Graduate School of Medical Sciences

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1 faculty of medical sciences Graduate School of Medical Sciences PhD Study guide 3rd edition General & Course information

2 Graduate School of Medical Sciences of the University of Groningen at the University Medical Center Groningen. Postal address: Hanzeplein 1, 9713 GZ Groningen HPC: FA33 Publication Graduate School of Medical Sciences PhD Study guide. December, 2014 Editors Prof. Robbert Sanderman Ms. Renate Kroese Ms. Riekje Banus The GSMS Degree program advisory committees Lay-out Maarten Strik, Strik Design Printing Grafische Industrie De Marne printed on Cocoon* (CSR**) * Cocoon is 100% recycled and chlorine-free paper, acknowledged by FSC, having the FSC 100% recycled-label. Cocoon certificates: ISO 9001, ISO 14001, OHSAS 18001, NAPM, EU ecolabel. ** Corporate social responsibility is the continuing commitment by business to behave ethically and contribute to economic development while improving the quality of life of the workforce and their families as well as of the local community and society at large

3 Overview of this study guide Welcome... 1 Contents... 2 Organization of the Graduate School of Medical Sciences... 7 Important Facts... 8 Organization and Contact Persons General Information for PhD students GSMS Courses General Competences Research Techniques Field Specific & Interdisciplinary Subjects Seminars / Symposia / Meetings External Courses Contact and Addresses GSMS - PhD Study guide

4 Welcome

5 Welcome to the Graduate School of Medical Sciences The Graduate School of Medical Sciences (GSMS) organizes all (research) master and PhD tracks within the University Medical Center Groningen (UMCG). In addition, the five research institutes of the UMCG are incorporated in the Graduate School of Medical Sciences. The Research Institutes are: 1. BCN (Behavioural and Cognitive Neurosciences) 2. CRCG (Cancer Research Center Groningen) 3. GUIDE (Groningen University Institute for Drug Exploration) 4. W.J. Kolff Institute (Institute for Biomedical Engineering and Materials Science) 5. SHARE (Science in Healthy Ageing and healthcare). These institutes regulate the research policy in their fields and organize institute-specific courses for the education programs of the Masters and PhD tracks. The University of Groningen and the UMCG focus on Healthy Ageing as a unifying theme of research. Every PhD student doing research in a medical sciences-related field is registered in the Graduate School of Medical Sciences. This applies for everyone preparing a PhD thesis (dissertation). There are several categories of PhD students, ranging from the regular 4 years PhD student to the research fellow and the external candidate (extraneous). From the very start you will register and control your research and development activities in the RUG registration system Hora Finita, while the Graduate School provides a balanced mix of expert supervision, tailor-made graduate training and the freedom to pursue your own ideas within relevant research themes. In some cases part of the research can be carried out abroad. Registration in GSMS gives access to the courses and activities in the graduate school s education program. Participation in the courses of the program is free of charge. Apart from taking courses, it is important that the PhD students become familiar with activities related to the transfer of knowledge, such as keeping up with professional literature, participation in work discussion meetings and reference meetings and active participation in national and international scientific meetings. This booklet will help find your way in the organization and educational activities of the Graduate School of Medical Sciences. All information and course registration is available at the GSMS website. I hope you will enjoy your time as a PhD student in our Graduate School and wish you success in achieving your ambitions, M.J. (Martin) Smit, PhD Director Graduate School of Medical Sciences Website and online course registration: Fan page: Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 1

6 Contents Organization of the Graduate School of Medical Sciences... 7 Important Facts... 8 Registration... 8 GS office... 8 Study Requirements... 9 Organization and Contact Persons Graduate School of Medical Sciences Behavioural and Cognitive Neurosciences (BCN) Oncology (CRCG) Chronic Diseases and Drug Exploration (GUIDE) Biomedical Engineering and Materials Science (KOLFF) Science in Healthy Ageing and healthcare (SHARE) Research Master s Programs Confidential Advisor General Information for PhD students Courses Foreign PhD students Funds and Financing Introductory Event University of Groningen PhD Communities at the University of Groningen PhD Council GSMS PhD Development Conference Degree Program Advisory Committees Principles of Scientific Integrity Guidelines and Requirements for Approval of a PhD Thesis GSMS Courses General Competences GUIDE Project Management and GSMS Introduction Entrepreneurship and Valorization for medical sciences Presentation skills Publishing in English Scientific Writing A-Z Technical & Ethical Aspects of Digital Image Manipulation BCN BCN Management Competences in your PhD Project BCN Orientation course BCN Poster Presentation SHARE

7 Critical Appraisal of Literature Ethics of Research and Scientific Integrity for Researchers Introducing New PhD Students to SHARE Science Writing Course Thesis Defence in Sight Ethics of Research on Human Subjects Research Techniques BCN BCN Introductory fmri Course BCN Advanced fmri course BCN Functional Neuroscience: EEG BCN Matlab BCN Statistics Course GUIDE Epidemiology and Applied Statistics Introduction to genetic epidemiological research and data analysis Advances in genetic epidemiological research and data analysis Data Integration for biologists Good Research Practices: GCP/GLP Methodology for Phase II/III Clinical Trials SHARE Applied Longitudinal Data analysis Clinical Epidemiology Clinical Relevance versus Statistical Significance Health Technology Assessment and Economic Evaluation Health Technology Assessment; Quality-of-Life and Patient-Reported Outcome Measures (PROMs) Incomplete Information: Non-response, Attrition, and Missing Data Measuring Concepts in Quantitative Research Medical Statistics Mixed Models for Clustered Data Multivariate Analyses: How to Handle Three Variables Psychiatric Epidemiology Public Health Epidemiology Study Design in Clinical Epidemiology Systematic reviews and meta-analysis Working with Questionnaires in Patient-related Research Other Cellular Imaging - Basic Image Analysis In Vivo Optical Imaging Analysis Microscopy Quartz Crystal Microbalance (QCM) and Low Load Mechanical Tester (LLMT) Surface Characterization X-Ray Photoelectron Spectroscopy Laboratory Animal Science GSMS - PhD Study guide 3

8 Microbiological Safety SMBWO Immunology Course on HLA Typing and HLA Antibodies Field Specific & Interdisciplinary Subjects BCN BCN Philosophy of Neuroscience Human Neuroanatomy GUIDE Advanced Drug Delivery & Drug Targeting High-throughput next-generation biology Membranes, Signal Transduction and Transport Quantitative Bioanalysis Course: Techniques in Molecular Biology SHARE Evolutionary Medicine Basics in Medicine Basics in Psychology and Psychosocial Factors Drug Utilization Research Health Psychology: Theory, Research and Practice Health Psychology; advanced course Modeling in Health Technology Assessment OTHER Blood-Material Interactions Cells, Materials & Biomaterials Colloid Stability Hydrophobicity-SFE-DLVO Implants for Application in Maxillofacial Surgery Implants for Application in Ophthalmology Introduction to Medical Product Design Polymers in Medicine Tissue Engineering An Introduction Immunology I Seminars / Symposia / Meetings BCN BCN Lectures BCN Master Classes BCN PhD Retreat BCN Symposium SHARE Seminar Series Molecular Medicine Seminar Series External Courses Basic Course Instructions & Organisation for Clinical Researchers Career Development & Training Central Medical Library Courses Information Technology

9 Contact and Addresses Research Institutes Contact Details GSMS - PhD Study guide 5

10 6

11 Organization of the Graduate School of Medical Sciences GSMS - PhD Study guide 7

12 Important Facts Registration Every researcher doing doctoral research in one of the research institutes of the Graduate School must be registered at GSMS. To register, please fill out the GSMS Registration Form and hand it in at your research institute s office (see below). Hora Finita RUG registration system Registration with the GSMS gives access to the Hora Finita registration system of the University of Groningen. In this system all details concerning the PhD student and the project will be registered, monitored and processed. This involves the admission to the PhD program, progress reports, courses taken, the assessment of the thesis and the organization of the Defence Ceremony. All PhD students have to use this system: www. horafinita.nl. Login with your RUG P-number and pass word. Registration with the GSMS gives access at no cost to participation in GSMS courses, and financial support for scientific activities. Registration forms can be downloaded from the website: PhD students from outside the Netherlands are supported by the International Office of the Education Institute of the UMCG and the International Service Desk of the University of Groningen. Here, assistance is provided with immigration procedures, visas, and initial temporary housing in Groningen. International Office Medical Sciences: International Service Desk: GS office The Graduate School Office on the 7th floor of De Brug is the organizational center of the Graduate School of Medical Sciences. The five research institutes (BCN, CRCG, GUIDE, W.J. Kolff Institute and SHARE) organize scientific activities that are tailored to the institutes specific fields of research (including field-specific and interdisciplinary subjects). Detailed information on these subjects can be obtained at these institutes. Contact persons and addresses are given on page 8. 8

13 Study Requirements The curriculum has a varied program, which gives all students working on a thesis the opportunity to join courses related to their research and circumstances. The GSMS curriculum is based on the European Credit Transfer System (ECTS). While carrying out the standard four-year research project, 30 credit points must be obtained by taking courses and research activities, as follows: 10 EC for courses 10 EC for research related activities (see list on page 7) 10 EC free to choose for courses and research related activities. As there are several categories of PhD students the required number of credits varies accordingly: 4 years: 30 EC 3 years: 22.5 EC 2 years: 15 EC 1 EC = 28 hours approx. (of contact time or working hours on a subject) The GSMS Degree program advisory committee is responsible for assigning the EC. ECTS credit points can be obtained by: 1. Taking courses in the GSMS education program 2. Taking courses at other institutes and organizations 3. Taking Research Master s program courses 4. Conducting research activities. It is important to know that the courses taken at other institutes and organizations are at least on Master s level. Bachelor courses cannot be accepted in the PhD education program. In addition to taking courses, it is important that PhD students familiarize with activities related to the transfer of knowledge, such as keeping up with professional literature, participation in work discussion meetings and reference meetings of the student s own research group and in consultation with their supervisor of other research groups, active participation in local and national scientific meetings, and in international meetings. EC for research related and academic activities This scheme describes how several activities will be rewarded. Please note that it shows a lot of opportunities for PhD students to get rewarded with credits beyond the regular course work. When things either are not clear or you have additions to suggest please ask one of the PhD representatives in the GSMS Education Committee Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 9

14 Credits Max 1 remarks Workshops/Master classes/summer schools Depending on time and literature (28 hrs per EC) Seminars / Journal clubs 0.1/seminar 2 EC Presenting data at international conferences (orally and poster) Invited lecture outside institute Prize for best abstract/poster/presentation Granted project proposal 1st author: < 10,000 Euro 10,000 <> 30,000 Euro > 30,000 Euro 0.5/conf 0.5/conf 0.5/prize 0.5 EC 1 EC 2 EC 6 EC Supervised reviewing of manuscripts (2) 1 EC/2 ms 3 EC Research stay abroad (minimum 2 weeks) 4 EC Depending on time invested (28 hrs per EC) Stay in Dutch lab Other academic activities 4 EC Is granted only in very special occasions. Prior to the visit to the Dutch lab, the supervisor and PhD student must - with arguments - appeal for granting with the PhD education committee of the Research institute. GSMS PhD council 1 EC/yr GSMS educational committee Research Institute s PhD councils Organisation of scientific meeting (symposium/ conference) 1 EC/yr 1 EC/conf 6 EC Depending on time invested and agreements within Research Institutes Teaching/Student supervision Tutor/mentor Lecture Coach master scientific thesis Depending on time invested 4 EC According to Institute for Medical Education Definitions: 1 Maximum EC for full time 4 years PhD students, 3 and 2 years students accordingly less Teaching can be for medical as well as other students at university level 1 EC = 28 hours invested 1 EC = ± 120 pages of obligatory literature 10

15 GSMS - PhD Study guide 11 Important Facts General Research Techniques Field specific Meetings External

16 Organization and Contact Persons Graduate School of Medical Sciences Visiting address: Building 3217 De Brug, FA33 Ant. Deusinglaan AV Groningen The Netherlands The Graduate School of Medical Sciences deals with five main scientific areas, along the lines of which the teaching program has been developed. The five areas are: Behavioural and Cognitive Neurosciences (BCN) Oncology (CRCG) Chronic Diseases and Drug Exploration (GUIDE) Biomedical Engineering and Material Science (KOLFF) Health Research (SHARE) Each subject is represented by an institute with its own office dealing with course organization and registration in its particular field. Behavioural and Cognitive Neurosciences (BCN) Scientific Director: Secretary: PhD and education coordinator: Director: Secretary: Education: Prof. H.W.G.M. (Erik) Boddeke Ms. E.T. (Evelyn) Kuiper-Drenth Ms. D.H. (Diana) Koopmans Prof. H.W.G.M. (Erik) Boddeke Ms. E.T. (Evelyn) Kuiper-Drenth Phone: +31 (0) Ms. D.H. (Diana) Koopmans Oncology (CRCG) Director: Secretary: Education: Prof. E. Vellenga Ms. M.T.L. (Mathilde) Pekelaer Phone: +31 (0) Ms. M.H. (Maaike) Bansema 12

17 Chronic Diseases and Drug Exploration (GUIDE) Director: Secretary: Education: Prof. D. de Zeeuw, PhD Ms. M.T.L. (Mathilde) Pekelaer Phone: +31 (0) Ms. M.H. (Maaike) Bansema Biomedical Engineering and Materials Science (KOLFF) Director: Education: Prof. H.C. (Henny) van der Mei T.G. (Theo) van Kooten, PhD Phone: +31 (0) Science in Healthy Ageing and healthcare (SHARE) Director: Prof. M.J. (Maarten) Postma Secretary and Education: Ms. R.C. (Renate) Kroese Phone: +31 (0) Research Master s Programs In addition to the PhD program the Graduate School of Medical Sciences administrates three Research Master s Programs: 1. Behavioural and Cognitive Neurosciences (BCN N-track) 2. Clinical and Psychosocial Epidemiology (CPE) 3. Medical and Pharmaceutical Drug Innovation (MPDI) ad 1. ad 2. and 3. Program coordinator I.A. (Ika) Neven, PhD Program coordinator D.F. (Désirée) Jansen, PhD The two-year Research Master s programs offer an excellent preparation for a research career in biomedical or health sciences. Only the best students from all over the world are admitted. Students will be supervised by the most outstanding scientists our University numbers. The training program is intensive and highly interactive. All three programs share the philosophy that research skills are best learned in a learning by doing approach. These programs prepare students for performing a PhD project, and give an extra boost to career perspectives. Talented students have the opportunity to design their own PhD project and the best proposals are granted. After successfully completing one of the Research Master s programs you will receive an MSc degree. Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 13

18 PhD-students have limited access to the courses of the Research Master s Programs. Detailed information: Confidential Advisor PhD students who experience undesirable conduct, unequal treatment of problems in cooperation at work may consult the confidential advisor. Name: Riekje Banus 14

19 GSMS - PhD Study guide 15 Important Facts General Research Techniques Field specific Meetings External

20 General Information for PhD students Courses The Graduate School of Medical Sciences (GSMS) offers a wide range of courses for additional training of PhD students, MD/PhD students, Top Master s students and Research Master s students. Included are courses in general competences, in research techniques and in field-specific and interdisciplinary subjects. Also listed are the seminars and meetings organized by the five research institutes. PhD students have limited access to research master s courses. Research master s students have precedence. Foreign PhD students The Medical Faculty has an International Office which provides advice and support to international students and guests. The Office cooperates closely with the International Service Desk of the University of Groningen. The International Office can provide detailed information on a variety of subjects such as health matters, visas, registration with the municipality, driver s licenses, University facilities, daily life in Groningen, etc. Detailed Information: Faculty of Medical Sciences International Office: University of Groningen International Service Desk: Funds and Financing Only registered PhD students can participate in courses for free and receive financial support for scientific activities such as external courses, science writing, attending conferences etc. Application forms can be downloaded from the website. In the near future application can be performed in the Hora Finita system. Financial support to a maximum of 600 a year p.p. for: National and international conferences External courses 16

21 STUDY LOAD Printing costs of the dissertation: All PhD students at the UMCG receive a financial contribution from the UMCG of 250. Additional to this, students registered at the Graduate School of Medical Sciences may receive a financial contribution to a maximum amount of 850 if meeting the criteria on 1) education, 2) speed, 3) quality. Each criterion renders 200. Information and application form: Name: Ms. J.W. (Mieke) Kapteyn Information for GRIP PhD students: GRIP PhD students must apply for financial support of the printing costs at the Graduate School of Science. Detailed information can be found at: gradschoolscience/. Important! GRIP PhD students are registered both in the Graduate School of Medical Sciences (UMCG) and in the Graduate School of Science. They make use of all facilities, and educational and financial GSMS support, mentioned above. The GSS ITB (International Training Budget) is NOT applicable to GRIP PhD students. Introductory Event University of Groningen Apart from local introductions, the Dean of the Groningen Graduate Schools (GSS), Prof. Lou de Leij, also invites newly started PhD students to join the GSS Introduction. This Groningen Graduate Schools (GSS) is the umbrella organization of all faculty based graduate schools at the university. Every PhD student starting a degree program receives an invitation. It is a two-day event, offering a variety of activities, giving an impression of the University and its faculties and facilities, the city and province of Groningen, and a taste of courses and other support activities offered by the University of Groningen graduate schools. 1 EC Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 17

22 PhD Communities at the University of Groningen There are two PhD associations in Groningen: GRIN (Groningen Graduate Interest Network) which represents and supports the interests and rights of PhD students, and Gopher (Groningen Organization for PhD Education and Recreation) which organizes informative and social events. Websites: PhD Council The PhD Council represents the interests of all PhD candidates within the GSMS. The council consists of two PhD students from each of the four research institutes. GSMS: GSMS PhD Development Conference Every two years the GSMS PhD development conference is organized for all GSMS PhD students. The conference focuses on creating awareness of the value of a PhD, discovering specific PhD talents and how to transfer your talents to your further career. A two day program will cover several lectures, workshops, discussions and a career market. More information: Study load: 1 EC Degree Program Advisory Committees Each research institute has a degree program advisory committee that is responsible for the education program. The GSMS Degree program advisory committee is the umbrella committee and consists of the chairs of the research institutes degree advisory committees and their PhD student representatives. Further information can be obtained at the education coordinators of the institutes. Principles of Scientific Integrity Code of Conduct for Scientific Integrity for courses organized by the Graduate School of Medical Sciences. 18

23 This document was drawn up at the request of the Degree Program Advisory Committee of the Graduate School of Medical Sciences (GSMS). The reason for drafting this document stems from the generally shared conviction that scientific education needs to be conducted in a proper way by all involved parties. In order to provide an indication of desired behavior, the following principles of scientific integrity have been established to promote the best scientific education. Scrupulousness: course participants have to take care that the data obtained by research is precise and nuanced and is not influenced by externalities. Reliability: course participants have to take care that their data acquirement, data processing and data reporting are honest and with true scientific motives. Verifiability: course participants have to take care that at all times it is clear where data and the conclusions are based on, where they were derived from and how they can be verified. Impartiality: students participate in a course with the intention to develop their academic knowledge and skills and use their full academic potential. Independence: course participants are not influenced by interests other than those aimed at conducting pure science. Examples of non-desired dependencies are personal financial gain or pressure of publication. Scientific misconduct, also named fraud or serious offense, is all behavior in contradiction with the above mentioned principles of scientific integrity in academic research. The RUG hereby declares that these behaviors are not accepted and need to be opposed. This could result in sanctions for involved parties. The authors of this document realize that participants of GSMS courses are in a learning situation. Therefore, not all conduct that opposes above mentioned principles can automatically be considered scientific fraud. When a serious scientific misconduct is observed by one of the involved parties, this should be discussed with both involved parties and an independent third. The allegations will be researched and evaluated so that can be judged whether scientific fraud has occurred. Any confidential information will be handled with care at all times by all parties involved. A result of arbitration by a third party or the Pro Dean of Education can be that a course participant has shown scientific misconduct and should be penalized. Possible penalties are, among other things, no allocation of the EC that stand for the concerned course, denying of any participation to a course organized by GSMS (for a certain period of time) and a mandatory participation to the GSMS course Scientific Integrity for participants in courses. Furthermore, the supervisor of the student concerned will be informed. The verdict of the Pro Dean of Education is binding. Further information: Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 19

24 Guidelines and Requirements for Approval of a PhD Thesis As of September 2013 the protocol for the conferral of a PhD has been renewed. A detailed description can be found at: In the following the general quality/quantity requirements for a PhD thesis at the UMCG are given, using three questions/answers: Question 1: Who decides whether a manuscript of a PhD thesis fulfils the requirements for a PhD degree a t the UMCG/RUG? Answer: The protocol mentioned above gives a detailed description on the procedure for approval. In short, the first judgment of the quality of the work done by a PhD student (promovendus) as reflected in the manuscript of the PhD thesis - i.e. whether he/she qualifies to be admitted to the thesis defence, or not, - is done by the supervisors (the promoters, who have the ius promovendi ). They indicate their approval in Hora Finita, submit the manuscript to the Dean and propose the Dean to start the procedure. The Dean appoints a reading committee, generally consisting of three professors of whom at least one must have an appointment outside the University of Groningen. The members of the reading committee judge the quality of the manuscript independently, and advise the Dean. The Dean decides. Question 2: Are there minimum requirements, e.g. regarding the number of experimental and published chapters, or the size of a thesis? Answer: The protocol given above does not mention an obligation to have (parts of) the thesis published and/or submitted/accepted for publication prior to the thesis defence. Also, there are no specific requirements with regard to the number of (experimental) chapters nor the size (the number of pages) of the thesis. However, since the PhD title is given as proof of being an independent researcher, it is clear that the manuscript should show sufficient indications that the candidate has mastered the entire cycle associated with performing scientific work. This includes the writing and, preferably, publication of research papers. As a rule of thumb the UMCG considers a thesis containing an introduction / outline of the thesis, two published/accepted/acceptable experimental chapters and, preferably, two additional (experimental) chapters as appropriate. However, as said before, in principle there is no absolute requirement for publication to be admitted to the thesis defence, nor for obtaining the PhD degree. A PhD student must finish the manuscript of the thesis within the allotted time period. It is important that a well-written, summarizing discussion should show that the candidate has mastered his/her field of research and is capable of independent, scientific reasoning. 20

25 Question 3: Is there a general guidance regarding the quality of the scientific journals in which articles should be published? Answer: It is important to strive for publication in high-ranked journals. This also holds for the publications that are included in a thesis. It is better to include experimental data that cannot be published in a high ranked journal in a chapter of the thesis than to publish these in a low ranked journal. To encourage publication in high ranked journals, the Graduate School of Medical Sciences offers financial support in printing costs as an incentive for quality, when at least two of the articles in the manuscript have been published or accepted for publication in the top 25% of the relevant ISI-field in Web of Science. More importantly, the manuscript of a thesis which contains publications in high-ranked journals and which is regarded as being in the quality top 5-10% of these can be taken as the basis for a cum laude application. The procedure for a cum laude application is given in the protocol for the conferral of a PhD as mentioned above. A cum laude PhD defense is not a prerequisite, but may be very helpful in starting a scientific career, e.g. as (pre)tenure track fellow at the UMCG. Important Facts General Research Techniques Field specific Meetings External GSMS - PhD Study guide 21

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