses.it.ox.ac.uk

Departmental IT facilities are managed by the IT staff located in the New Biochemistry Building:

Mr Martin Ackland, Support Team Manager 10-026 extension 13307 [email protected] Dr Richard Bryan, Research Computing Manager 00-069 extension 13332 12 [email protected] Dr John Elder, Infrastructure & Security Manager 00-070 extension 13333 [email protected]

Mr Julian Jordan, Web & Macintosh Officer 10-027 extension 13310 [email protected] Dr Jeremy Rowntree, IT Systems Manager 10-027 extension 13309 [email protected]

Biochemistry network accounts are available to all members of the Department and students of affiliated programmes. They provide personal disc space for secure storage of files. Please contact Dr John Elder (Room 00-070) in order to activate your network account.

More information on Biochemistry IT facilities is available at http://www.bioch.ox.ac.uk/itsupport

INTRODUCTION TO THE RADCLIFFE SCIENCE LIBRARY The Radcliffe Science Library (RSL), part of the Bodleian Libraries (http://www.bodleian.ox.ac.uk/science), is situated on Parks Road (5 minute walk from the Department of biochemistry). Admission to the RSL operates through a swipe card entry system. Have your University Card with you at all times when you visit the library.

The library is open 8.30 am till 10.00pm Monday-Friday during the term. Services available in the library include quiet and bookable group study areas, 3D printing, Virtual Reality lending, inter-library loans, and self-service printing, copying and scanning (PCAS). Further details on these services and change in the opening hours during the academic year are available on the RSL website at http://www.bodleian.ox.ac.uk/science, “Using this Library”.

The RSL holds a very extensive range of current print and electronic books and journals. Electronic journals as well as e-books can be accessed from all University workstations and personal devices with your Single-Sign-On login (SSO).

Printed and electronic collections of books, journals, and databases are searchable through SOLO (Search Oxford Libraries Online), the University’s online library catalogue. SOLO contains item records from over 100 University and College libraries. The system allows journals and books in any library in Oxford to be located as well as accessing the full text of journal articles, full content of e-books, and bibliographic databases, such as Embase, Medline, Scopus, Web of Science. SOLO also provides direct links to OxLIP+, http://oxlip-plus.bodleian.ox.ac.uk , our collection of databases, online encyclopaedias, e-books, and OU e-Journals (Oxford University e-journal subscriptions), http://ejournals.bodleian.ox.ac.uk. SOLO is accessible from any computer on the University network at http://solo.bodleian.ox.ac.uk.

The online Biochemistry subject guide, http://libguides.bodleian.ox.ac.uk/biochemistry is a comprehensive website to help students find resources and information they need during their studies. Some resources listed will require Oxford Single Sign-On login when working outside the University network.

Subject librarians regularly review and update holdings on the advice of graduate representatives and teaching staff. If you have suggestions for books, journals and other resources to be purchased for the library, you can use the forms on the Bodleian website: http://www.bodleian.ox.ac.uk/bodley/finding- resources/recommendations for books and http://www.bodleian.ox.ac.uk/bodley/finding- resources/recommend for e-resources or email your Subject Librarian, Karine Barker, [email protected], with your recommendation and any other queries you may have.

Karine Barker can help you with using the catalogue, finding resources, searching databases, carrying out a literature search, setting-up current awareness, tracking research impact, applying for open access publishing, and saving citations with citation management software.

Please remember to take your University Identity Card with you to the RSL (if you have had one issued) and indeed carry it with you at all times in the University.

B. STRUCTURE AND CONTENT OF THE GRADUATE COURSE

POST GRADUATE WEBLEARN There is a weblearn site [https://weblearn.ox.ac.uk/portal/hierarchy/medsci/bioch/pg] that contains a copy of this handbook along with further information about the graduate courses within the Department. It also contains the links to all the information outlined in this handbook and further information about skills training. This site will be kept up to date with any changes made to the graduate course. Relevant information can also be found at the Medical Sciences Graduate School weblearn site at https://weblearn.ox.ac.uk/portal/hierarchy/medsci/department/grad_school/page/home

YOUR RIGHTS AND RESPONSIBILITIES A full list of your rights and responsibilities and those of your supervisors’ are detailed in weblearn. Here we give a Departmental Charter introduced by Professor Raymond Dwek in 1996: Students have a right to know: 1. The aims of their project and where it is leading. 2. A rough time scale in which to operate. 3. That they have a right to their supervisor's time and input. 4. Where to turn to should they have concerns regarding their project/supervisor/personal problems. A number of avenues for help and discussion are available. The earlier they make an approach the sooner these issues will be resolved. No problem is too small to be discussed, and no problem is too big to be resolved. 5. That they are a vital part of this department and they have the right, and the responsibility, to make the most of the excellent facilities and opportunities that are available to them - in terms of seminars, discussion groups, libraries, visiting scholars and distinguished speakers, techniques, etc. 6. That they can take the initiative and explore! 7. That all information given in confidence is kept strictly confidential. 8. That they are entitled to 38 days holiday per annum, inclusive of 8 statutory bank holidays and the time at Christmas when the Department is closed. Please note: (a) Your report for transfer to D.Phil. status (or M.Sc. status, if required) should be submitted by the Friday of 10th week in your third term (except MSDTC & MPLS DTC 2nd year students, who should submit by Friday of 8th week). (b) Transfer of Status is conditional upon fulfilling the compulsory modules (see page 4). (c) Successful completion of a D.Phil. will require you to develop a knowledge and understanding of your field of research as well as training in experimental methods. By the time of your Transfer of Status viva you should be able to discuss any techniques you have used as well as related/alternative procedures. You should also be able to demonstrate an appreciation of work carried out by others in your own and related fields. To recommend Transfer of Status your assessors must be satisfied that the work that you have carried out forms the basis of a D.Phil. thesis, that you have made appropriate future plans and that you are developing the ability to work independently. (d) You have a responsibility to your research group and you must therefore negotiate with your supervisor when you wish to take your holiday leave, for which you should give at least one month’s notice.

FIRST YEAR

PROBATIONER STATUS All new graduate students admitted to D.Phil. or M.Sc. initially hold the Probationer Research Student (P.R.S.) status. Subject to satisfactory progress you should transfer to D.Phil. or M.Sc. Status in your third term of study (see guidelines on pages 17-20). In the course of your research you should become aware of skills you may need to develop in order to learn how to do high quality research and communicate your work to your research group and wider audiences. You should discuss any such needs with your supervisors and advisors and take opportunities for skills development. You will need to report on the progress of your training on the application form for Transfer of Status (Form GSO2MSD - see p.17). The graduate course is designed to assist with the awareness and practice of some essential skills, which can be further developed through the following course requirements: Graduate Induction, Presentation Skills, Writing Skills Courses, and submission of three assignments, one per term during your first year.

GRADUATE INDUCTION COURSE The induction course in Michaelmas Term aims to introduce support systems, course milestones, introduce students to each other and research possibilities in Oxford, raise awareness of Graduate Skills Training, the Oxford Research Environment, Facilities and Services, and promote networking within the department and related graduate programmes.

PREPARING POWERPOINT PRESENTATIONS & POSTER SESSION The Oxford University Computer Services (13 Banbury Road, Oxford, OX2 6NN) offer courses on preparing presentations using Microsoft PowerPoint. Attendance at one, or both, of these courses is strongly recommended, prior to the Presentation Skills course, for those unfamiliar with PowerPoint. For details such as course dates and registration, please contact OUCS by phone (01865 273200), email [email protected], or via the web http://ithelp-test.nsms.ox.ac.uk

EFFECTIVE SCIENTIFIC WRITING COURSE Effective scientific writing is an essential skill for scientific research and is also readily transferable to many other careers. The writing skills course will take place ahead of your preparation of the Transfer of Status report, and will cover topics such as: Good style in scientific writing; Preparing scientific papers; theses and reports; Focus on abstracts and summaries; Illustrating your writing; Perfecting your draft. Further to the attendance of the course, 1st year students will be required to write a critical review of a scientific paper, which will then be discussed within the student’s advisor group.

UNDERGRADUATE LECTURES (MASTER OF BIOCHEMISTRY COURSE) General Lectures If you do not have a good background in Biochemistry or in your particular field of graduate study, you may wish to attend some of the lectures provided for 1st, 2nd and 3rd year undergraduates in the Department. Lecture lists are available in the University Gazette, on the Department’s Web page (www.bioch.ox.ac.uk/lectures/). You should discuss your attendance at such lectures with your supervisor and also email the lecturer concerned.

F.H.S Molecular And Cellular Biochemistry Part II Lecture Series Part II options are provided by the Department for fourth year undergraduates reading Biochemistry. Each option consists of a series of twelve specialist lectures held in Hilary Term, and details can be found in Weblearn. First year graduate students are encouraged to attend relevant Part II options if this is considered appropriate after discussion with their supervisor(s). The following Lecture Series will be offered by the Department in the academic year 2017-2018: Microscopy for all: research and outreach, Dr R.M.Parton, Dr D. Ennis and Prof I. Davis Advanced structural biology, Prof R. Gilbert Clinical and Applied Immunology, Prof J. Austyn

Virology, Prof N. Zitzmann From DNA to Chromosomes, Prof R. Klose Membrane Transport, Assoc. Prof S. Newstead and Prof B. Berks

RESEARCH SEMINARS The Medical Sciences Division and the Department of Biochemistry attach a high priority to your attendance at seminars. They provide an important part of your course and you should endeavour to attend as many departmental seminars as possible. The Departmental seminar committee and OUBS organise a seminar programme jointly and the aim is to represent a broad range of topics at a level suited to a general audience. These departmental colloquia take place on Mondays at 1:00 pm as advertised along with other seminars at http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=seminars. All members of the Department, both staff and students, are welcome to propose future speakers. Please send suggestions to OUBS. Each week a notice is put on the entrance doors to the atrium listing the seminars in the building for that week, additionally upcoming seminars are listed on the homepage of the department website, there are also email reminders. In addition the subject areas have their own seminar programmes seminars held in the following departments may also be of interest, see links for updates on times and venues at http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=460.

ASSIGNMENTS (MANDOTARY FOR D.PHIL. IN BIOCHEMISTRY, M.SC. BY RESEARCH IN BIOCHEMISTRY STUDENTS. OPTIONAL FOR OTHER PROGRAMMES INCLUDING STUDENTS STUDYING D.PHIL. IN BIOCHEMISTRY AT HARWELL MRC UNIT) As part of your assessment, you are required to prepare, write and submit the following assignments during your first year (3 terms) as Probationer Research Student. Michaelmas term You are required to write a short report on a seminar you have attended in Michaelmas term. Although you may attend seminars in any of the departments or sub-departments listed above, your report should be written on one of the Departmental colloquia but not one that closely relates to your own research topic. If you work outside the South Parks Road Science area, you may write a report on a seminar in your institution/department/unit. The following guidelines should be followed: i) Word limit 300-400 words i.e. 1-2 pages. Looking at abstracts of published papers may help you to write your report in a concise style. ii) Points to include (a) An introductory sentence. (b) Main points from the seminar. (c) Final summary. (d) A personal comment. Your report should be submitted to the Graduate Studies Administrator Erol Canpunar [email protected] as an email attachment – please use rich text format (RTF) or Word (doc). Your report will be read by your Advisors and returned to you, with comments/suggestions. Deadline for submission: Friday of 8th week Michaelmas term.

Hilary term

You will be required to write a critical review of one scientific paper related to your research in Hilary term. The following guidelines should be followed: i) Write a critical review on a paper of your choice in the style of a News and Views article, no more than 2 sides A4. ii) Start with the article title, full reference and authors, and your name. iii) Introduce and describe how this work is relevant, trying to put the work into a wider context. iv) Critique key methods and results along with their strengths and weakness as approaches. v) Include references to other data in describing how this contributes to the field. vi) If using a large paper pick only the Key methods/results to discuss in detail. vii) Write a standalone piece that can be read without reference to the original article. viii) Finish with the wider significance of these data, what work could lead on from this paper and future directions.

Please note your paper should be sent to the Graduate Studies Administrator, Erol Canpunar [email protected] and it will be shared among your advisor group members for peer review. Deadline for submission: Friday of 8th week Hilary term Group discussion: Dates to meet and discuss with your advisor group will be arranged at a later stage.

Trinity term

You will be required to attend the Presentation Skills course and prepare a PowerPoint presentation and a Poster.

The following guidelines should be followed: i) A PowerPoint presentation with maximum 6-7 slides ii) The presentation shall not last more than 12 minutes iii) Prepare a Poster and submit to your advisors’ email address (before start of the Presentation Skill Course). Attend any subsequent meeting with group adviser for discussion.

Presentation Skills Course: dates TBC Deadline for submission: date TBC

TRANSFER OF STATUS

The Department of Biochemistry require Probationer Research Students (D.Phil.) to transfer status by the end of their third term. Students must apply to the University for transfer using form GSO2MSD (Medical Science Division) downloadable from: http://www.ox.ac.uk/students/academic/guidance/graduate/progression

TRANSFER TO M.SC. (RESEARCH) STATUS Students should submit a completed GSO2MSD (Medical Sciences Division) form together with an outline of their project of no more than 500 words, and a timetable leading to thesis submission. They will be asked to give a presentation on their work. Students should consult the Notes for the Guidance of Graduate students in the Medical Sciences Division corresponding to the year of their admission to the course, for further details.

TRANSFER TO D.PHIL. STATUS

Postgraduates in the Department of Biochemistry are required to attempt transfer to D.Phil./M.Sc. by Research status as indicated in the Table below. A Candidate’s Thesis committee may in exceptional circumstances advise them to apply by no later than Friday of 1st week of their fourth Term. Candidates of the Joint Scripps-Oxford programme taking their qualifying examinations at Scripps should transfer in the 1st or 2nd year, according to their specific course requirements at Scripps.

Submit application Form and Programme Name Programme Transfer Report to DGS D.Phil. in Biochemistry, Joint Oxford Scripps D.Phil./PhD in D.Phil. in Biochemistry 3rd Term, Friday 10th week Biochemistry (Starting at Oxford)

M.Sc. by Research in M.Sc. by Research Programme 3rd Term, Friday 10th week Biochemistry

Joint Oxford Scripps Joint Oxford Scripps 15 August of 2nd year; as D.Phil./PhD in Biochemistry D.Phil./PhD required by Scripps regulations (Starting at Scripps Research) D.Phil. in Chromosome and Chromosome & Developmental 6th Term, Friday 8th Week Developmental Biology Biology D.Phil. in Cellular Structural Cellular Structural Biology 6th Term, Friday 8th Week Biology Integrative Systems Biology D.Phil. in: Integrative Systems Doctoral Training Centre, Life Biology, D.Phil. in Life Sciences Interface Doctoral Sciences Interface, 6th Term, Friday 8th Week Training Centre, Systems D.Phil. in Systems Approaches Approaches to Biomedical to Biomedical Science Science DTC

TRANSFER OF STATUS PROCESS OUTLINE

Students must apply for Transfer of Status using Form GSO2MSD (Medical Sciences Division). Assessors must be selected by supervisors according to the guidelines, and be invited by the DGS. The DGS will invite assessors and send them guidelines, assessor forms and student research reports. When assessors accept their invitations, the DGS will notify students to make arrangements with the assessors for their interview.

Students

1. Prepare their transfer report (see report details below) 2. Fill in and sign relevant Part I of Application Form GSO2MSD (Medical Sciences Division) (http://www.ox.ac.uk/students/academic/guidance/graduate/progression) including any relevant skills sections at the back, and obtain a signed statement from a main supervisor in Part II, that ‘they have read the student research report, approve the proposed subject for a thesis and consider the candidate well-fitted to undertake advanced research’. 3. Obtain college approval on the form through their college office. The form must be returned to the student to submit with their transfer report to the DGS by the deadline. The assessment should not take place prior to the Application Form being completed and submitted along with the report to 19

4. the Graduate Studies Administrator, Erol Canpunar in the Graduate Studies Office, Department of Biochemistry, South Parks Road, OX1 3QU, Oxford. 5. Failure to complete transfer to either M.Sc. or D.Phil. status by the end of the 4th term of study (except for students on programmes in which transfer is attempted in the 6th term) will cause the student status to expire and the student’s name to be removed from the Register of Graduate Students. For Programmes in which a later transfer is allowed (see table above) transfer must be completed by the end of the 6th term.

Guidelines for Selection of Assessors

1. Two assessors are required for D.Phil./M.Sc. by Research. 2. Both assessors should be internal to Oxford, although an honorary contract (for NHS employees) would be sufficient. Likewise, a contract research (post-doctoral) staff member who is employed by University of Oxford would be acceptable. 3. Students admitted to research study at the MRC MGU Unit at Harwell may choose one assessor from the MGU, but the other assessor should be from the University of Oxford. 4. At least one assessor should have supervised a student in the University of Oxford to completion. 5. It may be desirable for one of the assessors to be external to the student’s department, where this can be achieved. 6. Neither assessors should have acted in a supervisory capacity to the student. This includes the student’s College Advisor, DGS, Graduate Advisor or Secondary Supervisor. Transfer assessors may subsequently be invited as degree examiners for the student, provided they have not given further help/assistance to the student between transfer viva and final submission of M.Sc./D.Phil. thesis. 7. Academic visitors to the University cannot be invited to assess.

Research Report The report must be about experiments carried out and data obtained by the student, and contain a section outlining clear aims, including experimental approaches and an approximate timetable for development of the study to a thesis. The report should be no more than 3000 words (including the main text and figure legends, but not including the references), and may contain an appendix containing up to a further 2000 words. The number of words in the report and any appendix must be specified separately on the front cover. Reports containing more than the specified number of words will not be accepted. Two soft-bound paper copies of the Transfer report must be delivered to the DGS together with their application for transfer.

Report structure

1. Abstract: summarising aims, research question(s), approaches, results and conclusions 2. Introduction: setting the study in context of the literature, not exceeding 600 words. 3. Materials and Methods: unless developing materials and methods is a main objective of the D.Phil. project, standard or slightly modified materials and methods may be put in the Appendix. 4. Results: Student’s own research data and interpretation 5. Figures should be included to present results and provide clarity. There is no limit on the number of diagrams, but they should only be used where necessary. 6. Collaboration with other research groups is encouraged and if a student has made a contribution to other researchers' work, this can be included in the report with colleagues’ written permission. 7. Discussion 8. Conclusions 9. Research Proposal for the D.Phil. Thesis: A final section describing a student’s future work in sufficient detail in about 500 words, including a time scale and outline of proposed experiments. 10. References: There is no limit on the number of references cited (up to 100 may be reasonable). The titles of the papers cited must be presented in the references section.

English Language If a student’s first language is not English their Assessors will also assess their written and oral communication skills. Students should seek their Graduate Advisors’ informal assessment of their skills by way of Seminar Report feedback. They may access English Language lessons if advisable. If a student feels that they may be at a disadvantage at viva, it is strongly recommended that they attend English Language classes to gain confidence in speaking, and to seek advice from their supervisors and advisors.

Transfer viva Two assessors will jointly interview the student, fill in a form and write a report. The interview will normally last about one hour. Having read the student’s research report, assessors will ask questions about the specific work undertaken and proposed. It is expected that the student will have good general background knowledge of the field related to their work and the assessors would test this. In particular, assessors will be looking for the following in a good transfer report and interview:

1. A comprehensive knowledge of the literature relating to the student’s subject. 2. Ability to express ideas clearly, in English, both in writing and orally. 3. A clear understanding of what the student is doing and why. 4. Evidence of the student’s own input into the project and ability to work and think independently. 5. The quality and standard of the work performed. 6. Novelty and originality of work. 7. Ideas and plans for future work. 8. Ability to work independently. 9. Evidence that the project is likely to yield sufficient results in the time available. 10. Prospect of the student finishing within 4 years from programme start date. 11. Student’s ability to defend their completed and future work. 12. Evidence that they are getting adequate supervision. 13. Would the student benefit from additional supervision to facilitate their studies?

Outcome The assessors’ report will expand on areas where they feel there are concerns and provide scientific feedback on work presented and proposed future work. The report should be brief, except where necessary to list problems for the attention of the student. Assessors may give feedback on the student’s science and report during the interview, but the transfer outcome is not known until it is approved by the Board, therefore it is best practice for assessors not to state their recommendation to the student at the interview.

Department and Board approvals, updating of student record and communication of the outcome to the student. The assessors should post the assessment form and report to Graduate Studies Office, Department of Biochemistry, South Parks Rd, Oxford OX1 3QU. The student’s application will be appended to the form, sent to the Medical Sciences Division Board for decision and communication with the student. It is important that students submit their reports on time.

SECOND YEAR

PUBLIC UNDERSTANDING OF SCIENCE, SOCIAL CONTEXT OF SCIENCE, INTELLECTUAL PROPERTY, ENTREPRENEURSHIP The Division lists training opportunities for awareness of Intellectual Property (IP), entrepreneurship, social context and public understanding of science, and you should attend as many of these as your research and thesis timetables allow (https://www.medsci.ox.ac.uk/study/skillstraining) . PI refers to ideas, information and knowledge and, in the University context, can be viewed as the results and outcomes of research: ‘Intellectual’ because it is creative output and ‘Property’ because it is a tradable commodity. The University's Intellectual Property Policy in relation to students can be found at http://www.admin.ox.ac.uk/researchsupport/ip/.

PREPARATION FOR D.PHIL. SYMPOSIUM Depending on your programme you may wish to start preparation to put yourself forward for your laboratory’s D.Phil. Symposium presentation. If you choose not to do this at this stage of your programme, you must participate in the D.Phil. symposium the following year.

THIRD YEAR D.PHIL. SYMPOSIUM Details of the symposium format are given in the Skills Training (Section A) section of this handbook. The Advisors from your laboratory group will contact you with information regarding this in your second or third year (students in 3rd or 4th year programme). You must participate in your third or fourth year. If you are on the M.Sc. by Research programme you will be required to take part in your first year. Talks will last for 15 min, including question time, and any appropriate media for presentation can be used. Speakers are required to submit an abstract of about 200 words, including speaker's name, supervisor(s), abstract title and text, to the graduate studies administrator. The abstracts will be published on the Department's web site prior to the symposium unless students specify otherwise. Prizes are awarded for the best presentations.

CONFIRMATION OF STATUS (This is different from the Transfer of status). D.Phil. students are required to apply for confirmation of D.Phil. status, ideally by the end of the 8th term and not later than the 9th term after their admission to the University (for exceptions see: https://weblearn.ox.ac.uk/portal/hierarchy/medsci/department/grad_school/page/home). The purpose of the confirmation procedure is to determine whether you have made adequate progress since transfer of status, and to ascertain whether or not you will be in a position to submit for examination in due course.

Confirmation of Status Procedure The procedure and requirements for Confirmation of Status are:

1) Complete form GSO14MSD (Medical Sciences Division’s application form can be downloaded from the website: (http://www.ox.ac.uk/students/academic/guidance/graduate/progression). This should include a statement from the candidate’s supervisor(s) and from the candidate’s college as specified by the regulations governing the degree of Doctor of Philosophy. A statement detailing the skills training that the candidate has undertaken should also be included, together with a full contents list for their thesis, details of any remaining work to be undertaken with milestones for its completion, and dates for the submission of draft chapters to their supervisor(s) for comment. The completed form and accompanying paperwork should be handed to the Director of Graduate Studies.

2) The members of the candidate’s Thesis Committee will normally act as assessors for the Confirmation of Status. The Director of Graduate Studies will notify the assessors that an application for

Confirmation of Status has been made and send them copies of the completed GSO14MSD form and associated paperwork. The student will then arrange a meeting with his/her Thesis Committee at which he/she will be required to deliver a formal, oral presentation of his/her work. Following the presentation the assessors will conduct an interview with the candidate.

3) The assessors will report to the Board on the candidate’s suitability for confirmation of D.Phil. status. This report will be based on the information provided in the statement from the supervisor(s) and the statement from the candidate’s college as specified by the regulations governing the degree of Doctor of Philosophy, and in the supplementary statement from the candidate in conjunction with their presentation and interview. In cases where confirmation of status is not recommended the assessors will attach a short written report detailing where the work submitted falls below the standard required. Note that it is the responsibility of the student to arrange the meeting’s time/location and the GSO14MSD form should be submitted prior the meeting taking place with the assessors.

POSTER PRESENTATION Department of Biochemistry A poster session will be held for third year graduate students. All 3rd year students are required to contribute to this event, which will be advertised by email. Abstracts will be made available prior to the poster session and all members of the Department are invited to view the posters. Presenters should be available during the session to discuss their posters. Prizes will be awarded for posters voted best. Posters can be printed at the Physics Department’s Media Services Unit or at OUCS (http://www.oucs.ox.ac.uk/printing/).

THESIS SUBMISSION [3rd or 4th year as advised by the supervisor(s)] All students on 3- or 4- year programmes must submit their Thesis by the end of Trinity Term of their 4th year after admission to the University. Most Research Studentships or other awards are awarded for three years and you should aim to complete your practical work and write up your thesis by the end of your third year. Four-year studentships require thesis submission by the end of the fourth year from commencement of your funding. If you are following a 4-year course, you must start writing after 3.5 years, if you are on a 3-year course you must writing after 2.5 years, i.e. six months before it is due for submission. Guidelines for thesis preparation and details of the submission procedure can be downloaded from the website: http://www.ox.ac.uk/students/academic/guidance/graduate/progression

C. GENERAL POINTS

For general information and links concerning the graduate programmes please see: https://weblearn.ox.ac.uk/portal/hierarchy/medsci/bioch/pg

RESEARCH INTERESTS IN THE DEPARTMENT OF BIOCHEMISTRY Current research interests in the Department can be found on the Department’s web page (http://www.bioch.ox.ac.uk/aspsite/index.asp?pageid=73).

NEW BIOCHEMISTRY Many of the research groups in the Biochemistry department moved into New Biochemistry in 2008, however, there are also research groups based in the Rex Richards Building and the Rodney Porter Building. New Biochemistry has research laboratories and write-up areas from the lower ground to the third floor, while the basement houses support labs and specialist equipment. Each floor (with the exception of the ground floor) contains a small kitchen and sitting areas. The Biochemistry café is located on the ground floor next to the main entrance to the department and opens from 8.30am to 4.30pm. In addition to a selection of hot and cold drinks the café serves a variety of snacks and cakes as well as hot food and salads at lunchtime. There is also a vending machine in the Basement by the lifts.

DEPARTMENTAL ORGANISATION For administration of departmental studentships please see Mr Chris Manning, 50-006 New Biochemistry, ext13208. The New Biochemistry Stores, run by Mr John Hill and Mr Chris Scott 20-010, ext13280, keeps limited stocks of commonly used consumables and cleaning materials. To obtain items from Stores you will require an appropriate purchase order, prepared through the web-based Oracle system, signed by a senior member of staff. Stores are open between 08:00 and 16:30, Monday - Thursday and between 08:00 and 16:00 on Friday. To order equipment or materials from external suppliers a purchase order must be generated through Oracle, signed by a senior member of staff and faxed (by reception), unless the order is electronic. Some details can be found in “Help” of the Purchasing area of the departmental webpage. A training course (organised by Chris Manning - New Biochemistry 50-006, phone 13208) is required before using Oracle. Incoming and outgoing mail is dealt with by the Reception 20-020 ext 13200, at the Reception Desk in the New Biochemistry building. Incoming mail must be collected from the A-Z mail boxes on the right side of reception desk. The University operates a Messenger Service, which can be used to send items to other Departments and Colleges within Oxford. Mail for this service should be marked MESSENGER and placed in the appropriate box in the Reception. All other post, both internal (i.e. within the Department) and external, should be posted in the box labelled "All Other Mail" and “Internal Biochemistry Mail”. Mail is collected at 15:00. Your supervisor or a senior member of staff must annotate all external mail that requires franking with your group’s allocated reference number. Urgent mail can be sent by the Courier Service. Items, accompanied by the appropriate requisition form and courier request form, should be taken to the Reception desk before 15:00.

MEMBERSHIP OF SOCIETIES Membership of learned societies (e.g. the Biochemical Society, the Genetics Society, the Society for General Microbiology, the British Society of Immunology, the British Crystallographic Association, the British Society for Developmental Biology and the Society for Cell Biology, The Society of Chemical Industry (SCI), The Royal Society of Chemistry) offers important opportunities. Most societies organise pre-doctoral meetings as well as major symposia, which are often free for members, and many offer bursaries for attendance at International meetings. In addition Society Newsletters are an important source of information.

All graduate students are encouraged to join at least one Society. Most offer reduced registration fees for students. You should seek advice from other members of your lab as to the most appropriate Society to join. THE OXFORD UNIVERSITY BIOCHEMICAL SOCIETY (OUBS) The Oxford Biochemical Society (OUBS) is the official graduate student association affiliated with the Department of Biochemistry. The primary goal of OUBS is to promote understanding, discussion and review of exciting and current topics in biochemistry. The society invites outstanding speakers from outside Oxford to give lectures in the Department of Biochemistry. These talks attract students, post- docs and senior members from all of the various life-science departments of Oxford University. Recent speakers have included Prof Venki Ramakrishnan, Prof Robert Huber, Prof Susan Lindquist, and Prof Brian Kobilka. The OUBS also organises a range of periodic social events, including the ‘Friday at 5’ social hour, movie nights and group trips, to promote exchange between students outside of the laboratory environment.

OUBS holds a careers day every year to provide students and post-docs with information about the careers available to people with science degrees. Presentations are given by representatives from various organisations and there are opportunities to meet the speakers during the day. A recent venture of OUBS is its biological sciences magazine Phenotype. The magazine is printed and distributed across the University. Contributions come from PIs, post-docs and students and the editorial team is made up of people from several departments. Funding for OUBS comes from the biochemistry department, scientific societies and companies, which means that we do not charge subscription fees. Our activities and events are open to all University members. More information can be found on the OUBS web page: www.bioch.ox.ac.uk/~oubs. Please get in touch if you'd like to get involved in OUBS.

TEACHING AND DEMONSTRATING The Department provides lectures, problems classes and practical classes for all undergraduate students studying Biochemistry. There may be opportunities for graduate students to participate in teaching problems classes and demonstrating in practicals. Additional undergraduate teaching is provided by the individual Colleges for their own students and is mostly in the form of tutorials, for one to four students. College Tutors do the majority of this teaching, but they may enlist outside tuition for particular subject areas. As a graduate student you are encouraged, but not expected, to participate in undergraduate teaching. Before undertaking any teaching you must seek and obtain advice from your supervisor as to whether your research is on track for timely publications and your thesis will be submitted within the timescale of your funding and be within 4 years from starting your graduate course. Before getting involved in any teaching, you must seek your supervisors’ permission. In any case, according to University Guidelines you must not spend more than an average of 5 hours per week teaching (including marking) during term time and you should not undertake teaching during your first year or the last term of your final year of study. You should be careful not to take on too much teaching, to the detriment of your research. As a general rule it is best not to undertake teaching until your second year. The Department provides support for anyone involved in teaching. This can range from advice and guidance on an individual level, to instruction on how to teach specific practical or problems classes, to more general courses on how to give tutorials and classes organised by the Department together with the University Learning Institute. The LI also provides a much wider range of courses and available to anyone within the University. A course on Teaching Undergraduates is available for graduate students (organised by Dr Mark Wormald). Course dates will be publicised via the Web and pre-registration will be required: https://weblearn.ox.ac.uk/portal/hierarchy/medsci/bioch/pg/teachertrain

ATTENDANCE AT CONFERENCES Attendance at conferences, as well as providing valuable experience in presenting your research, also offers the opportunity to meet others who work in your own, and related, fields and hence the possibility of establishing collaborations. Most UK funding bodies provide an allocation for attendance at conferences. The amounts available and application procedures vary and you should discuss this with your supervisor well in advance of attending a conference. All applications for funding should be submitted in good time. Contributions towards conference travel can also be obtained from individual Colleges. The Department receives a conference allowance of £300 per year for each graduate student funded by the MRC and the BBSRC. If your supervisor approves attendance at a particular conference, you should download a travel and subsistence claim form from http://www.bioch.ox.ac.uk/aspsite/index.asp?sectionid=adminforms to claim against provision of your scholarship and submit the form to Mr Chris Manning in the Accounts office, to recover costs towards the conference. Please note that only expenses for which you can provide receipts may be claimed. Postgraduates in Biochemistry may apply to the Biochemistry Postgraduate Conference Fund for a grant of up to £500. The Fund was set up with a generous donation from DE Koshland to the Department of Biochemistry to support postgraduate education. Information about how to apply can be found at https://weblearn.ox.ac.uk/portal/hierarchy/medsci/bioch/pg Other major sources of funding for students are the various scientific societies. The Biochemical Society has quite a lot of funding for travel to meetings etc. The British Society for Developmental Biology, and the Society for Cell Biology are also quite generous and will give up to £400. You will need to check the Web pages of each Society for their criteria. Of course, you will need to join the Society and usually, the longer you have been a member, the more likely you are to get funding. Some meeting organisers offer bursaries or scholarships to assist student delegates. For example, the Keystone Symposia on Molecular and Cellular Biology provides a yearly average of 400 student scholarships. These scholarships, of $1000 each, can be used to help defray the expenses associated with conference attendance. Abstracts submitted for poster presentation are used as the basis for awarding the scholarships. Conference organisers will select the scholarship recipients based solely on the quality of science of the abstract and the relevance of the abstract to the conference topic. Please visit www.keystonesymposia.org for more information on scholarships and how to apply, or email [email protected] See also https://weblearn.ox.ac.uk/portal/hierarchy/medsci/bioch/pg

ENGLISH LANGUAGE COURSES The University of Oxford Language Centre was established to help members of the University who need foreign languages for their study or research. Classes in English for Academic Studies are also available. The Department encourages participation in these classes, as involvement usually results in students enjoying their studies far more and they usually see a marked improvement in the quality of their written work. Full details can be obtained from the University of Oxford Language Centre at 12 Woodstock Road (tel: 283360; fax: 283366, e-mail: [email protected]). Alternatively, you can get these details from the web (www.lang.ox.ac.uk). If you are a postgraduate student at University of Oxford for whom English is a foreign or additional language, you are entitled to take two free courses in English (Academic Writing and one other listed below) and you have priority. How to Register You must go to the Language Centre reception in person to register and complete a registration form. Registration takes place in 0th Week of Michaelmas Term and continues until courses are full. You can join the waiting list for courses at any time during the academic year and will be contacted by email as 26 soon as a place becomes available. You should only register for a class when you know that you will be able to attend the class regularly.

Some of the Year-round courses are: Academic Writing; Advanced English; English for Social and Academic Purposes.

Recommended Books for all courses (available from Blackwells): Instead of relying on a bilingual dictionary, you should buy a monolingual dictionary for learners of English. There are several good ones to choose from (e.g. Macmillan English Dictionary for Advanced Learners, Oxford Advanced Learner's Dictionary, Collins COBUILD English Dictionary for Advanced Learners or Cambridge International Dictionary of English). These are available in paperback or hardback, and the most recent editions include CD-ROMs. You should also have an English reference grammar. Look through the grammars in the library to decide which would be most suitable for you. We suggest Carter, R., Hughes, R. and McCarthy, M. (2000) Exploring Grammar in Context. Upper Intermediate and Advanced. (CUP) or Swan, M. (1995) Practical English Usage. (OUP) or Vince, M. (1994) Advanced Language Practice (with key) Macmillan Heinemann ELT.

SICKNESS LEAVE Students must notify their supervisor about any absences and must write or send an email to their supervisor(s) informing them of their reasons for absence. Students are required to keep a record of these communications. For absences of more than seven calendar days that are due to illness, students must submit a doctor’s letter to their DGS for their file.

HOLIDAY ALLOCATION The amount of holiday you are entitled to is 38 days per year. This is inclusive of Bank Holidays (usually 8 days per year) and 5 days at Christmas when the Department is closed. When you take a holiday or a few days off work is a matter for you to discuss with your supervisor, ensuring you give sufficient advance notice. It is advisable that you take at least 2 weeks break each year.

If your work dictates that you are unable to take any of the "statutory'" days holiday, you may take time off in lieu subject to discussion with your supervisor. Students from abroad who wish to take a long single holiday, rather than a number of shorter breaks, should make suitable arrangements with their supervisor. When planning your holidays you should try to avoid dates that have been assigned for components of the graduate course.

CAREER OPTIONS AFTER YOUR DEGREE There is plenty of help available from Oxford University Careers Service, which is free and open to all our students, alumni and researchers. It provides careers guidance and information, as well as organising careers talks, fairs (including an annual Science, Engineering and Technical Fair) and skills training workshops, with events also tailored specifically for postgraduate students. Visit www.careers.ox.ac.uk where you can register, book an appointment with a Careers Adviser, search the vacancy database, see the term programme of careers events and lots more. Claire Chesworth, Careers Adviser, Oxford University Careers Service, www.careers.ox.ac.uk

THE UNIVERSITY COUNSELLING SERVICE Graduate students are expected to make a significant contribution to their field and this can be a very challenging experience. Students are responsible for becoming well informed about current knowledge and methods of study and must also become experts in specialised techniques and learn how to apply these. They need to take initiative in learning and suggest experiments and develop good working relationships with their supervisors and others in the lab, where many technical and research skills are employed. Students will learn to cope with failures and difficulties, and find ways to overcome problems. The website http://www.ox.ac.uk/students/welfare/counselling lists resources available to graduate students and how to access them.

LIVING IN OXFORD For information about things related to living in Oxford, whether it’s finding accommodation or somewhere to eat the daily info website (http://www.dailyinfo.co.uk/) has a lot of information. For places to eat close to the department there are a range of cafés and sandwich shops on Woodstock Road and Little Clarendon Street.

WHAT TO DO IN THE EVENT OF AN ATTACK

APPENDIX 1

Postgraduate Students, cohort 2017

Title Name Surname Programme Res. Dept Supervisor Supervisor Group Lab. Miss Srishti Arora DPhil in Biochemistry CRBG BIOC P Ligoxygakis 1

Mr Cillian Brophy DPhil in Biochemistry CRBG BIOC A Furger 2

Miss Paige Chandler DPhil in Biochemistry CRBG Harwell R Cox M Whitby 3

Mr Honglin Chen DPhil in Biochemistry CRBG BIOC A Castello S Mohammed 4

Mr Owen Crowther MRes in Biochemistry SBMB BIOC A Watts 5

Miss Laura Dyer DPhil in Biochemistry CRBG Harwell R Cox M Whitby 1

Mr Gavriil Gavriilidis MRes in Biochemistry CBDG BIOC A Woollard 2

Mr Thomas Harrison DPhil in Biochemistry IDP BIOC M Higgins 3

Mr Mark Hickling MRes in Biochemistry CRBG BIOC A Furger 4

Mr Patrick Inns DPhil in Biochemistry MSB BIOC C Kleanthous 5

Mr Malick Jagne DPhil in Biochemistry CRBG BIOC M Whitby 1

Mr Deniz Kaya DPhil in Biochemistry CRBG BIOC S Mohammed R Klose 2

Mr Young Seok Lee DPhil in Biochemistry CRBG BIOC I Davis 3

Miss Colette Lipp DPhil in Biochemistry CBDG BIOC M Cohn 4

Mr Patryk Ludzia DPhil in Biochemistry CRBG BIOC B Akiyoshi 5

Miss Yao Meng DPhil in Biochemistry CBDG BIOC P Handford 1

Mr Re’Em Moskovitz DPhil in IDP BIOC N Zitzmann 2 Biochemistry(OU/TSRI) Miss Silvia Raineri DPhil in Biochemistry SBMB BIOC J Mellor 3

Miss Jagoda Rokicka* DPhil in Biochemistry CRBG BIOC N Lakin 4

Mr Arne Scheu DPhil in Biochemistry CBDG BIOC M Howarth 5

Mr Che Chun Tsui DPhil in SBMB BIOC M Sansom 1 Biochemistry(OU/TSRI) Mr Menelaos Voulgaris DPhil in Biochemistry CRBG BIOC K Nasmyth 2

Miss Di Yang DPhil in Biochemistry CBDG BIOC M Cohn 3

Mr Kelvin Yaprianto DPhil in Biochemistry CBDG BIOC M Cohn 4

Mr Konstantinos Klaourakis DPhil in CDB WT CDB tbc tbc 5

Miss Clara Pavillet DPhil in CDB WT CDB tbc tbc 1

Mr Frederick Richards DPhil in CDB WT CDB tbc tbc 2

Miss Rosa Stopler DPhil in CDB WT CDB tbc tbc 3

Miss Komal Yasmin DPhil in CDB WT CDB tbc tbc 4

Ms Claire Coupland DPhil in SB WT SB tbc tbc 5

Mr Tomas Da Costa Cabral DPhil in SB WT SB tbc tbc 1 Gomez Mr Samuel Gérard DPhil in SB WT SB tbc tbc 2

Mr Rory Hennell James DPhil in SB WT SB tbc tbc 3

Mr Reinis Ruza DPhil in SB WT SB tbc tbc 4

Miss Céline Zheng DPhil in SB WT SB tbc tbc 5

* Starts Trinity Term 2018

SBMB: Structural Biology & Molecular Biophysics CRBG: Chromosomal and RNA Biology CBDG: Cell Biology, Development & Genetics MSB: Microbiology & Systems Biology IDP: Infection & Disease Processes

APPENDIX 2 Departmental Graduate Advisors

Advisor Group Research Laboratory Email

Group 1 Kathryn Scott Infection & Disease Processes [email protected]

David Staunton Structural Biology & Molecular [email protected] Biophysics

Group 2 Martin Cohn Cell Biology, Development & [email protected] Genetics

Philip Stansfeld Structural Biology & Molecular [email protected] Biophysics

Group 3 Stephan Uphoff Chromosomal and RNA Biology [email protected]

Felicity Alcock Microbiology & Systems Biology [email protected]

Group 4 Heather Coker Chromosomal and RNA Biology [email protected]

Tatyana Nesterova Chromosomal and RNA Biology [email protected]

Group 5 George Wadhams Microbiology & Systems Biology [email protected]

Joanna Miller Infection & Disease Processes [email protected]

Graduate Studies Office

E-mail: [email protected]

Director of Graduate Studies: Prof. Matthew Whitby

Graduate Studies Administrator: Erol Canpunar

APPENDIX 3

2nd Year Postgraduate Students, cohort 2016

Title Name Surname Programme Res. Lab. Dept Supervisor Supervisor Group

Mr Onno Akkermans DPhil in Biochemistry MSB BIOC E Seiradake 5

Mr Irsyad Anuar Khairil DPhil in Biochemistry CBDG BIOC M Howarth 1

Miss Nehir Banaz DPhil in Biochemistry CRBG BIOC K Nasmyth D Sherratt 4

Miss Theodora Bruun MRes in Biochemistry CBDG BIOC M Howarth 3

Mr James Collier DPhil in Biochemistry CRBG BIOC K Nasmyth D Sherratt 2

Miss Lucy Dunbar DPhil in Biochemistry CRBG Harwell M Bowl M Whitby 3

Mr Max Epstein DPhil in Biochemistry SBMB BIOC P Biggin 5

Mr Mario Hensen DPhil in Biochemistry IDP BIOC N Zitzmann 1

Miss Jia Hui Khoo DPhil in Biochemistry MSB BIOC J Armitage 2

Miss Walaa Khushaim MRes in Biochemistry CRBG BIOC J Mellor 4

Me Marian Kupculak DPhil in Biochemistry CBDG BIOC M Cohn 4

Mrs Jean Metson MRes in Biochemistry CRBG BIOC K Nasmyth D Sherratt 1

Miss Shanlin Rao DPhil in Biochemistry SBMB BIOC M Sansom 5

Miss Lisa Rodermund DPhil in Biochemistry CRBG BIOC L N Brockdorff 3 Schermelleh Mr Henry Sawczyc DPhil in Biochemistry SBMB BIOC A Watts 4

Miss Ülkű Uzun DPhil in Biochemistry CRBG BIOC J Mellor 2

Mr Yasunori Watanabe DPhil in Biochemistry IDP BIOC M Crispin M Wormald 1

Mr Joseph Bowness DPhil in CDB CRBG BIOC N Brockdorff 1

Miss Amy Hughes DPhil in CDB CRBG BIOC R Klose 3

Ms Anna Lamstaes DPhil in CDB CRBG BIOC J Mellor 4

Mr Jonathan Goult DPhil in SB MSB BIOC C Kleanthous 2

Miss Elizabeth Jefferys DPhil in SB SBMB BIOC M Sansom 3

Miss Iva Atanaskovic DPhil IITM MSB BIOC C Kleanthous M Maiden 4

Miss Juliane Brun DPhil IITM IDP BIOC N Zitzmann B Wills 5

Mr Zhiyi Wu DPhil Ion Channels & Disease SBMB BIOC S Newstead 2

Mr Oliver Adams DPhil Biochemistry IDBS SBMB BIOC S Newstead P Fowler 5

Mr Conor Kelly DPhil Biochemistry IDBS SBMB BIOC S Shammas C 3 Kleanthous/A Bowen Miss Harriet Lester DPhil Biochemistry IDBS CRBG BIOC A Furger 1

Mr Phillip Lorenz DPhil Biochemistry IDBS CRBG BIOC J Mellor 2

Miss Jisoo Jean DPhil Biochemistry IDBS CBDG BIOC M Howarth M Bedford 4

APPENDIX 4

3rd Year Postgraduate Students, cohort 2015

Title Name Surname Programme Res. Lab. Dept Supervisor Supervisor Group

Miss Sarah-Beth Amos DPhil in Biochemistry SBMB BIOC M Sansom 1

Mr Javier Camallonga DPhil in Biochemistry SBMB BIOC A Watts 4

Mr Marc Daemgen DPhil in Biochemistry SBMB BIOC P Biggin 1

Mr Thomas Dixon DPhil in Biochemistry SBMB BIOC S McLain 5

Miss Jodie Ford DPhil in Biochemistry IDP BIOC J Vakonakis 2

Miss Nadezda Fursova DPhil in Biochemistry CRBG BIOC R Klose 3

Mr Alberto Gonzalez DPhil in Biochemistry MSB BIOC A Angel J Mellor 2

Mr Li-Yao Huang DPhil in Biochemistry CBDG BIOC C Pears 4

Mr Steven Lavington DPhil in Biochemistry SBMB BIOC A Watts 1

Miss Caroline Lenz DPhil in Biochemistry CRBG BIOC A Castello 5

Mr Faiz-Hafiz Muhd Kipli DPhil in Biochemistry SBMB BIOC J Schnell 5

Mr Milan Muso DPhil in Biochemistry CRBG Harwell R Cox P 5 Ligoxygakis Miss Gemma Seabright DPhil in Biochemistry IDP BIOC/Sot’on M Wormald M Crispin 2

Miss Shahana Sengupta DPhil in Biochemistry CRBG Harwell R Cox L Vasilieva 4

Mr Doğukan Ülgen DPhil in Biochemistry CRBG BIOC L Vasilieva 4

Miss Nilanka Perera DPhil in Biochemistry IDP BIOC N Zitzmann 3

Miss Hannah Walters DPhil in Biochemistry CBDG BIOC L Cox 2

Mr Florian Zobel MRes in Biochemistry CRBG BIOC N Lakin 3

Mr Shidong Xi DPhil in Biochemistry CRBG BIOC J Mellor 4

Mr Miles Huseyin DPhil in CDB WT CDB BIOC R Klose 5

Miss Natalie Barber DPhil in SB WT SB BIOC M Higgins 5

Mr Phillipp Braeuer DPhil in SB WT SB BIOC S Newstead F Barr 1

Mr Augustinas Silale DPhil in SB WT SB BIOC B Berks S Lea 1

Ms Hannah Behrens DPhil in IITM WT IITM BIOC C Kleanthous 5

Mr Joseph Bluck DPhil SABS SBMB BIOC/STAT/ P Biggin S Conway/ 3 CRL G Morris Miss Liisa Parts DPhil Biochemistry IDBS CBDG BIOC A Woollard 4

Miss Kathryn Potter DPhil Biochemistry IDBS MSB BIOC G Wadhams 2

Miss Qinrui Wang DPhil Biochemistry IDBS SBMB BIOC M Sansom 1

Miss Sophie Williams DPhil Biochemistry IDBS SMBM BIOC P Stansfeld R Gilbert 5

Mr Gianni Klesse DPhil Systems Biology-Biochemistry SBMB BIOC M Sansom S Tucker 5

APPENDIX 5

4th Year Postgraduate Students cohort 2014

Title Name Surname Programme Res. Lab. Dept Supervisor Supervisor Group

Mr Josip Ahel DPhil in Biochemistry CBDG BIOC F Barr 2

Mr Juan Bada DPhil in Biochemistry SBMB BIOC A Watts 5

Miss Ying Bai DPhil in Biochemistry CBDG Harwell R Cox R Klose 4

Mr Can Buldun DPhil in Biochemistry CBDG BIOC M Howarth 1

Mr George Hedger DPhil in Biochemistry SBMB BIOC M Sansom 2

Miss Nadiya Ishnazarova DPhil in Biochemistry CRBG BIOC M Whitby 1

Miss Tea Kecman DPhil in Biochemistry CRBG BIOC L Vasilieva 4

Ms Lan Ngoc Le DPhil in Biochemistry IDP BIOC N Zitzmann 3

Miss Catherine Livermore DPhil in Biochemistry CBDG Harwell A Greenfield F Barr 3

Mr Alastair Louey DPhil in Biochemistry CRBG BIOC A Furger 2

Mr David Lopez-Martinez DPhil in Biochemistry CBDG BIOC M Cohn 4

Mr Nikolaos Michelarakis DPhil in Biochemistry SBMB BIOC M Sansom P Stansfeld 3

Miss Fiona Naughton DPhil in Biochemistry SBMB BIOC M Sansom A Kalli 4

Ms Nicola Steinke DPhil in Biochemistry SBMB BIOC S Mclain C Redfield 5

Miss Sanjeeta Tamang DPhil in Biochemistry CRBG BIOC M Whitby 5

Miss Jennifer Vibert DPhil in Biochemistry CRBG Harwell R Cox I Davis 4

Miss Florence Wagner DPhil in Biochemistry CRBG BIOC D Sherratt 5

Mr Jack Feltham DPhil in CDB WT CDB BIOC J Mellor 1

Miss Tamsin Samuels DPhil in CDB WT CDB BIOC I Davis 4

Mr Aidan Walker DPhil in CDB WT CDB BIOC A Woollard 5

Miss Jemma Day DPhil in SB WT SB BIOC J Vakonakis 1

Mr Ashley Gillum DPhil in SB WT SB BIOC S Newstead 2

Mr Johan Hill DPhil in SB WT SB BIOC N Zitzmann 3

Mr Felipe Ossa DPhil in SB WT SB BIOC J Schnell S Padilla-Parra 4

Mr Thomas Brown DPhil SABS MSB BIOC A Angel J Mellor 4

Miss Marie-Louise Francis DPhil Biochemistry MSB BIOC C Kleanthous 1 IDBS Miss Abigail Guillermo DPhil Biochemistry CBDG BIOC A Woollard 2 IDBS Mr Martin Hailstone DPhil in Biomedical CRBG BIOC I Davis 3 Imaging Mr Michael Hopkins DPhil SABS MSB BIOC B Novak 1

Miss Megan Sloan DPhil IITM CBDG BIOC P Ligoxygakis K Gull 5

Miss Beatrice Tyrrell DPhil IITM IDP BIOC N Zitzmann 1

Mr Naushad Velgy DPhil in Systems SBMB BIOC P Biggin 4 Biology-Biochemistry

APPENDIX 6

ACADEMIC INTEGRITY: GOOD PRACTICE IN CITATION, AND THE AVOIDANCE OF PLAGIARISM The University’s code of conduct concerning academic integrity is set out on the website at http://www.admin.ox.ac.uk/personnel/cops/researchintegrity/, and while the code’s principles relate specifically to the conduct of research, all graduate students are advised to make themselves aware of the document’s contents.

The code of conduct mentions plagiarism, and in this context it is important for all taught course and research students within the division’s subject areas, to be aware of and to follow, good practice in the use of sources and making appropriate reference. You will need to exercise judgement in determining when a reference is required, and when material may be taken to be so much a part of the ‘general knowledge’ of your subject that formal citation would not be expected. The basis on which such judgements are made is likely to vary slightly between subject areas, as may the style and format of making references. Your supervisor, or course organiser where appropriate, will be in the best position to advise you on such matters; in addition, these may be covered, along with other aspects of academic writing, in your induction training.

By following the citation principles and practices in place in your subject area you will develop a rigorous approach to academic referencing, and avoid inadvertent plagiarism. Cases of apparently deliberate plagiarism, while happily infrequent in the University are taken extremely seriously. Where examiners suspect that this has occurred they bring the matter to the attention of the Proctors. Your attention is drawn to the Proctors’ and Assessor’s Memorandum, Section 9.5, ‘Conduct in Examinations’, and in particular to sections 4 and 5 and the concluding paragraph of the section:

4. No candidate shall present for an examination as his or her own work any part or the substance of any part of another person’s work.

5. In any written work (whether thesis, dissertation, essay, coursework, or written examinations) passages quoted or closely paraphrased from another person’s work must be identified as quotations or paraphrases, and the source of the quoted or paraphrased material must be clearly acknowledged.

The University employs a series of sophisticated software applications to detect plagiarism in submitted examination work, both in terms of copying and collusion. It regularly monitors on-line essay banks, essay-writing services, and other potential sources of material. It reserves the right to check samples of submitted essays for plagiarism. Although the University strongly encourages the use of electronic resources by students in their academic work, any attempt to draw on third-party material without proper attribution may well attract severe disciplinary sanctions.

APPENDIX 7

GRADUATE SKILLS

Students are actively encouraged to make appropriate use of the teaching and learning facilities available within the University, which has a wealth of expertise and opportunities to further one’s professional development, training and skills, as expressed in the joint statement of the Research Councils. These skills may be present on commencement, explicitly taught, or developed during the course of the research. Different mechanisms support learning as appropriate, including self- direction, supervisor support and mentoring, departmental support, workshops, conferences, elective training courses, assessed courses and informal opportunities.

GENERAL TRANSFERABLE SKILLS Below is a comprehensive list of general transferable skills that a graduate student would be expected to acquire. It was compiled by Research Councils and has been adopted by HEFCE (The Higher Education Funding Council for England).

 These skills may be present on commencement, explicitly taught, or developed during the course of the research.

 You should use it with the guidance of your Supervisors and Advisors as a checklist to identify gaps/deficiencies in your training and prioritize your training programme.

 Please note that skills training should facilitate, not hinder your research or research training, which must lead to thesis submission, normally within 4 years from starting your degree.

 The core components of the Biochemistry Graduate Training Programme, as outlined on page 4 of the Departmental Graduate Handbook, are mandatory and address key training requirements. Most of the training below is also acquired in the normal course of doing a D.Phil. others can be accessed from the Graduate Training Programmes organised by the Medical Sciences or other Divisions within the University of Oxford, according to individual needs and preferences.

SKILLS CHECKLIST (A) COMMENT (A) RESEARCH SKILLS AND TECHNIQUES – TO BE ABLE TO DEMONSTRATE: 1. the ability to recognise and validate problems by e.g.: setting project objectives (if undefined at start of research); solving problems which arise in course of research; ultimately the preparation of the thesis 2. original, independent and critical thinking, and the ability to develop theoretical concepts through e.g.: data analysis; producing a literature review; preparation of the thesis 3. knowledge of recent advances within one's field and in related areas by e.g.: attendance at research seminars and group meetings; membership of cutting-edge research groups; postgraduate reading/discussion groups; literature review 4. understanding of relevant research methodologies and techniques and their appropriate application within one's research field: acquired through work within research group 5. ability to critically analyse and evaluate one's findings and those of others through e.g.: written and oral presentations of findings and dealing with criticism received from others; participation in presentations given by others; literature review; thesis preparation 6. ability to summarise, document, report and reflect on progress through preparation of papers/reports required at transfer and confirmation of status

SKILLS CHECKLIST (B) COMMENT

(B) RESEARCH ENVIRONMENT – TO BE ABLE TO: 1. show a broad understanding of the context, at the national and international level, in which research takes place, through eg.: subject specific seminars; student mentoring scheme: practised in research groups 2. demonstrate awareness of issues relating to the rights of other researchers, of research subjects, and of others who may be affected by the research, e.g. confidentiality, ethical issues, attribution, copyright, malpractice, ownership of data and the requirements of the Data Protection Act by attending lectures and courses and reading relevant university literature displayed on the university website, e.g.(copyright) https://innovation.ox.ac.uk/ ; (ownership of data http://www.admin.ox.ac.uk/researchsupport/integrity/); http://www.admin.ox.ac.uk/dataprotection/ (data protection); https://www.nuffieldbioethics.org (ethical issues) 3. demonstrate appreciation of standards of good research practice in their institution and discipline: as above 4. understand relevant health and safety issues and demonstrate responsible working practices, e.g.: attend departmental health & safety lectures and meetings; work specific training e.g. use of workshops, specialised equipment; required to complete COSHH forms before carrying out new experiments; easy access to information, e.g. https://www.admin.ox.ac.uk/safety/ (University Safety Office) 5. understand the processes for funding and evaluation of research, e.g.:lectures by senior staff from the University Research Services Office (RSO), which processes all grant applications, negotiates research-related contracts, advises researchers e.g. about external research funding opportunities, costing and pricing of research at Oxford, exploitation of intellectual property arising from research. The RSO also contributes to development and implementation of research-related policy and disseminates information about the University's research and related activities. https://www.admin.ox.ac.uk/rso/ 6. justify the principles and experimental techniques used in one's own research, e.g.: part of thesis, oral presentations, literature review; examined a) in 1st year before transfer to DPhil, b) final viva 7. understand the process of academic or commercial exploitation of research results, e.g. joint Research Council/ISIS training days; easy access to https://www. innovation.ox.ac.uk.

SKILLS CHECKLIST (C,D) COMMENT (C) RESEARCH MANAGEMENT – TO BE ABLE TO: 1. apply effective project management through the setting of research goals, intermediate milestones and prioritisation of activities, e.g.: part of regular discussions with supervisors; more formal review at milestones of transfer of status and confirmation of status; sessions on project management and time management as appropriate 2. design and execute systems for the acquisition and collation of information through the effective use of appropriate resources and equipment, e.g. undertaken as part of research project 3. identify and access appropriate bibliographical resources, archives, and other sources of relevant information, e.g.: course on library and information technology resources, undertaken as part of literature review 4. use information technology appropriately for database management, recording and presenting information, e.g.:as above, training also provided by supervisors; general and specialised courses & documentation freely accessible by https://www.it.ox.ac.uk/ (University Computing Service)

(D) PERSONAL EFFECTIVENESS – TO BE ABLE TO: 1. demonstrate a willingness and ability to learn and acquire knowledge 2. be creative, innovative and original in one's approach to research 3. demonstrate flexibility and open-mindedness 4. demonstrate self-awareness and the ability to identify own training needs 5. demonstrate self-discipline, motivation, and thoroughness 6. recognise boundaries and draw upon/use sources of support as appropriate 7. show initiative, work independently and be self-reliant

All of these skills are required to complete a research project and thesis. Effectiveness is monitored by regular meetings with supervisors, who formally report on progress termly, and by independent assessments (milestones)

SKILLS CHECKLIST (E,F) COMMENT (E) COMMUNICATION SKILLS – TO BE ABLE TO: 1. write clearly and in a style appropriate to purpose, e.g. progress reports, published documents, thesis, e.g.: regular support from supervisor and graduate advisors, written seminar reports, literature review, transfer of status reports, thesis 2. construct coherent arguments and articulate ideas clearly to a range of audiences, formally and informally through a variety of techniques, e.g.:mandatory and optional oral, poster and written presentations prepared throughout the three-years of the D.Phil., presentations at transfer and confirmation of status, conferences 3. constructively defend research outcomes at seminars and viva examination, e.g.: weekly participation in research group and departmental seminars, part of assessment procedures and the viva examination 4. contribute to promoting the public understanding of one’s research field, e.g.: as above, also presentation of research to peers in college based seminar series, contribution to SET week, optional participation in promoting science e.g. to schools, museums and broadcasting. 5. effectively support the learning of others when involved in teaching, mentoring or demonstrating activities, e.g.: graduate teaching course/seminars are provided by the ULI in association with the department.

(F) NETWORKING & TEAMWORKING- TO BE ABLE TO: 1. develop and maintain co-operative networks and working relationships with supervisors, colleagues and peers, within the institution and the wider research community, e.g.: present their work in conferences & local interdepartmental subject groups and form collaborations, talk to visiting seminar speakers, network within college and department 2. understand one's behaviours and impact on others when working in and contributing to the success of formal and informal teams, e.g.: team skills acquired through participation in a research group, attend Research Councils Graduate Student Program (RCGSP), review with supervisor 3. listen, give and receive feedback and respond perceptively to others , e.g.:- student presentations/discussion groups

SKILLS CHECKLIST (G) COMMENT (G) CAREER MANAGEMENT – TO BE ABLE TO: 1. appreciate the need for and show commitment to continued professional development, e.g.: attend RCSGP https://www.vitae.ac.uk/ 2. take ownership for and manage one's career progression, set realistic and achievable career goals, and identify and develop ways to improve employability, e.g.: register with the University Careers Service https://www.careers.ox.ac.uk 3. demonstrate an insight into the transferable nature of research skills to other work environments and the range of career opportunities within and outside academia, e.g.: individual departments may involve potential employers, industrial partners, and previous students in presenting students with a range of career opportunities, the Careers Service provides talks on career planning in departments (if asked to do so) 4. present one's skills, personal attributes and experiences through effective CVs, applications and interviews, e.g.: the University Careers Service offers courses on preparing CVs, preparing for interviews, and practice aptitude tests