Swiss TPH Student Handbook 2021-2022

2021-2022

Swiss TPH Student Handbook Department of Education and Training

Foreword The Department of Education and Training (ET) at the Swiss Tropical and Public Health Institute (Swiss TPH) is pleased to provide you the fall semester 2021/2022 version of the Swiss TPH Student Handbook.

It shall help you navigate your way through program requirements, the regulations of the University of Basel, Swiss TPH or the Swiss School of Public Health (SSPH+). Selected key information about living in Basel is provided, too. Whether you are new to Swiss TPH or continuing your graduate studies here, a visiting student from abroad or a native Basel citizen, we trust that the Student Handbook will be of assistance and use to you.

The Handbook contains all relevant information related to studying at Swiss TPH. It includes important and also NEW notes about rules and regulations for the Master and PhD students. It is crucial that students always use the newest manual rather than referring to previous versions as information, rules and regulations are regularly updated and often changed by the involved partners. Please take in particular note of the upcoming changes in the PhD programs with new information possibly emerging during the fall semester. As of now, nothing has changed given some delays in the launching of the new inter-faculty Graduate School Health Science of the University of Basel. We lead a University mandate at Swiss TPH to bring this vision to life.

To learn more about course offers, please check out the Directory of Uni Basel (Course directory of the University Basel) and the offers of the PhD Program Health Sciences (PPHS), coordinated and led by Swiss TPH. Of high interest are also the courses listed in SSPH+ Inter-university Graduate Campus (IGC) of the Swiss School of Public health. All Swiss TPH PhD students qualify to register in the IGC and are highly advised to do so.

For new students and for those who want a copy, the Swiss TPH Student Handbook will still be printed once a year (in autumn) and regularly up-dated in the online version (at least in February). For the most up-to-date version of the document, visit our website www.swisstph.ch/en/study-with-us/bachelor-and-master/.

If you have any suggestions to further improve the Student Handbook please let us know and we will consider your comments for future editions. Comments or suggestions can be sent to Nicole Peter at ET: nicole.peter@swisstph.ch.

Enjoy this resource and your studies!

Julia Bohlius Head of Department of Education and Training (ET), Swiss TPH

Nino Künzli Head of Unit Bachelor-Master-Doctorate (Department Education and Training), Swiss TPH Dean, Swiss School of Public Health (SSPH+) Introduction

Welcome to the Swiss TPH Dear students and colleagues A very warm welcome to Swiss TPH. My colleagues and I are delighted that you decided to pursue your studies at the largest public health institute in Switzerland. Hence, you are now part of the Swiss TPH family that consists of more than 850 people from over 80 nations. Come and join our vision that is to make the world a healthier place. With our upcoming move to the beautiful, multi-functional building “Belo Horizonte” in Allschwil, we will all work under one roof. This will allow us to fulfil our mission more effectively: we aim to improve the health and wellbeing of people locally, nationally and around the globe.

Swiss TPH is one of five associated institutes of the University of Basel, the oldest university of Switzerland founded in 1460. You will actively contribute to our three strategic goals, namely (i) excellence in science; (ii) taking science to impact; and (iii) mutual learning for sustainable development.

The entire teaching cadre at Swiss TPH – coordinated by the Department of Education and Training (ET) – is strongly committed to education and training, so that a next generation of skilled scientists, public health experts and specialists in the fields of epidemiology, infection biology, public health and global health are being nurtured. Please, take this unique opportunity, immerse yourself in the subject matters, be curious, share your knowledge with other students and faculty, and network for all you are worth. In turn, we promise that you will learn a great deal – and so will we. Our goal is to foster capacities in the public, international and global health sciences. In the midst of a global pandemic, this is needed more than ever!

Please note that you are a full member of Swiss TPH as you pursue your studies. Hence, we count on you from the first day you enter our doors. You are invited to interact with our staff and your fellow student colleagues during the course work – in-class and virtually. Exchange, debate and communicate with all our people, as this is part of our culture, provides mutual benefits and maximizes advantage of the rich knowledge across diverse backgrounds, disciplines and socio-cultural settings. As you shall witness, our teaching faculty is eager to share their experiences and expertise with younger colleagues and peers, and invites open communication and constructive debate with students whenever possible.

Swiss TPH is a vibrant and well-respected institute and your contributions will amplify each of our three strategic goals and contribute to our vision and mission.

On behalf of the whole Directorate, the teaching faculty and staff at Swiss TPH, I wish you an intellectually stimulating and productive time at Swiss TPH and the University of Basel. Thanks again for having chosen Swiss TPH to pursue your studies and much more!

Jürg Utzinger Director Swiss TPH Introduction

Important Contacts Emergency numbers

In case of an emergency or accident, the following phone numbers should be called: Police: Fire Brigade: Medical Emergency:

117 118 144

Swiss TPH Extensions

From outside Swiss TPH, dial +41 (0)61 284 and then the extensions given below: Main Office: Student Administration: Library: IT: Medical Services: Travel Clinic: Security Officer: Human Resources:

x8111 x8289 x8899 x8333 x8255 x8255 x8798 x9393

Swiss TPH Socinstrasse 57 4051 Basel Switzerland Tel.: +41 (0)61 284 81 11 Fax: +41 (0)61 284 81 01 www.swisstph.ch

Head of Department of Education and Training (ET) Julia Bohlius, +41 (0)61284 88 40 julia.bohlius@swisstph.ch

Head of Unit Bachelor-Master-Doctorate Nino Künzli, +41 (0)61 284 83 99, nino.kuenzli@swisstph.ch

PhD Student Office Christine Mensch, +41 (0)61 284 82 89, christine.mensch@swisstph.ch

Bachelor and Master Student Office Pascal Gschwind, +41 (0)61 284 83 60, pascal.gschwind@swisstph.ch

PPHS and Graduate School Health Sciences Coordinator Anja Matthiä, +41 (0)61 284 88 17, anja.matthiae@swisstph.ch, pphs@unibas.ch

Research Commission Coordinator, Student Handbook, Support PPHS & Graduate School Health Sciences Nicole Peter, +41 (0)61 284 83 59, nicole.peter@swisstph.ch, research.commission@swisstph.ch

Introduction

TABLE OF CONTENTS The Swiss Tropical and Public Health Institute

8

Safety, Intellectual Property, Data Protection

19

The Swiss School of Public Health (SSPH+)

21

Switzerland and Basel

22

Departments 9 Organigram 2021 10 Location 11 Facilities at Swiss TPH 11

Travel Safety 19 Intellectual Property Rights and Data Protection 20

Switzerland 22 Basel 23 How to get a Visa 25 University of Basel 26

Guidelines for the Master Degrees in Infection Biology and Epidemiology

27

Introduction for MSc Students General Information and Procedures Checklist for MSc Students

28 29 35

Guidelines for Doctoral Studies at Swiss TPH

36

Students’ Rights and Obligations

59

Student Representative’s Roles and Responsibilities

62

Overview of general guidelines for Swiss TPH PhD studies Doctor of Medicine (MD) at Swiss TPH Combined Medical Doctorate (MD-PhD) Administrative Checklist for New PhD Students Structured PhD Programs Relevant steps taken during the PhD studies at Swiss TPH Other opportunities

Table of contents

37 38 38 41 42 46 58

Overview of Courses Offered by Swiss TPH Specialised Master in Infection Biology Timetable Infection Biology Autumn Semester 2021 Specialised Master in Epidemiology Timetable Epidemiology Autumn Semester 2021

66 67 68 69 70

Appendices 71 Writing a MSc thesis proposal MSc Thesis Structure

71 73

Swiss TPH Academic Teaching Staff list Competences in Medical Parasitology and Infection Biology (MPI) Competences in Epidemiology and Public Health Guidelines for writing a PhD proposal Guidelines for the internal PhD proposal evaluation process PhD thesis structure

75 77 78 79 81 83

Ethical Clearance for Swiss TPH Projects Plagiarism Corporate Identity at Swiss TPH Accomodation for students Map of Basel

84 87 88 89 90

Download the latest pdf version of the student handbook Table of contents

The Swiss Tropical and Public Health Institute The Swiss Tropical and Public Health Institute (Swiss TPH), formerly known as the Swiss Tropical Institute (STI), was founded as a public organisation in 1943. In 2010, the Institute for Social and Preventive Medicine (ISPM) of the University of Basel Medical Faculty was integrated with the former STI, creating Swiss TPH as we know it today. Financial support comes from the Swiss Federal Government (State Secretariat for Education, Research and Innovation), the Cantons of Basel-Stadt and Basel-Landschaft and the University of Basel (ca. 20%), while competitively acquired project funds and service department earnings (Swiss Centre for International Health, Department of Medicine) make up the rest (80%). The Department of Education and Training (ET) of Swiss TPH coordinates the extensive teaching commitments of Swiss TPH, involving dedicated teachers from all Swiss TPH Departments. As an associate institute of the University of Basel, Swiss TPH offers a range of teaching activities in various faculties of the University. In the Faculty of Science we lead a wide variety of courses for the Bachelor degree in Infection Biology and Epidemiology (IBE), the Master of Infection Biology and the Master of Epidemiology. In the Medical Faculty, Swiss TPH is responsible for the Bachelor and Master level teaching in public health throughout the medical curriculum. Other teaching activities are based in the Faculty of Humanities and Social Sciences. Swiss TPH is also engaged in a range of post-graduate programmes and courses and the largest partner of the Swiss School of Public Health (SSPH+) - a foundation of (currently) 12 Swiss universities and universities of applied sciences which constitute the inter-university faculty of public health sciences.

The Swiss TPH mandate is to contribute to the improvement of the health of populations internationally, nationally and locally through excellence in research, services, and teaching and training. We fulfill our mandate and further develop our institutional profile by the pursuit of four strategic goals: • Strengthen our excellent standing in generating new knowledge on disease and health systems • Establish and apply interventions for health policy, strategies, clinical medicine and public health at local, national and global levels • Share knowledge with students, health professionals, relevant institutions, beneficiaries and other stakeholders • Promote and strengthen responsible interactions and exchange with individuals and communities in their social, cultural and ecological contexts. People and their well-being are the foundation and centre for our thinking and action

8 – General information

Departments Since January 1, 2017, Swiss TPH consists of the following five departments:

Epidemiology and Public Health (EPH) EPH explores new approaches in epidemiology; assesses interventions for disease control; investigates the environmental, social, economic and bio-genetic causes of health and disease and studies determinants of health seeking behaviour and health system organisation and planning in Africa, Asia and Europe.

Medical Parasitology and Infection Biology (MPI) MPI studies host-parasite relationships, determinants of infection and morbidity at the molecular, cellular, clinical and population levels and develops tools for diagnosis, prevention and treatment of infectious diseases.

Swiss Centre for International Health (SCIH) SCIH assists in health project implementation; acts as executing and support agency for health development; and offers short- and long-term consultancies and expertise in all aspects of health services management, planning, risk analysis and evaluation.

Medicine (MED) MED builds on a foundation of clinical medical services, diagnostics, pharmaceutical medicine and clinical research. It includes medical services, advice for travellers to tropical and subtropical countries, vaccination services and 24-hour emergency services, a reference diagnostic laboratory specialised for tropical infectious diseases, and a clinical research unit, as well as offers for professional support for clinical trials, services and training on regulatory topics and quality assurance of internally conducted trials.

Education and Training (ET) ET is the Swiss TPH hub for all teaching and student affairs (including PhD students). It coordinates teaching and training activities on all levels within Swiss TPH, University of Basel and external partners.

Scientists from all Swiss TPH departments contribute to the wide range of educational and teaching activities of the Swiss TPH. For further information (projects and staff) see: www.swisstph.ch

General information – 9

Organigram 2021

Organigram 2021 Board of Governors Members from the cantons of Basel-Stadt and Basel-Landschaft, Swiss universities and the private sector Chairman Andreas Burckhardt

Directorate Director Jürg Utzinger

Communications Sabina Beatrice-Matter

Deputy Director and Department Head Kaspar Wyss

Administration Mathias Kronig Finances / Controlling Deniz Gör & Stephan Schwarz

Department Heads Nicole Probst-Hensch, Sébastien Gagneux, Kaspar Wyss, Daniel Paris, Julia Bohlius

Human Resources Iris Haueter

Administrative Director Mathias Kronig

Internal Audit Vincent Bodenez Security, Safety and Health Marco Tamborrini Project and Grant Michael Käser

Informatics Alain Bertolotti Infrastructure Ursina Müller

Departments

Epidemiology and Public Health

Medical Parasitology and Infection Biology

Swiss Centre for International Health

Medicine

Education and Training

Nicole Probst-Hensch Deputy: Jakob Zinsstag

Sébastien Gagneux Deputy: Till Voss

Kaspar Wyss

Daniel Paris Deputy: Christian Burri

Julia Bohlius Deputy: Axel Hoffmann

Biostatistics Penelope Vounatsou

Clinical Immunology Claudia Daubenberger

Clinical Operations Elisabeth Reus

Chronic Disease Epidemiology Nicole Probst-Hensch

Helminth Drug Development Jennifer Keiser

Bachelor-MasterDoctorate Nino Künzli

Disease Modelling Melissa Penny Ecosystem Health Sciences Guéladio Cissé Environmental Exposures and Health Martin Röösli

Malaria Gene Regulation Till Voss Malaria Host Interactions Nicolas Brancucci Molecular Immunology Gerd Pluschke

Health Interventions Christian Lengeler

Parasite Chemotherapy Pascal Mäser

Household Economics and Health Systems Research Günther Fink

Tuberculosis Research Sébastien Gagneux

Health Systems Support Helen Prytherch Digital Health Martin Raab Systems Performance and Monitoring Odile Pham-Tan

Clinical Research Klaus Reither Diagnostics Beatrice Nickel

Library and Documentation Giovanni Casagrande

Medical Services Andreas Neumayr

Professional Postgraduate Training Karin Gross

Medicines Implementation Research Christian Burri

Teaching Technology and Didactics Axel Hoffmann

Human and Animal Health Jakob Zinsstag Society, Gender and Health

Sonja Merten

Vector Biology Pie Müller

Organigram valid August 2021

10 – General information

The Institute Location Swiss TPH is located at Socinstrasse (near Tram nos. 1 and 6, and bus no. 50 stop “Brausebad”), and is housed in several buildings (No. 55, 55a, 57, 59). No. 57 is the main building and home to the travel clinic, outpatient department and administration. No. 59 features offices, lecture and seminar rooms, the library and laboratory facilities. Newly built laboratory facilities and course administration centres are located at No. 55a. The former elderly house (Socin 55) is now also a Swiss TPH facility with a large teaching and meeting room on the top floor. Other Swiss TPH buildings are found at Eulerstrasse No. 54, 77 and 83.

Towards the end of 2021, Swiss TPH moves into its new building ‘Belo Horizonte’ at the corner of Kreuzstrasse and Hegenheimermattweg in Allschwil. Find more information and updates about the move on the intranet.

Facilities at Swiss TPH Staff and door badge

To get around Swiss TPH, students need to have a staff badge. The staff badge serves as an electronic door key and gives students access to the library and the teaching rooms. The badge can also be loaded with money and used for payment in the cafeteria (the machine to load the badge can be found on the main floor in Socinstrasse 57, in front of the elevator). Paying with the badge at the cafeteria gives you a 30% discount off the original price. Please make sure you have enough money on the badge prior to visiting the cafeteria. The badge can be obtained at the main secretariat. A deposit of CHF 100 is required and will be fully refunded upon return of the badge.

Please bring the badge back to the main secretariat if you leave Switzerland for a longer stay abroad.

Library

The Swiss TPH library offers books and journals on Public Health, Epidemiology, Global Health, Travel and Tropical Medicine, as well as on Medical Parasitology and Biology of Infection. An extensive electronic library is available via the University network: https://ub.unibas.ch/en/search-find/databases-e-journals-e-books/.

Library users can access our books and journals and almost all of the scientific media holdings in Switzerland via a single portal called swisscovery. To use swisscovery, you need to log in with your SWITCH edu-ID account (https://www.switch.ch/edu-id/).

The library welcomes suggestions for the purchase of new books and can order copies of journal articles that are not available at the Swiss TPH library or at the University Library. Documents available at the University Library must be obtained directly.

Find more information on the intranet: https://intranet.swisstph.ch/en/aoc/library-services/ or contact the library (library@swisstph.ch).

Literature searching and systematic reviews

When you start on your master’s or doctoral thesis, you will have to familiarize yourself with techniques of literature search. Our library offers courses on literature searching and reference management in cooperation with the University Library: https://fortbildung.unibas.ch/suche?search=medizin.

General information – 11

The University Medical Library offers help with systematic literature searching in bibliographic databases. A one-hour mentoring session including preparation and follow-up by the library staff is provided free of charge for Swiss TPH students https://ub.unibas.ch/en/locations/university-medical-library/support-for-literature-searching/. Students who endeavor to do a systematic review are especially advised to make use of this offer: https://ub.unibas.ch/en/locations/university-medical-library/systematic-reviews-and-mediated-searches/.

Find more information on our library services on: https://intranet.swisstph.ch/en/aoc/library-services/ or contact the library staff (library@swisstph.ch).

Printing and copying

All Swiss TPH printers, scanners and copy machines are connected to the central network and are operated with the personal badge. Both black and white and colour machines are available and costs are charged directly to the student’s account(s), set up by the supervisor. Library and IT staff can provide guidance and help if technical problems arise.

Swiss TPH fully supports open access (OA)

Free access to scientific information is of particular relevance for all our partners in low- and middle-income countries. In general, if you submit a paper to an OA journal you have to pay an Article Processing Charge (APC). APCs vary from journal to journal. Please read the journal’s submission guidelines thoroughly before submitting a paper. Many publishers offer waivers or discounts on the APCs, for example to corresponding authors with primary affiliations based in countries defined by the World Bank as ‘Low-Income Economies’. Please don’t forget to mention your affiliation to the University of Basel by submitting your paper (see our affiliation guidelines). As author affiliated with the University of Basel you can benefit from various Read & Publish agreements with scientific publishers (Elsevier, SpringerNature, Taylor & Francis, Wiley, etc.) or discounts (BioMed Central, British Medical Journal, MDPI, etc.). For more detailed information, please refer to our guidelines on the intranet.

Computers and e-mail

All MSc and PhD students who write, generate or use Swiss TPH data to write their thesis at the Institute are entitled to a computer provided and owned by Swiss TPH. With these devices, access to the wired network and the wireless network "swiss-tph" is possible. It is not allowed to use private computers for Swiss TPH related work / data.

WLAN access is available in all conference rooms, the library and the auditorium.

A limited number of public computers are available in the library and can be accessed via a personal account or by a temporary account provided by the library staff. All public computers are connected to the Internet.

For all networks, the Terms of Use of the Swiss TPH and the University of Basel apply and must be strictly adhered to. Private computers are not allowed in the networks of the Institute.

For MSc and PhD students, University e-mail accounts are provided by the University as part of the official matriculation process. In addition, Swiss TPH staff receive the @swisstph.ch email (usually with the same name as the unibas.ch email). You need the Swiss TPH email for all institutional matters; the unibas.ch email is therefore automatically forwarded to the swisstph.ch account.

Swiss TPH uses Lotus Notes software for e-mail. Remote access to e-mail accounts is available via www.webmail.swisstph.ch. VPN client software for remote access to the University of Basel and Swiss TPH network can be obtained from the University website www.mobile.unibas.ch

12 – General information

Please note that e-mail remains the primary official mode of e-communication at Swiss TPH. You are therefore required to read your swisstph.ch e-mail account and to promptly respond from this account where needed. You will also get your semester registration reminders sent by the administration office of University Basel via e-mail. Being registered at Unibas is absolutely essential for the whole period of your Master / PhD study.

Related Informatics Guidelines: www.intranet.swisstph.ch/en/regulations. Under “Filter list” select “Informatics”.

Project Communication

A fancy website does not guarantee efficient project communication. For collaboration in research projects in particular, the relevance of project communication should not be underestimated. The interplay between internal and external communications needs to be established from the outset. Effective and innovative project / research communications is a vital element in ensuring that research makes an impact.

Questions like the examples below need to be considered and discussed with the project team: • Which information needs to be shared – to whom and by whom?

• How can the appropriate tools be chosen and used efficiently?

• What is my responsibility as a student in terms of project communication?

For information and content support concerning the various Swiss TPH platforms for project communication, please contact the Swiss TPH communications unit at communications@swisstph.ch, or the following specialists:: • Head of communications: sabina.beatrice@swisstph.ch • Website/Newsletter (www.swisstph.ch): valerie.busson@swisstph.ch • Swiss TPH intranet (www.intranet.swisstph.ch/en): alain.hollfelder@swisstph.ch • Social Media (Facebook: Swiss Tropical and Public Health institute; Instagram: @Swiss_tph; Twitter: @SwissTPH, LinkedIn: Swiss Tropical and Public Health Institute): danielle.powell@swisstph.ch • Corporate Identity and Design: joanne.blackwell@swisstph.ch

IT Service Desk Compliance With the use of intranet, internet and e-mail of the Swiss TPH, the user confirms to acknowledge and comply to the Swiss TPH and University of Basel Terms of Use (DE).

Alfresco project collaboration platform For security reasons, the use of cloud storage devices, such as Dropbox, Sky-Drive, Ubuntu-One or iCloud is not permitted for the storage or exchange of data from the Swiss TPH. At Swiss TPH it is strongly recommended to use Alfresco for projects as a central data storage, collaboration platform and communication tool. The internal hosting as well as regular backups ensure the security of Alfresco. In addition to just sharing files, Alfresco supports different processes for working collaboratively on documents and includes different features for enhancing collaboration among the project partners both within and outside the Swiss TPH. All processes related to the Research Commission (more details see page 46ff) are managed with Alfresco. All PhD students will receive access permission to their relevant folders as soon as they start General information – 13

working for Swiss TPH (www.team.swisstph.ch/page/site/research-commission/documentlibrary).

Alfresco support is provided by the Swiss TPH IT unit: it-service@swisstph.ch How to get support The IT Service Desk team provides support in all areas related to the standard IT workstation – within the realms of their possibilities. Additionally, they help with the procurement of IT resources for our projects in Switzerland and abroad. To get support, follow ONE of the following steps, depending on your possibilities (VPN / Intranet Access) and the issues urgency.

Service Portal As standard procedure, kindly create an Incident Request in the IT ServicePortal www.itserviceportal.swisstph.ch. To do so, click on the Button “Create New Incidents” on the portals homepage.

After you fill in the required prompts, the system creates a ticket and displays the Incident Request Number. Your ticket will be forwarded automatically to our support team. Kindly note that you need to create one ticket per request!

Write: If you don’t have access to the Serviceportal, send an email to it-service@swisstph.ch.

Your email will be automatically forwarded to the IT Serviceportal and a ticket will be created. The IT Support Team will receive your Incident Request and will get in touch with you.

Call: In urgent cases or if the options above are not available, you can call the IT emergency phone, 333 (within Swiss TPH) or +41 61 284 83 33 (from outside Swiss TPH), on working days from 8:30-12:30 and 13:30-17:00.

Definition of urgent cases: • Reaction time shorter than one working day (deadline within 48 hours, event, travel...)

• Important service not available and no workaround possible (e.g., printing does not work at all) Visit: Please visit the IT office only after making an appointment and take the Incident Request (IRxxxx) ticket number and the name of the IT supporter (with whom you have an appointment) with you.

14 – General information

Please include answers to the questions below in every message to IT • Who – who is contacting and for whom are you contacting? Do you have an IT issue or does your colleague have one?

• What – what is the incident / request exactly?

• When 1 – when did the incident occur for the first time? Did you have this problem some time earlier already – if yes, how often?

• When 2 – when do you need support? Is there a deadline approaching? For instance do you need to submit an abstract this week and your software is crashed?

• Where – where did the incident happen? What were you working on when it happened?

For instance, were you writing an email or working on an Excel sheet?

• Why / How – do you know why / how it happened? Perhaps you know about an accident?

For further Information about Swiss TPH IT Support: https://intranet.swisstph.ch/en/aoc/informatics/it-service-support/ For students, there are special internal and external requirements and support offers, addressed in the IT introduction given at the beginning of each study.

Ordering software, hardware, access On the IT Serviceportal, the Swiss TPH Informatics offers different standard hardware and software, which you can order through the secretary of the department you are affiliated with. Please note that only software approved and licensed by Swiss TPH may be used on your rental laptop. It is not permitted to install any third party software by yourself. If you need any software that is not in the catalogue, please contact your department’s secretary.

General information – 15

Kindly clarify the needs and the budget with your supervisor in advance for avoiding delays and incorrect orders.

1. Login in the IT Serviceportal and check under orderable items what you need.

2. If the software is listed under the category Self-Service then follow the steps, described below.

As soon as your device is accessing the Swiss TPH network (also via VPN), the installation starts automatically. For all other Software / Hardware / Access needs, follow step 3.

3. Send an E-Mail to your Department secretariat with the follow information: Hardware: Type, Model, quantity, Recipient, Cost Centre, Preferred Delivery Date (at least 10 working days from approval), Delivery Location Software: Product Number, SW Name, Recipient, Cost Centre, Inventory Number from the Laptop / Desktop 4. Your Department Secretariat will place the order at the IT Serviceportal. Afterwards, your order has to be approved by the referring cost center owner in the Serviceportal directly. The time the approval takes depends on the reaction time of the cost centre owner and can’t be influenced by the IT. 5. After being approved by the cost centre owner, the hardware or software will be ready for delivery after ten days at the latest. For hardware orders you will be informed from the IT when the order is ready for delivery. Software will be automatically installed on your laptop / PC. As soon as your device is accessing the Swiss TPH network (also via VPN), the installation starts automatically, it can take from 30 minutes up to 3 hours, depending on the software.

Available in Software Center If you want to install software that is available in the Software Center, kindly follow these steps: 1. Start the Software Center application 2. Click on the “Available Software” tab 3. Search for the required software using the search bar 4. Select the required software package 5. Click on the “Install” button to start the installation procedure.

16 – General information

Depending on the selected software package, your PC will need to reboot once or multiple times during the installation. Once the installation procedure is completed, you will see a notification in you taskbar, and the new software will be available in the start menu.

Telephone and fax

International phone calls using the traditional infrastructure can be expensive; national as well as international calls from mobile phones are always very expensive. Whenever possible, e-mail and Internet-based phone services such as Zoom should be used instead. The phones in student offices can be used for work-related national calls. For international work-related calls, the line has to be activated (call the central secretariat 111 to ask for an international line). Office phones should not be used for private calls. A central fax machine is available in the EPH department, and should only be used for work-related transmissions. The number is +41 (0)61 284 81 05.

Post

Staff members have a letter-tray in the corridor of their respective floor, which should be checked regularly. At the same location, there are trays for internal Swiss TPH mail and for outgoing external mail.

Internal mail is sent in special envelopes; while official Swiss TPH envelopes should be used for external project-related mail (both are obtainable from Eliane Kobel, Zsuzsanna Györffy, Sabine Zbären and Nora Bauer). Swiss TPH pays for the cost of postage for work-related correspondence. Personal post can also be deposited in the tray for external posting, but stamps have to be bought privately. Stamps for personal post are available from the main secretariat. Indicate priority mail by using the “Priority” label or by writing “A-Post” in the upper-right corner of the envelope. The Institute’s address should not be used for receiving personal bills (utility, etc).

The Institute’s postal address is: Swiss Tropical and Public Health Institute From 1 January 2022: <Your Name> Swiss Tropical and Public Health Institute Socinstrasse 57 <Your Name> P.O. Box Kreuzsstrasse 2 4002 Basel 4123 Allschwil Switzerland Switzerland

Cafeteria

The cafeteria is located in the Eulerhof. Coffee, tea, soft drinks and various snacks are available during opening hours. Additionally, three different menus are offered every day during lunchtime. You can pay directly with your staff badge and receive a 30% discount or pay cash (no discount). Please make sure that you have enough money loaded on your badge prior to visiting the cafeteria (the machine to load your badge is on the ground floor in Socinstrasse 57, in front of the elevator). Please note: due to Covid-19, picnic is currently not allowed in the Eulerhof anymore (both inside and outside on the terrace).

Additionally, masks must be worn at all time in the building of the Eulerhof, until seated at a table.

There are several take-away shops on Allschwilerstrasse, close to Swiss TPH, as well as Migros, Coop and Aldi supermarkets. Two affordable restaurants are also in close proximity to Swiss TPH. In both places you can receive a discount if you show your student card: • Uni-Mensa, Bernoullistrasse 16, Basel • Cantina e9, Eulerstrasse 9, Basel At Restaurant Marmaris, Spalenring 118, Basel, a discount is also given if you present your Swiss TPH badge. At lunch, the MARKTHALLE close to Bahnhof SBB offers a very broad international variety of food vendors, at reasonable prices, in a nice urban atmosphere.

General information – 17

Football at Swiss TPH

The Swiss TPH offers its employees and students the opportunity to play football in a casual manner once a week. Men and women are most welcome independent of their talents and skills. In winter (OctMar) it takes place indoors at Hermann Kinkelin-Strasse 6, 4051 Basel on Monday from 18:15 to 20:00 and in summer (Apr-Sep) outdoors at Sankt Galler-Ring 80, 4055 Basel on Tuesday from 18:15 to 20:00.

Appropriate shoes are recommended. Contact Anja (anja.schreier@swisstph.ch) for more information.

Yoga

Swiss TPH is offering lunch yoga classes to all the employees and students. Vinyasa yoga and fun is taking place every Thursday at lunch-time (12:15 to 13:15). You are most welcome - independent of our talents and skills - to join Sonia Borrell (Scientist Swiss TPH and certified yoga teacher) at Turnhalle Mission 21. Contact Sonia Borrell (sonia.borrell@swisstph.ch) for more information.

Parking

Parking for bicycles (partly covered) is available outside the Institute. There is no car parking available for students. At the new building in Allschwil there will be a parking garage nearby.

Smoking

Smoking is not allowed inside any Swiss TPH building – and is generally discouraged for public health reasons. If you want to smoke, leave the building or use the designated places outside for smoking. It is not allowed to smoke in front of the windows nor in front of the main entrances.

Environment

Swiss TPH cares about the environment and the sustainable development goals locally as well. Indeed, Basel played a leading role in the “green movement” of Switzerland. This included the development of the environmental health research agendas, now all clustered at Swiss TPH. Please support all efforts to save energy in summer and winter, separate waste that cannot be prevented to support recycling, use public transport and limit your business trips to the minimum essentials as air traveling is by far the largest contributor to the climate relevant foot print. In your research teams, you may encourage the use of online conferencing to limit travel or promote piggy-bagging project workshops to conferences where most would go anyway. Favour seasonal and regional food for PhD defences and other work-related social events. Basel has high quality tap water – no need to invest in bottled water. Moreover, in the buildings of Swiss TPH there are several cold drink water machines (dispensers) which can be used.

Many student groups engage in environmental movements and activities (e.g., www.urbanagriculturebasel.ch).

Meetup

On meetup.com you can find lots of various socializing groups: www.meetup.com/cities/ch/basel A group of greatest interest, and in which many PhD students are registered, is the “Computational Methods for Research Community”: www.meetup.com/Basel-Computational-Methods-for-Research-Community-BCMRC.

18 – General information

Safety Travel Safety

Swiss TPH staff extensively travels to various countries, including fragile regions and conflict areas. Swiss TPH takes safety and security of its staff very seriously and has developed processes and tools which all staff must respect and use for a shared understanding of safety and security management.

Students who will travel abroad as part of their research project must adhere to the Swiss TPH travel safety and security regulations which can be found on the Swiss TPH intranet (www.intranet.swisstph.ch/en/aoc/health-safety-and-security/swiss-tph-travel-safety-security-concept). Should you for any reason not have access to the Swiss TPH intranet please request the material provided there through alexander.knup@swisstph.ch.

Swiss TPH key principles in safety and security • Principle of precaution: Take a preventive and proactive approach. Identify the risks and develop a plan to mitigate them.

• Primacy of life and personal well-being: safety and security always comes first. Your valuables are not worth your life or those of your colleagues. Likewise, pressure of work must never override safety and security.

• The right to withdraw: you have the right to decline if you think the risks are too high.

General travel requirements 1. Make yourself familiar with the Swiss TPH values and regulations by reading the Manual for Employees and the Code of Conduct.

2. Prior to leave for your first business trip abroad (out of Switzerland), you must complete the online security awareness training BSAFE : www.training.dss.un.org/ (send the certificates to hr@ swisstph.ch). Without this you are not eligible for business trips nor any reimbursements of any related travel costs.

3. Attend the Swiss TPH travel clinic for a pre-departure health check. A first medical check is paid by Swiss TPH. 4. Your private home emergency contact details need to be available and kept updated in your dossier at Swiss TPH Human Resources (hr@swisstph.ch) 5. Register yourself on GardaWorld Travel Security website for travel insurance (www.travelsecurity.garda.com/home) 6. Attend the two-day course on Swiss TPH safety & security risk management.

-> Travel recommendations during Covid-19: https://intranet.swisstph.ch/en/coronavirus/travelling/

Before each trip 1. Fill in the Travel Safety Form (take a copy with you and send one to your HQ and local contact) 2. Register your trip on GardaWorld Travel Security (mandatory for travel insurance cover).

3. Set up a communication protocol according to the security needs of the country.

General information – 19

4. Acquaint yourself with the local context and recent developments. Get help from your supervisors, they are responsible to ensure safety and practical arrangements.

5. Inform your embassy of your presence in the destination country (e.g., Itineris registration).

Accommodation Carefully plan your accommodations with your supervisor for stays abroad in case your research requires it (e.g. field work). Accommodation is often offered by the host institution abroad; else book safe and trust-worthy hotels (avoid using “couch-serve”, Airbnb and similar offers).

In case of an incident or an emergency, act as follows: 1. Look for local aid and inform your local contact and line manager (the numbers are those you filled-in on your Travel Safety Form).

2. If local help is not an option, call your line manager, HQ contact person or the Swiss TPH 24/7 Hotline. The hotline will offer you guidance and may trigger the emergency cascade if needed.

Intellectual Property (IP) rights and Data Protection

Working on a thesis as an MSc or PhD student may result in discoveries and inventions. Of note, discoveries or inventions – whether or not patentable – may include computer software, research data (e.g., novel diagnostic, drug or vaccine targets) or research tools, and all proprietary information associated with any of these items. Swiss TPH is a co-owner of discoveries and inventions made by MSc or PhD students during their work at Swiss TPH or while under supervision by Swiss TPH employees. The level of IP rights of the student depends on various issues, including the funder of the project and / or the supervisor, the rules established among research partners of networks the thesis may belong to, or the level of independence of the student work. With regard to the latter, Swiss TPH theses are often based on on-going projects and partly existing data where students may add a component or further analyse existing data. Whereas students have copyrights and co-authorship rights for their publications as generally defined in science, IP rights may be more restricted in such cases. Instead, in cases where the student generates genuinely new inventions entirely independent of pre-existing data or resources of Swiss TPH supervisors, IP rights of the student may be more substantial, though shared with Swiss TPH (for a brief overview of useful guidelines, the student is encouraged to consult the following website posted by the University of Toronto.

Thus far, IP rights have never been a source of conflict in the long history of Swiss TPH research. However, if you work on a specific domain where you anticipate IP rights to become a potentially conflicting issue, we recommend reading the aforementioned guidelines and discussing the issue early on with your direct supervisor. In such rare cases, details may be clarified in advance and become subject of special agreements.

The ownership of research data generated as part of the thesis need to be clarified with the supervisor.

In the majority of Swiss TPH theses, data used in the research may originate at least in part not only from the work done by the student but generated in the framework of larger projects. All rules of data ownership, data use and publication of such projects may thus apply, including the request to delete data on any private (non-Swiss TPH) hardware at the end of the theses work. Before using such data for further research beyond the thesis, supervisors and / or the principal investigators of the projects need to be informed to establish a new agreement.

Data protection

Please remember that data used for research must in all cases, and with no exception, be fully anonymous. If you collect or use data of subjects, files that contain personal data (e.g. name, date of birth, address, contact details etc.) must be safely stored and protected. Such personal information must be separated from the files used for the data analyses, using an anonymous ID number for the linkage to the full data, if needed. You should under no circumstances keep such personal files on your computer. Files containing names of subjects should never be sent by e-mail or other media.

20 – General information

The Swiss School of Public Health (SSPH+) Initiated in 2005, with funds from the State Secretariat for Education, Research and Innovation (SERI), the Swiss School of Public Health (SSPH+) became a foundation in 2008 and is currently supported by twelve Swiss universities (Universities of Basel, Bern, Fribourg, Geneva, Lausanne, Lucerne, Neuchâtel, Svizzera Italiana and Zurich and Universities of Applied Sciences Bern (BFH), ZHAW in Winterthur and SUPSI in Southern Switzerland). The visionary model of SSPH+ is based on the view that in a small country like Switzerland, no single institution has the critical mass to cover all public health relevant areas. As of 2019, a total of ~20 institutions affiliated with the ten founding universities build the core of SSPH+. As a foundation, SSPH+ does not have a “faculty”. However, counting all public health oriented faculty members at the partner universities, the SSPH+ “faculty” consists of more than 200 SSPH+ Fellows, supervising over 400 PhD students. Given the strong commitment of the University of Basel in public health, Basel has become the strongest pillar of SSPH+, with six partner institutes and over 50 University of Basel faculty members affiliated with SSPH+ (of which ca. 40 from Swiss TPH). Whereas the Dean, Nino Künzli, since 1 January 2015, is an employee of Swiss TPH, the other Directorate positions (in total two full-time-equivalents) are employees of the partner institutions in Zurich, Lugano and Geneva.

As SERI’s central funding contributions came to an end mid-2017, SSPH+ moved into a new innovative era where funding from its twelve universities and other partners now secures the mission of SSPH+ and ensures provision of central services to its prime partners.

Highlights of the collaborative SSPH+ activities relate to teaching and training offers on the PhD and post-graduate level. These courses and programmes are led by network partners. The most relevant one for Swiss TPH PhD candidates is the SSPH+ Inter-university Graduate Campus. It is open to all PhD candidates formally registered and approved as PhD candidates in one of the SSPH+ partner universities and supervised by any SSPH+ faculty member. More information on page 44.

The current E.U. funded PhD Fellowship Program GlobalP3HS is another flagship of SSPH+, bringing 50 competitively selected PhD students to Switzerland – with some dozen soon settled at Swiss TPH. Global P3HS students at Swiss TPH are expected to join the PPHS programme.

For further information see: www.ssphplus.ch and the recent commentary in Lancet. SSPH+ is also the owner of the International Journal of Public Health (IJPH). With its global public health focus, IJPH is a potential outlet for publishing PhD thesis papers. The editorial office, led by Dr. Anke Berger, is located at Swiss TPH.

General information – 21

Switzerland and Basel Switzerland Environment, people and language

Situated right in the heart of Western Europe, Switzerland (size: ~ 41,000 km²) is landlocked and shares borders with Germany, France, Italy, Austria and the Principality of Liechtenstein. About 60% of the country is covered by the Alps mountain range. Most of the approximately 8.5 million (June 2019) inhabitants live in the plains (so-called “Mittelland”), where the major cities of Zurich, Geneva, Basel, Lausanne and Bern (capital) are also found. Switzerland has four official languages: German (66 %) spoken in a variety of “Swiss-German” dialects, French (23 %), Italian (8%) and Rhaeto-Romanic (0.6 %), spoken in the South-Eastern canton of Graubünden. The largest constituencies among the ~2 Mio. foreign residents come from Italy, Germany and Portugal (270-310’000), followed by France, Kosovo and Spain (80-125’000) and Turkey, Serbia and Macedonia (~65’000 each). The far largest foreigner community in Basel comes from Germany.

State and currency

The Swiss Confederation (official English country name – or Confoederatio Helvetica (CH) as the official latin name) was founded in 1848, though the first nucleus – a confederation of three cantons (provinces) – dates back to 1291. Today it consists of 26 cantons, which operate with a large degree of autonomy, each with their own health, education and tax systems, legal authorities, parliaments and governments, among other things. Swiss national day is celebrated on August 1st though Basel starts with major festivities along the Rhine on July 31st already.

The currency in Switzerland is the Swiss Franc (CHF). One Swiss Franc is 100 cents (Rappen in German or Centimes in French). It is advisable to change money upon arrival in Switzerland, since exchange rates may be more favourable than abroad. Credit cards (VISA, Mastercard, etc.) and debit cards (Maestro, PostFinance) are widely accepted throughout the country. Apple-pay and similar (esp the Swiss app TWINT) are becoming more popular as well.

Education

The vast majority of Swiss children go to tax-financed free public schools. After compulsory education, adolescents transfer to upper secondary level, which can be subdivided into general education programmes, and Vocational Education and Training (VET) programmes. Adolescents can learn a profession through VET, which is mostly completed at training companies (apprenticeship) and combined with teaching at a VET school.

The University system in Switzerland is decentralised and is the responsibility of the cantons. Undergraduate “Bologna” Bachelor and Master Degrees and the graduate PhD education are also publicly funded. However, the post-graduate advanced education programmes must be fully paid by student fees.

There are nine cantonal universities, of which Basel is the oldest. Founded in 1460, the University of Basel is among the 20 oldest universities in the world. Two federal Universities have also been established, one in Zurich (Eidgenössische Technische Hochschule, ETHZ) and one in Lausanne (École Polytechnique Fédérale de Lausanne, EPFL).

More information about Switzerland can be found on the Internet at www.ch.ch.

22 – General information

Basel The city: culture and history

Basel is located in the northwest of Switzerland, where the river Rhine turns northwards. In the north of the city, the borders of three countries (Switzerland, Germany and France) meet.

Basel has about 199,000 inhabitants; the local language is a dialect of Swiss-German.

The Basel airport is located about 10 km north of the city on French territory (Euro Airport Basel-Mulhouse). The airport is accessible from Basel via a customs-free road.

When arriving by plane, make sure you take the exit to Switzerland to come to our Institute, and not the one to France! Basel has two major railway stations, the Swiss Basel SBB, including the French Bâle SNCF parts, and the Basel Badischer Bahnhof owned by the German railways but located on Basel territory.

The town was officially founded in 44 AC by the Roman local ruler Munatius Plancus. In the roman historiography, Basel is mentioned for the first time in 374 AC as Basilea. In 740 AC Basel became an Episcopal city (Bischofsstadt), which lead to its development as a trade and market town. In the 14th century, Basel experienced a plague epidemic and a devastating earthquake (1356). The city became world famous for hosting the great Council of Christianity from 1431 to 1448, and, as a consequence, the pope granted Basel the right to establish a full university from 1460. In 1501, Basel joined the Swiss Confederation and shortly thereafter, the Bishop was expelled during the Protestant reformation. However, the bishop’s crook (in German “Baslerstab” - see image) was kept as the city’s coat-of-arms. In 1833, the canton was separated into Basel-Stadt and Basel-Landschaft.

Basel has a great variety of museums, and is famous for its trade fairs, most notably the world-largest Watch and Jewellery Fair “Basel World” and Art Basel. The city centre retains many beautiful old buildings from the late Middle Ages. The local carnival, “Fasnacht”, lasts for 3 days and is traditionally and socially the most important annual festivity of the locals.

Climate and clothing

Basel is one of the warmest and sunniest spots in Switzerland. However, long periods of stable weather are rare. Summer (Jul-Aug) temperatures usually vary, and a rise to over 35°C on some days is often followed by thunderstorms and a cooler period (~25°C). The degree of humidity is moderate. Visitors from tropical countries may find the weather during the rest of the year to be ‘chilly’. In winter (Dec-Feb), temperatures regularly fall below 0°C and precipitation may take the form of snow. Rain falls throughout the year.

In winter, foreign students should bring warm clothing and rain protection. Buildings and public transport vehicles are adequately heated but in summer, air conditioning is usually not available.

Eating and drinking

There are many restaurants and take-away-stands throughout the city, although some (especially the restaurants) are quite expensive. It is cheaper to buy food in one of the many supermarkets (Migros, Coop, Denner, Aldi) offering a wide variety of ingredients and products, as well as ready-made meals and an ever-growing selection of organic food (labelled as “BIO”). The largest “BIO-only” store is close by, at the corner Eulerstrasse / Schützenmattstrasse (Höheners). Most shops have fixed opening hours, usually Monday-Friday 8 am – 7 pm and until 6 pm on Saturday. Supermarkets around the railway station are open till late and on Sundays, as are a few smaller local shops and shops at gas stations.

General information – 23

Swiss TPH students interested in African and Asian food recommend the two shops located at Viaduktstrasse 10 (A-Chau) and Missionsstrasse 15 (Mini-Market).

Typical Swiss specialities include “Fondue” and “Raclette”; both of which are based on melted cheese.

Muslim, Jewish and vegetarian students should watch out for pork meat (“Schweinefleisch”), which is often included in various restaurant dishes. A few restaurants are “vegetarian only” (e.g. Tibits which might be more expensive), although most restaurants have a growing list of vegetarian and vegan dishes on their menus, too.

Religious services

Switzerland has a Christian tradition, so there are many different Protestant and Catholic services offered in different languages in Basel. The website www.baselfellowship.org gives information about Protestant services held in English. There are also several mosques (close to Swiss TPH: Friedensgasse 18) and a synagogue (close to Swiss TPH: Eulerstrasse 2). Note that 45% of all ‘Basler’ do not belong to any church, 17% are protestants, 15% catholics and 10% muslim.

Language

German is the main language spoken in Basel and is the official teaching language of the University of Basel, thus, undergraduate students (BSc) must be proficient in that language.

MSc and PhD-level teaching at Swiss TPH is mostly English (except at the Medical faculty). Students fluent in English can participate comfortably in all Swiss TPH activities. Most teaching and administrative staff (and many people in shops, offices, etc.) can communicate in German, French and/or English.

Swiss TPH students from abroad are expected to have excellent English skills (corresponds to Cambridge certificate C1-C2). You might benefit from checking out the University of Basel Sprachenzentrum (Language Centre). They offer conversation and intensive courses in various languages. www.sprachenzentrum.unibas.ch

Travelling in and around Basel

Basel is a rather small city and it is quite easy to get around on foot or by bicycle. There is also a well developed public transport network that includes trams, buses and trains.

Regular users of the public transport system should consider buying a monthly pass (‘U-Abo’), which entitles you to unlimited travel for a fixed charge (CHF 80 for residents, CHF 105 for visitors, 53 CHF for PhD students as it is subsidized by the Institute) or a Half-Fare travel card (swisspass) that allows you to buy train and public transport tickets for half the price (see www.sbb.ch/en/travelcards-and-tickets/ railpasses/half-fare-travelcard.html). Alternatively, it is also possible to buy day tickets (1-7 days). Also note that SBB has started to sell tickets and day passes at discount prices, based on demand. Those are available only online or via the SBB app.

Tickets: www.sbb.ch/en/travelcards-and-tickets/tickets-for-switzerland/supersaver-tickets.html Day passes: www.sbb.ch/en/travelcards-and-tickets/tickets-for-switzerland/day-pass.html Basel has become a very bike-friendly city, thus, we encourage the use of bicycles as a healthy mode of mobility. However, be aware of the dangers posed by tram tracks! Cross the tracks only in steep angles!

Help preventing or reducing the number of bike accidents along the tram ways! Second hand bicycles are for example available via UniMarkt or at the Fleamarket on Petersplatz.

With its location at the German and French borders, your identity might be checked at any time and any place in the city. Hence, it is essential that you always carry your picture identity card or passport with you. If you cross the border it is crucial to have your swiss permit AND your passport with you.

24 – General information

How to get a visa For students from countries requiring a visa for entry into Switzerland, you have to apply for the visa at the Swiss embassy in your country. This must be done well in advance, as it will take at least 6-8 weeks for the visa to be issued. Only apply for a visa once you have received the ok from the student administration and your letter of admission from the University of Basel. More information can be found on: www.eda.admin.ch/eda/en/home.html.

In most cases, the Swiss TPH will assist PhD candidates requiring a visa or residence permit and will also help arrange accommodation, insurance and travel. Sometimes, however, this is not possible and candidates must apply for a visa on their own.

Master students are responsible to apply for their visa and residence permits themselves - see information below.

All foreign students (EU or non-EU countries) need to obtain a residence permit. It is your responsibility to check with the Migration Office Basel-Stadt “Migrationsamt Basel” or Migration Office Basel-Land “Migrationsamt Basel-Land”.

What you need to get a visa or a residence permit 1. A Letter of Admission from the Study Secretariat of the University of Basel (or for PhD-Students, a confirmation from the Swiss TPH Student Administration).

2. A written application indicating the reason for travel, duration of stay (length of your whole stay for study purposes), degree you will study, your plans for the future (work).

3. Curriculum vitae.

4. Evidence of sufficient financial resources to live in Switzerland. This usually involves providing proof that a solvent person will cover all the living expenses of the student, or providing a statement of account, a grant, or – for PhD-students – the contract of employment.

5. Written declaration that you will leave Switzerland after completion of your studies. After registering at the University of Basel, students must present in person at the Migration Office in Basel (Spiegelgasse 6) to get a biometric residence permit.

After having arrived in Basel, be prepared to show the following documents at the relevant migration office/community (PhD candidates: only if you are staying longer than 4 months in Switzerland) 1. Your passport (with visa, if required).

2. Valid students ID-card (“Legi”) of the University of Basel.

3. Proof of financial means.

4. Documents indicating your civil status, as appropriate (marriage certificate, divorce certificate, family register, etc.).

5. Copy of rental agreement.

The residence permit is only valid for one year. The immigration office will send out instructions for renewal. Students are responsible to inform ET or HR about expiry of their permit so that ET/HR can appy for a renewal of the Swiss permit if necessary.

General information – 25

The University of Basel The University of Basel is the oldest university in Switzerland and one of the 20 oldest universities of the world. It was founded on 4 April 1460, with a foundation ceremony held at the Basel Münster. During the 16th century, the Faculty of Medicine was renowned throughout Europe and could easily compete with the best faculties in Italy, France, the Netherlands and England. Early influential medical teachers include Paracelsus, Andreas Vesal, Felix Platter, Caspar Bauhin, Theodor Zwinger and Johann Niklaus Stupanus.

Other illustrious figures that have been lecturers at the University of Basel include Friedrich Nietzsche, Karl Barth, Daniel and Jakob Bernoulli, Jacob Burckhardt, Karl Jaspers, August Socin, among others.

The variety of people involved in academia turned Basel into an early centre of printing and humanism.

The University library was founded shortly after 1460. Today, with more than 3 million books and manuscripts, it is one of the biggest libraries in Switzerland. The University is supported by the cantons of Basel-Stadt and Basel-Landschaft. The University has been self-administered since 1996, with the “Universitätsrat” as the highest decision-making and supervisory body. Members of this body are elected by the two cantons of Basel. Dr. Beat Oberlin chairs the Universitätsrat. The current rector is Professor Andrea Schenker-Wicki (since 1 August 2015). The University counts approximately 12,000 students and 320 professors.

The University of Basel has produced five Nobel Prize winners in Physiology or Medicine: Paul H. Müller (1948) for work on DDT; Tadeus Reichstein (1950) for work on hormones; Werner Arber (1978) for work on restriction enzymes; and Niels K. Jerne and Georges J.F. Köhler (1984) for work on the basic immunological theories and mono-clonal antibodies.

Students at the University of Basel can take advantage of a variety of activities on offer, including sports, language courses, music, etc. An online marketplace is available at www.markt.unibas.ch, where students can buy and sell all kinds of goods for reasonable prices.

26 – General information

Guidelines for the Master Degrees in Infection Biology and Epidemiology

Guidelines for the Master Degrees in Infection Biology and Epidemiology – 27

Introduction for MSc Students We would like to welcome you to our specialised Master programs in Infection Biology and in Epidemiology. Some of you might already be familiar with Swiss TPH, having come through the University of Basel’s BSc programme, while others are new to the Institute. Over the last few years, the proportion of international students at Swiss TPH has increased substantially and we welcome this trend.

Students with a special interest in basic biology and laboratory work will consider the Specialised Master of Infection Biology, while students with a primary interest in epidemiology and statistics will be more interested in the Specialised Master of Epidemiology. Swiss TPH’s philosophy is to cover topics in international and global health from the laboratory to the field and to the beds of patients and the homes of the populations concerned. Hence, we encourage lively and meaningful cross-communication between the two Master programs.

This handbook aims to give you (and your supervisors!) practical information about being a student at Swiss TPH and answers a number of frequently asked questions. This section in particular provides guidance and information for Master students and covers topics ranging from admission requirements to program requirements and expectations. We hope this handbook will allow you to find information easily, saving you time and energy that would be better spent on getting the most out of your training at Swiss TPH and discovering the attractions of Basel and its surrounding areas.

Prof. Till Voss

Prof. Pascal Mäser

Prof. Christian Lengeler

28 – Guidelines for the Master Degrees in Infection Biology and Epidemiology

Prof. Martin Röösli

General Information and Procedures Admission

The Specialised Master of Science in Infection Biology is a 90 ECTS1 Bologna-compatible degree, requiring three semesters for completion. The Specialised Master of Science in Epidemiology is a 120 ECTS Bologna-compatible degree, requiring four semesters for completion. All lectures and courses are conducted in English. To be eligible for Master level studies at Swiss TPH, students must have the pre-requisites requested by the University of Basel according to the Bologna system for graduate studies. A Bachelor Degree with at least 180 ECTS credit points is required, of which at least 150 ECTS must have been acquired from the corresponding field of study (eligible BSc degrees are listed below).

Since autumn 2016, the program may host a few guest students from the MSc in Global Health offered by University of Geneva. This program offers students the option to take one semester in partner programs such as the MSc in Epidemiology for those who like to focus on epidemiology. These guest students do not complete their degree in Basel, but University of Geneva accepts the credits taken in Basel towards the MSc in Global Health.

Admission requirements for the Specialised Master of Infection Biology

A Bachelor of Science degree in Biology, Biochemistry, Medicine, Veterinary Medicine or Pharmaceutical Sciences with a minimum average degree score of 5.0 (according to the Swiss grading System, not rounded)2 and basic knowledge in infection biology / microbiology (at least four ECTS). Alternatively, students who pass the GRE® General Test in the area of «Quantitative Reasoning» or pass the GRE® Subject Test «Biology» with a score in the top 35th percentile will also be considered for admission (www. ets.org/gre).

Admission requirements for the Specialised Master of Epidemiology

A Bachelor of Science degree in Biology, Medicine, Dental and Veterinary Medicine, Pharmacy, Nursing Sciences, Agricultural and Forestry Sciences, Nutrition, Applied Biomedical Sciences, Sports Sciences, Biochemistry, Psychology, Sociology, Geography, Environmental Sciences, Mathematics, Computer Science and Economics, with a minimum average degree score of 5.0 (according to the Swiss grading system, not rounded) and basic knowledge of mathematics / biostatistics (at least four ECTS). Students with degrees in other disciplines will be considered on a case by case basis. Alternatively, students that pass the GRE® General Test in the area of “Quantitative Reasoning” with a score in the top 35th percentile will also be considered for admission (www.ets.org/gre).

Detailed guidelines regarding admission requirements are explained in the corresponding Studienordnungen and Wegleitungen (in German) and Infosheets (in English), which can be found at www.unibas. ch/en/Studies/Degree-Programs.

Applications for Master studies are made online on the University of Basel website www.unibas.ch, following the links: “Studies” -> “Application and Admission” -> “Application” -> “Master program” -> “Online application”.

1 The European Credit Transfer and Accumulation System (ECTS) was developed by the European Commission in order to provide general and accepted procedures for the recognition of study qualifications gained by students on courses outside their home country.

2 grades 1 - 6, 1 being the lowest, 6 the highest grade, 4 - 6 are passing grades

Guidelines for the Master Degrees in Infection Biology and Epidemiology – 29

The application AND authenticated copies of degrees and transcripts must be uploaded on the application platform of the University of Basel. Documents sent by post and scanned copies sent via e-mail will not be accepted. A letter of motivation explaining what you plan to study and why you wish to do your Master studies at Swiss TPH is also required. The application will be reviewed by the University of Basel and Swiss TPH and assessed according to the admission criteria.

Additional information on conditions of admission can be obtained online: www.unibas.ch/en/Student-Administration-Office-Enquiry.html.

The application window for both Specialised Master Programs is from 1 February to 30 April (the University of Basel is very strict and does not accept any delayed applications). There is a special deadline for University of Basel Bachelor students (around mid-August).

Late application (for holders of a recognised bachelor’s degree of a Swiss university, university of applied sciences or university of teacher education) is possible until 31 July - acceptance is not guaranteed.

Timeframe

Our Master programs usually last for three semesters (Infection Biology) or four semesters (Epidemiology) and can only be started in the autumn semester, beginning in mid-September. During the first semester, students in Infection Biology focus on lectures and course work. In this period, the students will also choose a MSc research topic that they will conduct during the following spring and autumn terms followed by write-up of the MSc thesis. This timeframe is extended by an additional semester for the MSc Epidemiology. An oral MSc examination completes the degree requirements. In special cases, it is possible to prolong thesis completion until the end of the next semester. An extension beyond four / five semesters will only be considered in the case of documented exceptional circumstances.

First steps

It is recommended that you organise suitable accommodation as soon as you are accepted into the Master program, as it is quite difficult to find affordable accommodation in Basel and nearby on short notice. You should also check whether or not you have adequate insurance coverage. Health insurance is mandatory in Switzerland and it is the student’s responsibility to arrange for the appropriate insurance coverage (e.g., www.swisscare.ch). It is also your own responsibility to organise your journey to Basel and apply for a visa (see page 25), if necessary.

At the beginning of the program, students must provide personal information (Student Data Sheet).

A photo will also be taken after arriving at Swiss TPH. After registering at Swiss TPH, students must undertake a medical examination, which is done free of charge by the Swiss TPH medical services department. In addition, all students have to complete a security test to show that they have read and understood the safety rules at the Institute.

Lecture selection

Once registered at the University and in possession of an official student card, it is still necessary to register for every lecture separately. This allows for the accurate calculation of ECTS credit points, which are awarded after completing all the lecture requirements. While it is possible to attend the same lecture twice, ECTS credit points can only be obtained once. Students have to register for lectures online via “Student Services” https://services.unibas.ch from the beginning of August until mid-October and from the beginning of February to mid-March.

30 – Guidelines for the Master Degrees in Infection Biology and Epidemiology

To use Student Services, you must have a University of Basel (Unibas) e-mail account and relevant password. Log in at https://services.unibas.ch - a detailed guideline in English for using Student Services can be found there.

1. Log in to the Student Services account.

2. Choose “Belegen” (i.e., “register”).

3. Switch to the “Vorlesungsverzeichnis” view and add your lectures to the list.

4. Register the selected list with “Student Services”.

5. Check your selected lectures at any time with the “Belegen” service. You may change, add, or drop lectures freely up until the end of the registration-period.

Choosing a thesis topic

A list of available Master thesis research topics will be distributed to all students. It is not possible to receive Master thesis topics in advance since all students should have the same chance of working on a specific science project. Once the student found his/her favourite Master project, he/she should contact the responsible supervisor for further discussions. As soon as the arrangement between student and supervisor is finalized, students will receive a contract outlining procedures, and the rights and responsibilities of the student and supervisor. Please note that the contract must include the supervisor’s academic title.

All students will be given a laptop for their research work and thesis write-up during their study time at Swiss TPH. The laptop remains the property of Swiss TPH and must be returned to the IT department after completing your Master degree. Please be aware: laptops that are returned damaged or not returned at all, will involve personal charges, to be paid by the registered individual, of up to CHF 2,500 for compensation. Treat the rental laptop as if it was your own property please!

Study goals

Master in Infection Biology Students acquire solid theoretical and practical knowledge of infection biology with emphasis on pathogens causing poverty-related infectious diseases. They are able to plan and conduct their own research project, to work in a research team and to analyse, interpret and present their findings orally as well as in written form.

Master in Epidemiology Students develop solid theoretical and methodological knowledge of key concepts in epidemiology and applied biostatistics. They acquire the ability to design and execute basic field studies, collect and analyse data, report results in written and oral form as well as collaborate in multidisciplinary teams.

For further information please read the degree profiles on our website: • Degree Profile Master in Infection Biology • Degree Profile Master in Epidemiology

Social competences

Students should develop a sense of responsibility in relation to their scientific activities. They should recognise ethical considerations in research and in the application of research results. Students will learn that addressing interdisciplinary questions requires teamwork among specialists of diverse disciplines and these skills will be practiced in seminars and during the completion of the Master thesis.

Credit point system

The requirements for Master studies are based on the European Credit Transfer and Accumulation System (ECTS). One ECTS corresponds to 25-30 hours of student work. For example, if one ECTS is assigned Guidelines for the Master Degrees in Infection Biology and Epidemiology – 31

to a one hour lecture during one semester of 14 weeks, this includes 14 hours of course attendance and for each of the 14 lectures one additional hour of student work to prepare or follow-up on course work.

To obtain a Specialised Master of Science in Infection Biology degree students need to collect 90 ECTS credit points (30 ECTS lectures / courses, 50 ECTS MSc thesis, 10 ECTS final exam).

For the Specialised Master of Science in Epidemiology degree students need to collect 120 ECTS credit points (60 ECTS lectures / courses, 50 ECTS MSc thesis, 10 ECTS final exam). ECTS credit points collected from lectures and courses are given for completing them with a “pass” grade. The criteria for achieving a pass grade are specific to each course, and may involve completion of assignments and / or written or oral examinations. A failed lecture can be repeated. Note that half-ECTS (0.5; 1.5 etc.) are not awarded.

For the Specialised Master in Infection Biology, the thesis research project focuses on laboratory work and is usually carried out at Swiss TPH under the supervision of a teaching staff member.

For the Specialised Master in Epidemiology, thesis research focuses on epidemiological field studies, bibliographic research, analysis of existing epidemiological databases or on epidemiological modelling.

A Swiss TPH teaching staff member supervises this work. For projects involving field work overseas, external experts usually provide additional on-site supervision.

Members of the Swiss TPH academic teaching staff who are affiliated with the Science Faculty of the University of Basel as Group I or II members (see Teaching Staff List, Appendix p.75) are formally responsible as supervisors (Beurteiler/in) for the Master students and their work. They can delegate supervisory work to other members of the teaching staff or to project leaders at Swiss TPH, but remain responsible towards the faculty. Supervisors advise students throughout their studies, oversee and grade the Master thesis and assess students in the final Master degree examination.

MSc courses (total 30 / 60 ECTS)

Each semester, Swiss TPH publishes a list of available lectures and courses, indicating the number of ECTS awarded by each. These lists are updated each autumn semester. See pages 67 and 69 For the Master in Infection Biology curriculum, students must acquire 30 ECTS credit point through lectures and courses. Of these, 18 ECTS are acquired from a list of mandatory lectures and courses at Swiss TPH. Students are free to choose the remaining lectures as they see fit, but these additional lectures should be agreed upon with the thesis supervisor and have to be approved by Till Voss.

For the Master in Epidemiology, 60 ECTS credit points from lectures and courses are required, of which 45 are mandatory. In order to pass your MSc studies in Epidemiology you need: • Exactly 15 CP from module (a) “Foundation in Epidemiology” • Exactly 15 CP from module (b) “Biostatistics and Computing” • At least 10 CP from module (c) “Global & Public Health” - with the possibility to take additional CP by visiting the Monday seminar more than once.

• At least 5 CP from module (d) “Transferable Skills and Competences”, of which two courses totalling 2 CP are compulsory (Good scientific conduct in health sciences and Application to an ethics committee).

• 15 CP from module (e) “Advances in Epidemiology, Statistics and Global & Public Health” Surplus credit points from non-compulsory lectures out of “Global & Public Health” (c) as well as “Transferable Skills and Competences” (d) may be counted towards “Advances in Epidemiology, Statistics and Global & Public Health” (e). But the reverse is of course not possible. With regard to transferring CP from (c) or (d), please note that you cannot split credit points between modules, if lectures award more than one credit point. In other words, if you want to shift a course with 2 CP from (d) to (e), you should make 32 – Guidelines for the Master Degrees in Infection Biology and Epidemiology

sure that the remaining courses in (d) still total the 5 required CP. In module (e) credit points from other study programmes of the University Basel may be used in agreement with your Swiss TPH supervisor and approval by Christian Lengeler.

If you plan to attend lectures at other universities in Switzerland or abroad (in agreement with your supervisor), you must request permission from the teaching commission (walter.salzburger@unibas.ch, cc to Christian Lengeler resp. Till Voss, and Pascal Gschwind) BEFORE you take that course.

Credit points from other universities will only be granted if at least 3 CP. Please make sure that you register for all the mandatory lectures of your particular Master course. If you fail to do so, the University of Basel will not be able to issue your final degree and you will have to register for another semester.

Students are advised to take most of their lectures before they embark on their thesis work - especially if field work abroad is required.

Master thesis (50 ECTS)

The Master thesis (see Appendix pages 71 & 73), including preparation for the final examination, usually takes one year to complete and is carried out under the supervision of one (or more) Swiss TPH lecturer(s) habilitated at the Faculty of Science (see Appendix page 75). 50 ECTS are granted for an accepted Master thesis. The thesis topic must have been approved by one of the Faculty Representatives at Swiss TPH. Late completion (after the end of the second thesis semester) is considered a ‘failure to complete’ unless supervisors have given the student formal permission to extend the submission date.

The thesis is evaluated and graded by the Faculty Representative, together with the supervisor of the Master project (if different from the Faculty Representative), on a scale from 1 (worst) to 6 (best). If the resulting grade is a fail (less than 4) or a 6, an additional person from the Faculty of the University of Basel, who is not directly involved in the project, will be asked to give an independent expert assessment of the thesis.

Final examination (10 ECTS)

The final examination is an oral test covering (1) the topic of the thesis, including the relevant scientific literature, and (2) the topic of infection biology /epidemiology more generally. The examination lasts 60 minutes. Examiners include the main thesis supervisor and a second person from the Swiss TPH teaching staff serving as a chairperson. One of these two persons should also be the Faculty Representative.

An additional examiner can be invited at the discretion of the student and / or the supervisor.

The oral final exam can only be taken when the thesis has been accepted and 30 (IB)/60 (Epi) CPs from specialised studies have been accumulated. The examination can be held at any time during the final semester. The examination is graded on a scale from 1 (worst) to 6 (best). The student earns 10 ECTS if s/he re-ceives a passing grade (score of 4 or more) at the oral exam. The general structure of the oral examination is as follows: 1. A short (max 10 minutes) summary of the MSc thesis work that was done, to start off the examination.

No formal presentation (Powerpoint, etc.) is required.

2. Approximately 20-30 minutes examination on the thesis and the specific field of investigation, including the relevant scientific literature.

3. Approximately 20-30 minutes section on general concepts of Infection Biology or Epidemiology to test general knowledge in the two subjects (according to MSc course taken).

Guidelines for the Master Degrees in Infection Biology and Epidemiology – 33

Pick up the relevant examination forms 1-2 weeks before the exam from the Swiss TPH student administration office.

Specialised Master degrees in Infection Biology or Epidemiology

The degree is completed once the following ECTS credit points have been acquired: • 50 ECTS from thesis work; • 30 / 60 ECTS from lecture work, including all compulsory lectures and courses; and • 10 ECTS from the final oral examination.

The final thesis grade is calculated by averaging the grade of the final examination (weight 1/3) and the grade of the written thesis (weight 2/3). The written certification of the MSc degree details the topic of the MSc thesis as well as the various grades.

After the final oral exam, the cover page of the Master thesis as well as the marked grading sheet and the other exam forms (all signed by the supervisor and chairperson) must IMMEDIATELY be taken by the student to the Swiss TPH student administration office. An electronic copy of the final Master thesis must be given within 2 - 3 weeks after the exam to the student administration office and to the Swiss TPH library (including the ‘Declaration of consent’), as well as to other appropriate recipients (persons involved in the work, etc.).

Salaries and scholarships

Swiss TPH (or the University of Basel) does not pay MSc students a salary nor are any scholarships offered, as funding for MSc studies is generally unavailable.

Study fees of currently CHF 850 per term (“Semestergebühren”) have to be paid by the student, as do health insurance costs and living expenses. Study fees at the University of Basel are the same for Swiss and international students. From the 2nd semester of registration onwards, a 10 CHF membership fee for the SKUBA (University of Basel student union) is charged as well, the first semester is free.

Program contacts and course guidance

The following people are responsible for the Swiss TPH Master programmes at the University of Basel: Prof. Till Voss Specialised Master in Infection Biology till.voss@swisstph.ch (Deputy: Prof. Pascal Mäser, pascal.maeser@swisstph.ch) Prof. Christian Lengeler Specialised Master in Epidemiology christian.lengeler@swisstph.ch (Deputy: Prof. Martin Röösli, martin.roosli@swisstph.ch ) Pascal Gschwind Administrative Course Coordinator pascal.gschwind@swisstph.ch

34 – Guidelines for the Master Degrees in Infection Biology and Epidemiology

Checklist for MSc Students To apply to an MSc course, complete the application form available on the University of Basel website and submit the application along with a letter of motivation explaining your research interests and why you wish to study at Swiss TPH. Once students have been accepted to the Master program, they should follow the checklist below. Students already registered at the University of Basel can start with point #6 of the checklist.

1. After receiving your admission letter from the University, apply for a Swiss residence permit and, depending on your country of origin, for a visa to enter Switzerland (see page 25).

2. Find accommodation in or around Basel, as soon as possible.

3. Ensure that your health insurance covers your stay in Basel. Be aware that health insurance is mandatory in Switzerland and you need to arrange for this before coming to Switzerland (e.g., www.swisscare.com).

4. Arrange your travel to Basel by yourself.

5. Register formally and in person at the University of Basel at the given time. Bring along original certificates, including high school certificates, as requested in the admission letter. You will then get a student card. The email address you will receive together with your Swiss TPH laptop at the welcome day.

6. In the first two weeks choose the lectures you want to attend and register (“belegen”) online at the University of Basel, using the Student Services program MOnA. Final registration has to be done by October.

7. When the autumn semester starts, get your personal Swiss TPH ID-badge (deposit CHF 100) to be able to access all learning and teaching rooms at Swiss TPH. 8. Complete the student data sheet (part two) and return it to the Swiss TPH student administration.

9. Make an appointment at the Swiss TPH health clinic for a free medical check-up (paid for by Swiss TPH).

10. Familiarise yourself with the Swiss TPH library. To use a printer, you need your personal IDbadge.

11. When writing up the Master thesis, decide with your supervisor on a date for the oral exam and who will be the chair of the exam. Register for the Master exam by completing the “Anmeldung zur Masterprüfung Biologie” form. Take the registration form to the University study secretariat (Faculty of Science), Mrs Susan Kaderli, “Studiensekretariat”, Klingelbergstrasse 50, 4056 Basel, no later than four weeks before the exam and inform Swiss TPH student administration accordingly.

12. Pick up the relevant forms for the oral exam from the Swiss TPH student administation.

13. After the oral exam, return the Master agreement and additional exam forms (signed by the supervisor and chairperson) to the Swiss TPH student administration.

14. When you have successfully finished your Master course, provide within two weeks an electronic copy (PDF) of your thesis to the Swiss TPH student administration. At the same time fill out and sign the form “Declaration of consent for the publication of the Master thesis on the Intranet” and send it with an electronic copy of your thesis (PDF) to the library. The library guarantees the long-term digital archiving of your thesis.

15. Complete outstanding administrative and academic formalities: Return your badge and collect the deposit; return all books to the library; provide copies of the data collected and other essential computer or archive files to your supervisor; return the laptop/notebook.

Guidelines for the Master Degrees in Infection Biology and Epidemiology – 35

Guidelines for Doctoral Studies at Swiss TPH

36 – Guidelines for Doctoral Studies at Swiss TPH

Guidelines for Doctoral Studies at Swiss TPH Overview of general guidelines for Swiss TPH PhD studies The University of Basel offers PhDs1 in many subject areas or disciplines/subjects, called “Promotionsfächer”. Formal responsibilities for those are rooted in the respective Faculties, thus, depending on the chosen subject, rules may partly differ.

Swiss TPH’s academic faculty supervises PhD studies in various faculties, though most frequently in the Faculty of Science followed by those enrolling in a Faculty of Medicine discipline.

PhD subjects offered by the Faculty of Science (of relevance at Swiss TPH): • Cell Biology • Epidemiology • Microbiology • Zoology PhD subjects offered by the Faculty of Medicine: • Biomedical Engineering; • Clinical Research (incl MD / PhD) • Public Health / Epidemiology, including Insurance Medicine (incl MD / PhD) • Medicines Development (incl MD / PhD) • Biomedical Ethics • Nursing Sciences • Sports Science According to the current regulation, the Medical Faculty awards the title Dr. sc. med. (Doctor scientiarum medicarum / PhD in English). For details, see the Faculty of Medicine website. The Faculty of Science awards the title Dr. phil. (PhD).

PhDs offered by the Faculty of Economics Students with a master’s degree in economics can also earn a PhD in economics under the supervision of Prof. Günther Fink. Students will have to apply to the economics department, and will then be enrolled in the Basel Graduate School of Economics. Course work typically entails 18 ECTS, and should focus mostly on economics courses.

Find out more: https://wwz.unibas.ch/de/graduateschool/

General rules and requirements

A completed Master degree, comprising at least 90 ECTS2 credit points3, is a prerequisite for doctoral studies at University of Basel. A Master of Advanced Studies (e.g. MPH) or any other MSc with only 60 ECTS credit points do NOT qualify for doctoral studies at the University of Basel.

The general rules for PhD candidates are outlined in the PhD rules and regulations (“Promotionsordnung”), which can be downloaded from the faculty websites, e.g. the Faculty of Science’s: https:// philnat.unibas.ch/de/forschung/promotionphd/immatrikulation-ab-hs-2016-registered-fall-semes1 PhD: Doctor of Philosophy; latin: philosophiae doctor 2 European Credit Transfer and Accumulation System (ECTS) was developed by the European Commission in order to provide general and accepted procedures for the recognition of study qualifications gained by students on courses outside their home country.

3 One ECTS credit point is equivalent to 25–30 student working hours.

Guidelines for Doctoral Studies at Swiss TPH – 37

ter-2016-or-later/, or the Faculty of Medicine site www.medizin.unibas.ch/de/karriere/doctoral-degrees/ (an English version can be requested from the Faculty of Medicine), respectively. PhD canditates are expected to know their respective regulations and adhere to them.

One important difference: • Faculty of Science: Not all Master degrees qualify for unrestricted access to the PhD. Candidates holding a not fully qualifying MSc (e.g., a MSc in economics, social sciences or a Medical Master degree) may be required to do extra course work (which comes in addition to the course work needed for the PhD).

• Medical Faculty: The regulation is open to inter-disciplinary research beyond faculty boundaries, thus, all MScs (from qualifying universities) are eligible for a PhD in one of the above mentioned subjects of the Medical Faculty as long as those MScs build a relevant background for the PhD research (according to the judgment of the supervisor).

Doctor of Medicine (MD) at Swiss TPH The 1-year MD studies can also be done at Swiss TPH provided the supervisor of the MD thesis has an academic position at Swiss TPH. The “Dr. med.” (MD) degree requires one year of scientific activity. To register as a doctoral student, a Master degree in Medicine is required. The thesis can only be submitted one year after obtaining the Master degree and after successfully completing the federal “Staatsexamen”. Work on the Dr. med. thesis can begin during the Master programme and can be a continuation of scientific work performed for the Master thesis. Details are available at the „Ordnung für den Erwerb der Doktorwürde „Dr. med.“ and the Wegleitung. The student must be registered for at least two consecutive semesters as a doctoral student at the University of Basel. A Dr. med. thesis can only be led (Thesis Leader - “Dissertationsleitung”) by one with an academic degree, such as a PD or a Professor, of the Faculty of Medicine. Please see the faculty affiliation list. Academically qualified staff from other faculties can be involved in thesis supervision as “Dissertationsbertreuer/in” and must be mentioned in the thesis, though it is the Thesis Leader (“Dissertationsleiter”) who will evaluate the final thesis. Though the MD is often a default in careers of physicians, the MD alone does not qualify for a scientific career.

Those interested in academic tracks may profit from the MD-PhD:

Combined Medical Doctorate (MD-PhD) The MD-PhD title allows research-oriented physicians to do the MD and a PhD in a combined way (Dr. med. and Dr. sc. med.). A major advantage of this combined track is to limit the total time needed for this double-title to the 3+ years of a usual PhD. In general the first first-author publication counts as the MD and the following 2+ provide the PhD, resulting in the MD / PhD. Doing first an MD-thesis only (usually approximately 1 year) followed by a PhD later on results in investing some 4+ years. MD-PhD theses can be lab-based, thus, can be performed in any of the disciplines of (basic) sciences but as well in epidemiology and public health or in clinical research – thus, all the above listed “subjects” / Promotionsfächer qualify for the MD-PhD track. At Swiss TPH, all rules set up for PhD students also apply to MD-PhD students, thus, all information provided below for PhDs also apply to MD-PhDs. Most MD-PhDs may be funded through projects like all other PhDs. However, Swiss Academy of Medical Sciences organizes a competitive scholarship program funded by the Swiss National Science Foundation (SNSF) and other donors. Scholarships are open to MD-PhD candidates for all disciplines, and the selection process is highly competitive, with pre-submission deadlines (pre-selection at Uni Basel level) usually mid December and decisions taken in the following May. Details are available at www.medizin.unibas.ch/de/karriere/doctoral-degrees/md-phd/. Contact person at Swiss TPH is Nino Künzli (nino. kuenzli@swisstph.ch)

38 – Guidelines for Doctoral Studies at Swiss TPH

Application

Persons interested in pursuing a PhD at Swiss TPH have two possibilities: Apply for an advertised position here: https://recruitingapp-2698.umantis.com/Jobs/All or send in an unsolicited application.

Unsolicited application: 1. Find a supervisor: If you are interested in becoming a PhD candidate at Swiss TPH, please be aware that finding a supervisor is the most important step for prospective candidates. Swiss TPH does not offer PhD candidate fellowships, rather, PhD candidates are funded through projects, led by potential supervisors. Candidates may also be funded by competitive external fellowships to which they apply on their own. In both cases, a Swiss TPH supervisor is required for eligibility. Please explore the Swiss TPH website to find a field or team of interest and relevance to you.

2. Documentation: Please send a detailed motivation letter and current CV to the Swiss TPH PhD Student Administrator, Christine Mensch, christine.mensch@swisstph.ch. In the motivation letter, specify any plans to apply for externally funded fellowships or whether you expect to be funded through our projects. Please also contact her to help clarify eligibility questions or concerns. After a first departmental screening, unsolicited applications will be shared with all potential supervisors at Swiss TPH. You will be notified directly if an opportunity is available and asked to submit further information. Please do not send your applications to Swiss TPH scientists directly.

Swiss TPH makes the final decision on whether or not to accept a PhD candidate who formally qualifies for PhD studies at the University of Basel. Acceptance of PhD candidates is very restrictive and competitive. As mentioned above, Swiss TPH does not offer fellowships, all PhDs are either financed through projects of supervisors or through fellowships acquired by the candidates to join Swiss TPH (e.g. Swiss Government Excellence Scholarships for Foreign Scholars and Artists - ESKAS). Funding must be secured and guaranteed for the entire PhD period, therefore, the funding mechanism has to be explained in the proposal.

Candidates and supervisors will agree on the PhD subject to be enrolled in (as explained below). Once the research project and logistics, including the mode of financing, have been agreed on with the supervisor and the formal eligibility of the candidate is confirmed by the Swiss TPH student administration, he/ she needs to start the registration process at the University of Basel (Immatrikulation, see next page).

Choosing the PhD subject

It is the responsibility of the supervisor to choose the right PhD subject with / for the PhD candidate. The choice is usually driven by the content of the thesis as well as the background of the candidate.

However, there is certainly some overlap among the life science research areas. The strongest and indeed complete overlap consists for the two options to do a PhD in epidemiology. The traditional choice for Swiss TPH students has been the Faculty of Science programme, established by Marcel Tanner already in 1992. The Faculty of Medicine offers PhDs since 2009, including the subject “Public Health / Epidemiology, including Insurance Medicine”. From the research and student perspective, the two options are the same. The major difference originates from the different faculty affiliation (see Staff list).

The various faculties define their own regulations and rules about the supervision. Those rules are partly in conflict with the need for inter-faculty multidisciplinary teams of supervisors as often needed in epidemiology and in many domains of public health sciences. Thus, your choice of the subject, and, eventually, the faculty, ultimately depends on who your supervisor(s) is/are.

Guidelines for Doctoral Studies at Swiss TPH – 39

For PhD studies in epidemiology where supervisors (or at least the Group I Full or Associate Professor supervisor (see staff list) are affiliated in the Faculty of Medicine (or got the permission to act like Group I professors in the Faculty of Medicine), the PhD in Public Health / Epidemiology including Insurance Medicine will be the easiest choice.

If supervisors (or at least the Group I Full or Associate Professor) are rooted in the Faculty of Science (or got the permission to act like Group I professors in the Faculty of Science) the PhD in Epidemiology of the Faculty of Science will be the optimal choice.

In general, the supervisor requirements are: • Faculty of Science: Both supervisors need to be members of the Faculty of Science (one of them Group I). If the non-Group I supervisor is rooted in a different faculty, permission to supervise must be requested from the Dean’s office.

• Faculty of Medicine: One supervisor needs to be a member of the Faculty of Medicine (Group I), the other supervisor may be from another Faculty.

The rules in the Faculty of Economics are similar to the one in the Medical Faculty.

Please discuss with your supervisor or feel free to contact Nino Kuenzli or Christine Mensch anytime in case of uncertainties on how to find solutions in the complex forest of the current University of Basel regulations. Please discuss uncertainties prior to the submission of your registration to the University to avoid time-consuming administrative changes.

University registration (matriculation)

PhD candidates at Swiss TPH need to be matriuclated at the University of Basel for the entire duration of their PhD studies.

Candidates already holding a Master degree from the University of Basel continuing towards a PhD must re-register at the University of Basel (via MOnA) and indicate their new status. The “Application for admission to doctoral study”-form must be completed and signed by the First Supervisor and submitted along with a fee of CHF 100 to the Admission Office of the University of Basel. A copy of this form must also be submitted to the Student Coordinator, Christine Mensch.

Candidates coming from outside the University of Basel need to be formally registered at the University of Basel. A registration fee of CHF 100 is required.

Registration details and online registration in German and English are available under: https://www.unibas.ch/en/Studies/Application-Admission/Application/Doctoral-Studies.html.

Some important points: • Required documents include a letter signed by the supervisor confirming the candidate’s acceptance. The student coordinator will arrange this letter. (The full list of required documents can be found in the application set for doctoral studies section of the University of Basel website (link above)).

• Medical Faculty: - a short proposal of the thesis is required - the potential second supervisor must be named • Science Faculty: - a provisional working title of the thesis is sufficient

40 – Guidelines for Doctoral Studies at Swiss TPH

• Deadlines for registration for doctoral studies: 31 July (autumn semester) 5 January (spring semester) Please also send scans of all application documents to Christine Mensch.

Upon registering at the University, you will receive a student card (which has to be activated every semester in the Kollegienhaus) enabling you to benefit from the many discounts offered to students/ doctoral candidates.

Administrative Checklist for new PhD candidates upon arriving at the Swiss TPH 1. Visit the Student Administration Office (Christine Mensch, Student Coordinator) to take care of administrative details. Complete the Data Sheet PhD Student.

2. Go to the library to have your photo taken for the ID / access badge (dates (no appointment necessary): 4 Aug, 1 Sep, 6 Oct, 3 Nov, 1 Dec 2021, 9-11am) (library@swisstph.ch).

3. Collect your badge (and hand over deposit of CHF 100) from the main secretariat (Socinstrasse 57, ground floor).

4. Sign your work contract (available from HR) or PhD regulation (available from ET). Upon signing the contract or regulation you will receive an information package, including important material about security, job ticket for public transportation, etc. Read it carefully.

5. Make an appointment with the Swiss TPH medical services department (located at Socinstrasse 57, first floor, open until 2 p.m.) for your compulsory medical check-up, which is free of charge for the student, but paid for by the institute.

How to get a bank account (for foreign / scholarship PhD candidates)

Please note that it is mandatory for all scholarship recipients to open a bank account so that the stipend can be transferred to the relevant accounts starting from the second month onwards. Cash payments will only be done in the first month.

We recommend to open a bank account either with Postfinance or UBS. Get in touch with christine. mensch@swisstph.ch to discuss the options.

The following documents have to be presented: • Identification paper (passport).

• Copy of regulation with Swiss TPH • Swiss permit or document “Ermächtigung” (which was issued by our migration office for entering Switzerland) which shows the duration of the stay in Switzerland After receipt of the first scholarship, it is possible the bank will block 200 CHF (or a similar amount) for safety reasons. Of course this amount will be reimbursed (some tax fees will be deducted) when leaving Switzerland.

Scholarship holders are obliged to inform christine.mensch@swisstph.ch immediately about the bank account details.

Guidelines for Doctoral Studies at Swiss TPH – 41

Structured PhD Programs Swiss TPH PhD candidates are highly encouraged to enrol in structured PhD programs within the first 4-6 months of the PhD. Structured PhD programs support PhD candidates during their studies and with finishing their PhD. PhD candidates registered in structured PhD programs must fulfil additional requirements (such as at least 18 instead of 12 ECTS of course work). This comes with a range of extra benefits though, such as: • Participation at special courses and events with small or no fees, • Access to funding of courses or conferences, • Career training, and • Networking among a critical mass of PhD candidates.

Please discuss this option early on (i.e. at the very beginning of your PhD period) with your supervisor.

Admission rules and procedures may differ across programs, thus, check out the websites and approach the programme coordinators. Typically, registered students who fulfil all requirements will get a programme certificate once they have received the PhD title from the University. These certificates are not a “PhD degree” but confirm the range of additional achievements. NOTE: If you do not accumulate the required ECTS until the defence, you may be charged the course fees in retrospect.

The world of PhD programs is changing: we are currently in the process of combining a few PhD programmes into one school, the graduate school health sciences (GSHS). The GSHS planning group is led by an inter-faculty team chaired by Nino Künzli and coordinated by Anja Matthiä.

All Swiss TPH PhD candidates will have to get enrolled in the GSHS together with students of the former structured PhD programs, namely the University of Basel Medical Faculty PhD Program in Health Sciences (PPHS, see below) and the University of Basel Science Faculty international PhD program Infection Biology (IPPIB, see below).

The large SSPH+ PhD program in Public Health doesn’t accept new students anymore, those already enrolled continue to benefit from the program though. Furthermore, all Swiss TPH PhD candidates are welcomed to the SSPH+ Inter-University Graduate Campus – the hub of inter-university high quality SSPH+ PhD courses, trainings, and events (see below).

All these changes are due to fundamental changes in the funding mechanisms of all PhD programmes.

These should though not affect PhD students already enrolled in any programme. Given the many PhD candidates of Swiss TPH still enrolled in those programmes, we keep some basic information of all here below. Feel free to approach Nino Künzli at anytime in case of uncertainties.

42 – Guidelines for Doctoral Studies at Swiss TPH

PhD Program in Health Sciences (PPHS)

Funded by the University of Basel and chaired by Nino Künzli, this program offers, among other things, free courses, networking, career training, and funds for external courses. Even though the program is rooted in the Medical Faculty, PhD candidates in the Health Sciences from Medical and Science Faculty in any of the following PhD subjects are eligible: Clincal Research, Nursing Science, Sports Science, Public Health/Epidemiology including Insurance Medicine (all Medical Faculty) or Cell Biology, Microbiology and Epidemiology (Science Faculty). Registration is online. Eligible students must agree to acquire at least 18 ECTS. The PPHS website, www.pphs.unibas.ch, provides all information. PPHS is coordinated by Dr. Anja Matthiä at Swiss TPH, contact: pphs@unibas.ch.

PPHS is particularly attractive as it has a formal agreement with the SSPH+ IGC: all courses offered by the two programs are freely accessible to the enrolees of both programs (for SSPH+ IGC courses a registration fee of 30 CHF is charged).

International PhD Program Infection Biology (IPPIB)

This PhD Program ended in 2019 but will continue its aims in the new Graduate School Health Sciences.

Until the official start of the Graduate School Health Sciences, current PhD students can use the offerings by PPHS, PhD Program Health Sciences. New students in the Swiss TPH Department of Medical Parasitology and Infection Biology (MPI) are encouraged to register to PPHS, https://pphs.unibas.ch/ registration/ Contact person for PhD students in the area of infection biology is Pascal Mäser (pascal.maeser@swisstph.ch).

Guidelines for Doctoral Studies at Swiss TPH – 43

SSPH+ Inter-university Graduate Campus

Since 1 June 2019 (following the previous SSPH+ PhD program in Public Health), PhD candidates have the opportunity to enroll in the Inter-university Graduate Campus of the Swiss School of Public Health SSPH+ to benefit from its offers to strengthen their academic skills, competencies, career paths and networks.

The only eligibility criteria for enrollment are the following: • The primary supervisor of the PhD candidate must be an SSPH+ Faculty member (note: Swiss TPH facutly are by default SSPH+ faculty member) • PhD candidates must be formally registered and approved as a PhD candidate in one of the SSPH+ Foundation partner universities.

The SSPH+ IGC is not a structured PhD program, but it offers courses in public health research, advanced methods, and thematic workshops as well as SSPH+ seasonal schools. Courses are taught by national and international experts and aim to provide high-level training for PhD students as well as stimulating networking opportunities. Registered SSPH+ students can attend PhD courses for free (apart from a processing fee of 30 CHF per course) and the SSPH+ seasonal schools (and courses by other partners) at reduced fees. There are no additional requirements in terms of ECTS, publications etc. apart from the ones of the home university of the PhD candidate. It is highly recommended for all PhDs at Swiss TPH to join the SSPH+ IGC. The SSPH+ IGC is managed and coordinated by Ann Walser (awalser@ssphplus.ch), Graduate Campus Manager, at the Institute of Social and Preventive Medicine, University Bern. For all information see www.ssphplus/en/graduate-campus/. Anja Matthiä, PPHS coordinator, is in close contact with Ann Walser. Nino Künzli, Head of BMD unit and Dean of SSPH+, is the local (Basel) representative and steering board member of IGC.

International Graduate School (IGS) North-South

The IGS North-South is not a structured PhD program but a graduate school of the Universities of Bern, Basel, and Zurich, www.igs-north-south.ch. It is dedicated to establishing an international research network that analyses the impacts of global change, with a view to advancing sustainable development worldwide through interdisciplinary collaborations. It emphasises an integrative, partnership-based research approach encompassing higher education at the PhD level, innovation and application. Upon completion of course work (at least 12 ECTS), the IGS North-South offers their students a Certificate of Specialization in Sustainable Development, which supplements the degree they receive from their home institution. The PhD students may choose from a broad range of disciplinary and thematic courses offered at the participating Swiss institutions. The three partner universities usually rotate the leadership for the annual IGS North-South Summer School (5 ECTS). If your research and training needs fit into IGS North-South, discuss this option with your supervisor. IGS North-South summer schools may be of particular value also for students from the global South.

44 – Guidelines for Doctoral Studies at Swiss TPH

Graduate School Health Sciences – the future highlight

To strengthen the PhD tracks in health sciences, the University of Basel will launch the Graduate School Health Sciences (GSHS). Though administratively rooted in the Medical Faculty, the GSHS expands the vision of inter-faculty multi-disciplinary health sciences in line with long traditions of PhD tracks at Swiss TPH. It is planned that the GSHS will have an inter-faculty regulation (Promotionsordnung) approved by both the Science and the Medical faculty. It will be mandatory for PhD students at the Medical Faculty and be open to all health sciences PhD candidates of other faculties and PhD subjects of the University of Basel who would like to join. It will become the “one-stop-shop” for PhD candidates and supervisors engaged in PhD studies in health sciences. GSHS will offer courses, seminars, seasonal schools and access to networking opportunities as needed in the interdisciplinary fields of health sciences. It guides PhD candidates to comply with regulations and requirements set by the faculties of their subject. It assists supervisors in selecting the most talented PhD candidates. The GSHS Steering Board (PhD Ausschuss) will secure the quality of PhD tracks, profile the academic content and the development as well the strategic orientation of the GSHS as a platform tailored to the academic needs of PhD tracks. The GSHS Coordination Office guarantees the administration and coordination of the GSHS and its academic board.

GSHS replaces and consolidates various parallel governance structures, commissions and boards currently involved in the parallel management of health sciences PhD tracks including the above mentioned PPHS and IPPIB and others. Thus, stay tuned and watch out what’s coming next. PhD candidates are also represented and most welcome in the GSHS development group, coordinated by Anja Matthiä at Swiss TPH, anja.matthiae@swisstph.ch.

Mailing list: pphs@maillist.unibas.ch Information about courses and events in the public health and related is sent to this mailing list and published online: https://pphs.unibas.ch/program/training-offers-overview/ and https://pphs.unibas. ch/events-in-the-health-sciences/.

Everyone can register for the mailing list. We will include your email address to the mailling list automatically. You can unsubscribe again at any time.

Everyone can write to the list (pphs@maillist.unibas.ch), e.g. in case you know of an interesting event to share. Interested people, e.g. Master or prospective PhD students, are welcome to join the list. In case you have any questions, please contact Anja Matthiä: pphs@unibas.ch.

Guidelines for Doctoral Studies at Swiss TPH – 45

Relevant steps taken during the PhD studies at Swiss TPH At the beginning of the PhD, discuss with your supervisor the aims and objectives of your PhD, which will be written in a proposal in the first six months. Throughout the PhD studies the student and the supervisor need to meet regularly to discuss the required next steps of the PhD process (annual meeting mandatory, copies thereof need to be given to the Student Administration Office). The final product of PhD study and research are peer-reviewed publications and/or a written thesis. Following the completion of the thesis, an oral exam is held. The below sections outline these processes.

PhD proposal

Swiss TPH procedures do not depend on the faculty of your PhD subject, thus, information below applies to all PhD candidates at the Swiss TPH.

New PhD candidates are required to first prepare a PhD proposal in collaboration with their supervisor – use the proposal template available at the Research Commission coordination. Guidelines for writing a proposal are available.

Candidates have to indicate whether their proposal is part of a research project which has already been peer-reviewed by a funding agency (such as SNF). If the PhD study is part of a larger research project, it is important to outline the specific role and responsibility of the PhD candidate. In addition to the description of the research planned, information about the composition of the doctoral committee, ethical issues, internal and external support, a budget plan, training to be undertaken during PhD studies (see below) and a detailed timeline must be provided. The planned research should allow for production of at

least three scientific manuscripts although a target of five publications is desirable.

Once your supervisor agrees with your proposal, all PhD proposals are thereafter reviewed by three senior Swiss TPH staff members (including one statistician).

Once the supervisor and reviewers agree with the revised version, it will be discussed for approval at a meeting of the Research Commission of the Swiss TPH (The PhD proposal evaluation process). The Research Commission meets regularly and the meeting dates are communicated in advance on the Intranet and the Institute’s hompage www.swisstph.ch/teaching/doctorate.html (see list of links towards the bottom on the right).

46 – Guidelines for Doctoral Studies at Swiss TPH

The aims of the PhD proposal review process are to: • Achieve high scientific quality of the proposals.

• Assure optimal use of internal collaborations.

• Foster collaborations across units and departments.

• Assure a comparable and high training standard of all Swiss TPH PhD students.

• Critically review the funding situation of each PhD student.

• Evaluate ethical issues of each proposal (Appendix).

• Allow an efficient exchange of information about ongoing research activities within Swiss TPH. The PhD proposal evaluation process (see also here) All candidates must submit their proposal three (to maximum six) months after having registered as PhD candidates at the University of Basel to the Research Commission: The date for your presentation to the Research Commission should be decided in collaboration with your Supervisor. Once you agreed on a date, please inform the Research Commission (research.commission@swisstph.ch) about the planned presentation date.

• Six weeks prior to targeted meeting: Upload the proposal labelled ‘proposal draft for review’ to the provided personal folder on Alfresco (link will be shared with you).

• The supervisor should ask two Swiss TPH colleagues and the statistical support group to critically review the proposal. The reviews should be carried out within two weeks.

• Reviewers upload the their review to the candidates Alfresco folder • The PhD candidate should organise a meeting with the reviewers, the designated statistician and their supervisor to discuss the reviewers’ comments. Required adaptations of the proposal should be made by the PhD candidate and the version labelled as the “revised proposal” uploaded together with the completed cover page into the Alfresco folder at least one week prior to the Research Commission meeting.

• The reviewers check the revised proposal and complete the review by filling in the second column in the reviewers’ form. The completed review has to be uploaded to the candidate’s folder two days before the Research Commission meeting.

• At the Research Commission meeting, each PhD candidate presents his / her revised proposal within five to max. seven minutes. The short presentation should be understandable for a mixed audience. The reviewers and the designated statistician give a short comment. All Research Commission members can then provide input. In general, the proposals will not need more than 15 minutes (in total) to be discussed with the Research Commission.

Guidelines for Doctoral Studies at Swiss TPH – 47

Special to PhD Candidates enrolled to the Medical Faculty: Please fill in the cover page required by the Commision of the Medical Faculty (‘PhD Ausschuss’). It is extremely similar to our own but has some special requirements, in particular the roles of the supervisors have to be described in detail. Please submit your final proposal (after passing the Research Commission meeting) together with this PhD Agreement to Christine Mensch, christine.mensch@swisstph.ch.

She will submit all documents to the Faculty of Medicine. Do not submit the documents directly to the Faculty of Medicine yourself.

Doctoral/PhD committee

As this information has changed in the past (autumn 2016), do not use older Student Handbooks.

The PhD committee consists of at least three mandatory members, namely the First and Second Supervisors (“Erst- & ZweitbetreuerIn”) and one external expert / examiner (formerly Ko-Referrent).

Required members of the PhD committee: First Supervisor Second Supervisor External Expert (see below) Further/additional advisors

Faculty of Science mandatory mandatory mandatory (NOT from University of Basel) possible

Faculty of Medicine mandatory mandatory mandatory (NOT from University of Basel) possible

Faculty of Economics mandatory mandatory

possible

Please abstain from assigning a “faculty representative” as this role does not exist anymore in any PhD regulation.

Faculties have slightly different rules about minimal requirements for the First and Second Supervisors but in any case it is required that at least one of the two supervisors is a Group I (Full or Associate Professor) faculty member. A group of Swiss TPH Professors not in Group I or not in the Faculty of Science got the Faculty’s permission to act like Group I members in PhD committees of our students - please see the detailed list of these Swiss TPH academics.

Moreover, new models emerge where the role of the First Supervisor can be shared (First Supervisor and First Co-Supervisor). This model, with in essence three “main supervisors”, allows to officially have e.g. a junior scientist, who is not yet a faculty member, assigned in the role of the First Supervisor (conditional on the First Co-Supervisor fulfilling the formal role as a Professor). The Science Faculty accepts this model according to an official Memo approved by the Dean. The commission / PhD Ausschuss of the Medical Faculty is also open to consider such proposals.

The External Expert(s) (formerly Ko-Referrent) may be any scientist in good standing (at least PhD) and familiar with the research. They must come from an academic institution outside Swiss TPH / University of Basel and must not be connected in any way to the PhD thesis (for example as associated expert or collaborator). Most importantly, the External Expert does not co-author any manuscripts of the PhD thesis. Preferrably he/she should also not be a regular co-author of the supervisors. A request has to be filled at the Faculty of Science or the Commission of the Faculty of Medicine to approve the external advisor (via student administration). The External Expert will be reading and marking the thesis and will be invited by the Dean’s office to attend the thesis examination.

The Chair of the Examination Committee is responsible for the organisation and the correct procedures of the thesis defence. In case of a Science Faculty defence, the supervisor can propose the Chair. In case of Medical Faculty and Faculty of Economics it is usually the PhD committee of the faculty who 48 – Guidelines for Doctoral Studies at Swiss TPH

assigns a chair although a suggestion can also be made. In case of Medical Faculty PhDs, the Dean’s office (Moira Lux (phd-med@unibas.ch)) prepares all the documents for the defence and delivers them directly to the Chair.

Course work and training

As per University of Basel regulations, PhD candidates are required to complete a minimum of 12 ECTS of formal training (1 ECTS = 25-30 student hours of work). The skills and competences needed for a successful completion of the PhD in Infection Biology and the PhD in Epidemiology (Science Faculty) are listed in the Appenices. The PPHS website describes the minimal standards for PhDs in the disciplines of health science.

These guidelines should be used to assess the training needs of individual students. In addition to subject specific knowledge, students need to acquire research skills and to develop personal and management skills (“transferable skills”). The 12 ECTS represent a minimum number and students lacking required qualifications should consider additional training after discussion with their supervisor. Also check the information on structured PhD programmes as attractive additional options – it is highly recommended to enrol in such program although they require at least 18 ECTS. The total ECTS required are decided by the doctoral committee together with the students and must be indicated as the Learning Agreement in the research proposal.

Swiss TPH courses offered through the Master programs in Epidemiology and in Infection Biology present additional training opportunities for PhD candidates. Also note that PhD candidates registered at Uni Basel have free access to all courses offered in any Bachelor or MSc-Program by the University. The University of Basel also offers relevant lectures and courses in transferable skills, most of which are open to all PhD students. Please use the course directory to search for relevant courses. Transferable skills courses, many of which are offered through the Graduate Center of the University of Basel (GRACE), may have a separate enrolment procedure, which can be found be at the GRACE web site. Please note though that most of the GRACE offers are currently unable to comply with the enormous demand. Other courses can e.g. be found on the SSPH+ website where a large set of offers are constantly updated. Also consult the PPHS webpage and discuss with your supervisor about best options to tailor your courses to your needs.

It is also required that all PhD candidates present at least once, usually in their last year, in the ‘Monday Seminar’ (Advances in Infection Biology, Epidemiology and Global Public Health).

Learning contract For courses outside the course directory of the university, candidates need to create a learning contract (Studienvertrag) in MOnA BEFORE taking/registering for a course. Your supervisor needs to approve the course before you can take part. After the course, your supervisor confirms the participation. The process is completely online and there should be no need for printouts. A step-by-step documentation is available on MOnA (online services).

Candidates of the Medical Faculty must also make sure that their courses are listed in the Learning Agreement (approved by PhD commission) before creating the learning contracts – any changes (e.g. courses added to the Learning Agreement) need to be approved again by the PhD commission. It is also recommended to send a copy/scan of certificates from all completed external course to Moira Lux (phdmed@unibas.ch).

For candidates enrolled at the Faculty of Science, see point 1.2: https://philnat.unibas.ch/fileadmin/ user_upload/philnat/3_Forschung/Doctoral_studies_-_Guidelines_Version_06.2021_english_01.pdf

Guidelines for Doctoral Studies at Swiss TPH – 49

Non-academic internships

There is also a strong trend and demand toward integrating a non-academic internship into the PhD track as a way of getting insights and possibly finding opportunities for non-academic careers after the PhD – indeed the ultimate track of many PhDs. SSPH+ has launched the SSPH+ Internship Program to assist you in finding and arranging such internships. Please discuss this option with your supervisor early on as it raises a range of questions you need to clarify upfront, including the ideal timing, conflicts with your research and funding issues. Recipients of a GobalP3HS fellowship of SSPH+ are required to integrate an internship into their PhD (therefore, the fellowship runs for up to 42 months). For all other PhD students, internships are optional. Depending on the host institution internships may be part-time and/or of different duration.

Financial support

As mentioned earlier, Swiss TPH does usually not accept unfunded PhD candidates; i.e., all PhD candidates must have some funds from either grants, fellowships, or other external funders or employers. In case of an external employer, PhD candidates / supervisors must provide proof of guaranteed funding that is not less than the models mentioned further below, whichever may apply, and that at least 50% FTE of the time can be dedicated to the PhD studies. If contracts of external employers end prior to the end of the PhD, supervisors need to cover the remaining monthly allowance.

Although Swiss TPH pursues fairness and equity in the salary structure, the level of the PhD student stipends are not fully under control of Swiss TPH, but partly determined by the funder. One default is the stipend as defined by SNSF, mandatory for all SNSF project funded PhDs. The same stipends should be applied for all other funders unless the funding agency has set different (higher) stipends.

For students from the global South, we have in particular County of Basel-Stadt (AFA) and Swiss Embassy (ESKAS) scholarships that have pre-set financial rules, which include stipends and other contributions (such as insurance, university fees etc.). As of 2019, Swiss TPH also welcomes GlobalP3HS fellowships from SSPH+, co-funded by the EU and the supervisors.

The net amounts of those stipends are lower than SNSF salaries but these stipends are tax exempt, have no social security deductions, and often include other support the usual PhD stipends do not cover. All those stipends are topped up to the fixed amount of CHF 2’350 per month. Taking all inherent differences into account (e.g. taxes, health and liability insurance, social security, semester fee, etc.). SNSF and other stipends do now provide rather similar amounts for the cost of living.

Approximately 75% of Swiss TPH PhD students regularly stay abroad during longer periods of the studies. Indeed the visionary Swiss TPH “sandwich model”, which entails research for, in, and with partner institutions in low and middle-income countries (LMIC), requires regular stays in the LMIC. Thus, in June 2020, ILK decided to harmonize payments while abroad and to make sure all PhD candidates receive 12 monthly payments per year from the start month (not later than the month after the matriculation date) to the end month of the PhD studies, assuming a duration of PhD studies of three up to a maximum of four years.

The new regulations applies to new incoming PhD students (matriculation since January 2021). The transition rules applies to those with a first matriculation between 2018 and 2020. For those previously enrolled as 100% FTE PhD students at Swiss TPH, no changes are forseen. PhD studies should not take longer than 3-4 years full-time equivalents (FTE).

New rules for all PhD students starting 1.1.2021 or later (matriculation date) Irrespective of the source of funding, all PhD students receive 12 monthly payments from the start month (not later than the month after the immatriculation date) to the end month of the PhD studies – typically 3 to max 4 years. Each PhD student gets contracted under one of the following three models: 1) SNSF Default, with 12 monthly payments from the start to the end of the PhD studies. The amount is defined by the Swiss National Science Foundation. The model includes a regular Swiss TPH employment 50 – Guidelines for Doctoral Studies at Swiss TPH

contract, managed by the HR office. The full costs of this model, to be guaranteed by funds of the supervisor, include the salary, social security, and the usual Swiss TPH overhead.

2) Swiss TPH Stipend: The stipend model is typically adopted for PhD studies under the “sandwich model”. The stipend model comes with 12 monthly payments of CHF 2’350 made by Swiss TPH from the start date to the end date of the PhD studies, irrespective of the physical stay. The model includes the signing of the Swiss TPH PhD Regulation, coordinated on behalf of HR through the Doctoral Student Office (ET / Christine Mensch).

3) Special Regulation: Occasionally, the 12 monthly payments may be defined and organized differently, such as being instead on the payroll with employment by third parties while working on the PhD studies.

Thus, employment rules and salary scales of those parties may apply. Details need to be described and signed in the Swiss TPH PhD Regulation prior to the matriculation as PhD student (application step, supported by ET). As in the other two models, agreements guarantee 12 monthly payments per year.

Transition rules for PhD students with PhD start dates prior to 1.1.2021 PhD students who started the PhD at Swiss TPH prior to 2021 shall finish their PhD studies under the currently agreed model.

Exceptional transition rule: As of 2021, PhD students with start date (matriculation month at Uni Basel) in 2018, 2019 or 2020 qualify for a top-up payment from the supervisor to reach CHF 1’000 during the full months stayed abroad in case the currently agreed payments were below CHF 1’000 during those months abroad.

Read the full Memo regarding the new rules here.

Please also make sure to wisely manage the monthly income as you have to pay all expenses, including housing, food, yourself. Depending on the funder, you may also need to pay the health insurance plan, which is mandatory in Switzerland, and tuition fees. Also note that health insurances have a self-pay fraction and dentists are not included in the health insurance plans.

A budget section outlining how the candidate will be paid and how additional research, travel and study costs will be covered must be part of future PhD proposals. Candidates and supervisors must make sure that the PhD related project is also fully funded (not just the stipend of the student).

IMPORTANT: For international students with a scholarship (according to 2) and 3)) and a residence permit B, the taxation office of Basel will send a tax declaration form once a year. It is of utmost importance to inform the taxation office IMMEDIATELY by registered letter that you are a student with a scholarship provided by the relevant sponsor to avoid having the scholarship funds taxed. You need to sign and return the tax papers with your scholarship notification letter and, if applicable, your student ID. Do not just ignore them, because then you might face serious problems with major financial consequences you will need to cover yourself and in addition, this might also affect the renewal of your residence permit!

Duration of PhD studies and extra tasks

Full-time PhD (or MD-PhD) candidates are expected to complete their thesis within 3 to 3.5 years, while part-time PhD candidates may extend the duration of their studies accordingly. For candidates conducting research abroad, a minimum residency in Basel of 4 months at the onset of studies and of 6 months at the end for finalising the PhD is required. For non-academic internships taken during the PhD studies see above and discuss with your supervisors. Most internship hosts might require full- or parttime presence of at least 6 months. Those internships may also build the link between the end of the PhD studies and the post-PhD live.

PhD candidates are expected to devote up to 20% of their time to support general tasks of Swiss TPH irrespective of the funding source. Please make sure to also volunteer in those tasks and to have your supervisor encouraging you in volunteering. If all Swiss TPH students equally contribute Guidelines for Doctoral Studies at Swiss TPH – 51

to those tasks, the contribution of a student will be far less than 20%. Student representatives (and supervisors) manage the assignment of such tasks: • • • • • •

Supervise during an exam (presence).

Correct exams and evaluation forms.

Assist with cocktail hours or coffee breaks.

Assist with the organisation of conferences or workshops.

Technical support (data cleaning and analysis, teaching, Master student’s support, etc.).

Assist the administration team.

Time off and PhD parental support

In the case of an unanticipated extended leave from studies due to illness, health problems or other personal reasons, the candidate is asked to inform and consult with his/her supervisor. For more information please refer to the human resources guidelines available from the HR department.

For PhD candidates who are parents, Uni Basel has special support in the get-on-track funding scheme (www.unibas.ch/en/Research/Financing/Doctorate/get-on-track.html). Additional information is available on the Family Services page: https://www.unibas.ch/en/Staff/Family-Health/Family-Services.html.

Portfolio and assessment

All Swiss TPH PhD candidates maintain a portfolio documenting their learning progress. Throughout the PhD studies the student and the supervisor are expected to complete the required next steps of the PhD process.

Regular meetings with the doctoral committee (at least annually) are accompanied by an evaluation based on the student’s self-assessment.

The student’s self-assessment is an opportunity to reflect on the experiences that improved his / her ability to conduct research and to suggest how other competences could be acquired and how to further develop and improve personal, managerial and leadership skills. Based on this assessment a working plan for the following year is developped. The self-assessment includes, but is not limited to, the documentation of formal training, conferences attended, presentations given or papers published. The self-assessment form stays with the student.

Students are responsible for organising the annual committee meetings. Each year, an annual meeting confirmation form must be submitted to the Student Coordination to be entered in the student database. After the first year of doctoral studies (usually 12 months after registration), a formal decision is made regarding whether or not the PhD studies should continue.

Upon completion of the PhD, the complete documentation of formal training, conferences attended, presentations given and papers published is sent to Christine Mensch.

PhD thesis

The final product of PhD study and research is a written thesis. Students of the Science Faculty have the choice of producing a monograph thesis or a publication-based thesis, whereas students of the Medical Faculty must write a publication-based thesis that includes at least three publications; the latter being the clear preference for all Swiss TPH PhD candidates.

In general, a publication-based thesis consists of 3-5 peer-reviewed articles and includes a general introduction, literature review, discussion section and conclusion. The student should be the first author of at least two publications and at least two manuscripts need to be published or accepted for publication at the time of thesis submission. The typical structure of a thesis is given in the Appendix. Theses are written in English.

Publishing your manuscripts

Swiss TPH PhD candidates usually publish at least three first-authored articles and thus exceed the 52 – Guidelines for Doctoral Studies at Swiss TPH

basic requirements of the University of Basel. Please discuss and plan the target journals very carefully with your supervisor. Open Access (OA) is becoming a default, and all journals, both traditional “subscription based” and true “Open Access“-journals, offer this option. Also be aware that SNSF-funded projects must be published OA, in return, SNSF pays the publication fees (ACPs). However, SNSF does not pay the ACP in case you choose OA in a hybrid journal (i.e. subscription based, with OA as option). In those cases, your supervisor needs another funding source. Please be aware that authors/supervisors (namely, the “corresponding author”) are responsible for the payment of the APC. Swiss TPH has no funding contribution to APC. However, many funders - not only SNSF - allow charging the APCs toward the projects. Also note that the University Basel has some institutional agreements with many scientific publishers. Given that all Swiss TPH “corresponding authors” include “University of Basel” as the second affiliation (after Swiss TPH) by default (see below), we automatically qualify for those special waivers or rebates.

Find more information on the Intranet: https://intranet.swisstph.ch/en/aoc/library-services/open-access-and-apc-discounts/ or contact the library (library@swisstph.ch) … but do not publish in predatory journals However, the move towards OA publishing has created thousands of fake/predatory journals. Make sure to never ever submit your work to any of these predatory journals. These journals violate all codes of scientific publishing and conduct. A website listing such journals (“negative list”) has not been continued.

Please refer to the more reliable web site listing all high quality open access journals (“positive list”): www.doaj.org.

If your target open access journal is not on that list: be aware and clarify this in all details prior to submission. Also be aware if you get invited to co-author a paper: make sure your first / corresponding author does not choose such a predatory journal! It is your co-responsibility as a co-author to check this too! The Swiss TPH library and the Editorial Office of the International Journal of Public Health (IJPH) at Swiss TPH (Anke Berger) may assist you too in case of questions. We highly recommend to read this Commentary in IJPH of Anna Severin – a PhD student in Bern doing research on these topics – and Nicola Low.

Authorship

It is recommended to discuss (co-)authorships rules for your thesis papers and / or all papers where you may contribute apart from the ones of PhD thesis early on with your supervisor, particularly also if you are part of large consortia. Publications do matter in academia, thus, you should make sure to get credit where appropriate and to also promote your co-authors where appropriate, as you may indeed know best who made crucial scientific contributions to your work. Whereas rules about the qualification for authorship are usually clear and internationally agreed, the positioning in the list of co-authors needs clarification early on to prevent any misunderstandings or disappointments. In most cases it is rather clear who takes the primary lead in analysing, reviewing the literature, writing up the paper within a PhD thesis – typical qualification as a 1st author. But occasionally this needs clarification as the major load may sometimes be equally shared by two, thus, one should discuss “equal first authorship” where both the first and the second are officially considered “first authors” (journals usually put a symbol to explain this). For those pursuing an academic career, a “first authorship” (or “equal first”) counts clearly stronger than a “normal” 2nd position.

All other author positions are less clearly defined, thus, subject of early discussions and decisions. Very often, the second most involved contributor to a paper (apart from the senior leader – see below) may be listed as “second author”. In most cases (in the typical fields of science prevalent at Swiss TPH), the leading senior scientist (i.e. the one in the driving seat of a project, a thesis etc. who is though not doing all the analyses and manuscript developments but rather acts as the primary supervisor giving feedback, revising manuscripts, etc.) may opt for “last author” positions. However, this is not universally true. Indeed, you may work with partners whose academic systems value the “second author” much higher than the “last author” position (thus, offering “last authorship” may be misinterpreted as Guidelines for Doctoral Studies at Swiss TPH – 53

an offense). Moreover, in large collaborations, more than one researcher may possibly qualify as “last author” and your supervisor will know this. For example, some networks have adopted the (unwritten and not universally equally understood) “rule” to position the most senior leaders as the “second last” and “third last” authors whereas the more junior 2-3 key researchers may appear as 1st, 2nd and 3rd. In such large groups of co-authors, one may typically opt for positioning the key contributors at the above mentioned positions whereas all the others may appear in between, in alphabetical order. These are just some guiding principles, to be defined case-by-case with your supervisor. Remember that as the first author of a paper, it is your responsibility to make sure (with the supervisor) all authors who qualify have been considered (thus got the opportunity to contribute) and that no one is listed who does not qualify as author (but, e.g., as “acknowledgement”). All your co-authors must have read at least the final or pre-final version and given feedback and the “ok” to co-author your paper. This needs some time you have to include in your planning.

IMPORTANT NOTE ABOUT SHARED AUTHORSHIPS: Collaborating in interdisciplinary research results usually in multi-author publications, including shared first authorship. This is highly welcomed and offers opportunities also to PhD students to co-author more publications than the “minimal essentials”.

Please be aware that the “core part” of your PhD thesis cannot at the same time be the “core part” of another student’s PhD thesis. Given that most PhD students go far beyond the “minimal essential requirements”, we have never seen conflicts with this rule. In case of uncertainties, discuss it with your supervisor early on. Some subtleties also differ between faculty regulations: The PhD Regulation of the Medical Faculty requires three first-authored publications as the “core”. Those three publications can be claimed as “core part” by only one PhD student (i.e. no other co-author can claim any of these three “core” articles to be the main part of his/her own PhD thesis as well).

The PhD Regulation of the Science Faculty refers to the same issue more generally with a reminder that if you do a “collaborative theses” (Gemeinschaftsarbeit), your own contribution must be well identifiable and circumscribed, and it must, by itself, fulfil the requirements of a PhD thesis.

Affiliation of Swiss TPH authors

Your PhD thesis will consist of several scientific articles, published in peer reviewed journals. All authors must always provide their affiliation. Swiss TPH researchers must by default provide two separate affiliations, namely the following two, in this order: 1. Swiss Tropical and Public Health Institute, Basel, Switzerland 2. University of Basel, Basel Switzerland As an independent institute, associated with the University of Basel, this double affiliation is required and non-negotiable. As leading author / PhD candidate you are responsible for providing correct affiliations, too. We do not add the Department to any of these two affiliations and most journals agree to skip this.

Submitting the thesis

Please read and study the relevant PhD regulations carefully: www.philnat.unibas.ch/de/forschung/promotionphd/ & https://medizin.unibas.ch/fileadmin/user_upload/medizin/Dokumente/Lehre/doctoral_degrees/PhD_Ordnung_2015.pdf For additional information, contact the responsible dean’s office, dekanat-philnat@unibas.ch (Science Faculty) or phd-med@unibas.ch (Medical Faculty). Further it is mandatory to inform the Administration Office of Swiss TPH if you plan to finish the PhD studies.

The thesis should represent original work on the part of the student. Plagiarism is a serious offence at Swiss TPH and the University of Basel. Please see Appendix page 87 for a definition of plagiarism.

54 – Guidelines for Doctoral Studies at Swiss TPH

Thesis evaluation

Faculty of Science: https://philnat.unibas.ch/fileadmin/user_upload/philnat/Doctoral_studies_-_Guidelines_Version_03.2019.pdf Faculty of Medicine: https://medizin.unibas.ch/de/karriere/doctoral-degrees/phd-dr-sc-med/timeline/graduation/ Please make sure that the gradings are submitted IN TIME at the relevant faculty. Late submissions will not be accepted.

Grades are given on a scale of 1 (worst) to 6 (best); half grades are possible. A minimum score of 4 is needed to pass. In cases where the primary supervisor is not a Group I Faculty member (or entitled as such), both the First and Second supervisor must sign the evaluation sheet. A positive evaluation ends with the following sentence (Faculty of Science): Ich (wir) beantrage(n) der Philosophisch-Naturwissenschaftlichen Fakultät der Universität Basel, die von XY vorgelegte Dissertation als xxx Arbeit (Note xx) anzuerkennen und XY zum Doktorexamen zuzulassen.

Translation I / we request the Faculty of Science to accept the thesis presented by XY as [good / excellent, etc.], with a mark of [4 - 6] and to admit the student for the oral doctoral exam.

PhD defence

Following the completion of the thesis, an oral exam is held. The candidate and the supervisor, in consultation with the PhD committee, arrange the date, time and location of the defence. In case of PhD defences at the Medical Faculty, the commission likes to delegate the Chair for the defence, thus, inform Moira Lux (phd-med@unibas.ch) at the earliest possible time once you start planning the defence.

Details of the PhD degree completion process can be found on the homepage of the Faculty of Science or the Faculty of Medicine. Details of the defence must be communicated to the Dean’s Secretary at the Faculty of Science or Faculty of Medicine well in advance of the date to allow official invitations to be sent to the examiners and to prepare the necessary documentation.

Please also contact the student representatives (studreps@swisstph.ch) in advance to request a PDA (PhD defence assistant), who will be responsible for the technical aspects during online/hypbrid defences via Zoom with remote participants!

Additional to the faculties, candidates must immediately provide the details of the defence to: • the Head of ET (Julia Bohlius) & head of BMD Unit (Nino Künzli) • the ET PhD coordinator (Christine Mensch), • the Head of the Department of the PhD candidate (Nicole Probst, Sébastien Gagneux, Daniel Paris or Kaspar Wyss), • the Director (Jürg Utzinger) • all Supervisors of the candidate • the Chair of the defence • the departmental support team contacts (Dagmar Batra for EPH, mpi.order@swisstph.ch for MPI and Sabine Luetzelschwab for SCIH) – they will be in charge of preparing the flyers to be featured on the boards and at meetings Infomation to include Date, time and location of the defence, title of thesis, supervisor(s), faculty representative (only if old Promotionsordnung), external expert (co-referee if old Promotionsordnung), further examiners (if any), Guidelines for Doctoral Studies at Swiss TPH – 55

Chair of the defence, name of PhD defence assistant and the Zoom link.

It is the candidate’s responsibility to collect the required documents from the Dean’s Secretary one day before the defence takes place and (in case of Science Faculty) to hand them over to the Chair of the Examination Committee. In case of Medical Faculty the Dean’s office sends the material to the Chair directly.

The defence can be public or closed, depending on the student’s preference. A closed defence includes a 10-minute oral presentation of the PhD project, followed by a 50-minute question and answer period.

An open defence includes a 20-30-minute presentation, followed by a 40-50 minutes question-and-answer period. Questions are usually related to the thesis, but more general questions about the field of investigation are to be expected.

The Chair of the Examination Committee is responsible for the organisation and the correct procedures of the thesis defence. The Staff List indicates which faculty members of Swiss TPH can serve as an examination Chair.

At the defence, the following persons need to be present in person or via Zoom: The Chair, the First supervisor, the Second supervisor, and the external Expert listed on the PhD application form “Promotionsantrag” submitted to the Faculty of Science.

In addition to these four members, other scientists involved in the thesis work can be invited to the thesis defence, if they were involved with the candidate’s work as collaborators. The choice of such individuals is up to the Primary supervisor and the candidate.

Grading

The overall grade of the thesis is a weighted average, with 1/3 of the grade given for the oral exam and 2/3 for the written thesis. It is only at the last step of calculations where the final mark is rounded off to the nearest half mark. Marks range from 1 to 6, with 6 being the best and 4 being the minimum grade for a pass.

Latin epithets corresponding to these grades are used: 4.0 4.5 5.0 5.5 6.0

rite (pass) bene (good) cum laude (with praise) magna cum laude (with great praise) summa cum laude (with the highest praise

After the PhD defence

Following the defence, the examiners will inform the candidate of her/his grade and the candidate will be asked to take an oath of academic integrity. It is customary to celebrate the defence with an Apéro or reception immediately afterwards. Due to Covid-19, this might be not possible. Please check the updated guidelines on the Intranet about current rules. If they can take place, it is the responsibility of the fellow students in coordination with the Swiss TPH supervisor to organise these events. Swiss TPH support staff does not organise such events nor does the Swiss TPH Directorate or ET finance them.

The supervisor is responsible to inform the Student Administration about the mark so that the PhD tracking can be completed.

De-register from the University and de-register from the relevant community if you are leaving Switzerland to avoid future visa problems when entering the SCHENGEN area.

56 – Guidelines for Doctoral Studies at Swiss TPH

Post PhD actions 1. Make final corrections to the thesis and arrange for printing according to the „Submission Regulations for Final Copies of Doctoral Dissertations“ of the University of Basel (https://philnat. unibas.ch/fileadmin/user_upload/philnat/3_Forschung/Pflichtexemplare_neue_Ordnung_E.pdf).

Please note: Although University of Basel states that the submission of the final corrected PhD thesis may take up to 2 years after the defence, we highly recommend to finish this step within a few weeks. Please make this step prior to departure / move into the post-doc live. This step is required to use the title “PhD”, thus, do not delay the submissions.

It is mandatory: - to print three copies of the dissertation (“Pflichtexemplare”) on archivable paper for the Dean’s Office and - to send an electronic copy (PDF) of the dissertation to the Swiss TPH library (library@swisstph. ch) - to upload the dissertation to the institutional repository of the University of Basel (edoc) You can print additional copies (booklets, more colourful) to distribute to home institutions, colleagues and other interested parties. Contact the library (library@swisstph.ch) for detailed instructions and full support on printing your thesis.

The hard copies must be turned in within two years after the PhD defence, otherwise the PhD defence may be declared void. In special circumstances, students may ask for an extension in writing, providing reasons for the delay.

After submission of the printed (final) copies of the dissertations to the Dean’s Office, you have to upload an electronic copy accompanied by an abstract to the institutional repository edoc (https://edoc.unibas.ch/). For this purpose, you will get an access code to edoc by email. You have to upload the dissertation and abstract files to edoc.unibas.ch within 30 days after receiving the access code. Only after checking that your files have been uploaded in the appropriate manner the Dean’s Office will provide you the Diploma.

2. Handover the raw and clean datasets including the data documentation, analysis R scripts or STATA do-files of reproduce results and other relevant documents to your Supervisor. Note: All produced datasets, documentations, analyses protocols and queries belong to Swiss TPH. 3. Provide copies of the datasets for the Swiss TPH Data Repository. The data repository stores datasets collected by students and staff and allows them to be potentially re-used for further studies. Information about each study is stored in a searchable data-base. If the data is requested, permission is then sought from the Supervisor. Sufficient information for the search terms and a brief description of the study should be provided. Exceptions are allowed if ethics agreements or contracts prohibit the storage of databases (contact regina.ducret@swisstph.ch and amanda.ross@swisstph.ch).

4. Archive all physical material (completed questionnaires, signed consent forms, field-work material, project manual, etc.) according to the Swiss TPH archiving regulations (contact marco. waser@swisstph.ch).

5. Please send a copy of your final doctoral degree to Christine Mensch.

Transition into post-doc

Please discuss your transition from PhD into the next phase of your career early on with the supervisor (or feel free to approach Nino Künzli). The PhD rarely ends with the defence but may typically need a few more months to finish up. Occasionally, there are some extra funds available to finish up for 2-3 months Guidelines for Doctoral Studies at Swiss TPH – 57

some additional papers. However, you should define the “end of PhD period” and plan the next phase early on. If you attempt to pursue an academic path, the next phase will be your time as a post-doc (defined as up to six years after the PhD). As a general rule, it is highly recommended to do your post-doc elsewhere. Continuing the post-doc where one does the PhD may penalize your academic track towards assistant or “Förderprofessor” positions given that “mobility” is seen as an asset of an academic career.

Other opportunities Contribute to Young Researcher Editorials

A primary objective of the PhD is the publication of peer-reviewed research papers. A Swiss TPH PhD student initiated a discussion about the lack of opportunities for PhD students to debate and express their views about public health sciences more broadly. This resulted in a new educational initiative of the International Journal of Public Health (IJPH) of SSPH+: The Young Researchers Editorials (YRE). It was launched in September 2017 to strengthen the academic voice of students in the public health scienc¬es. YRE is an independent editorial board of SSPH+ PhD students. They acquire, review and publish Ed¬itorials written and submitted by PhD students from all over the world. As all IJPH Editorials, these are citable open access publications. Please note that YRE is not the place to publish parts of your thesis. Editorials may refer to public health topics or papers published in IJPH or in any other journal or the news. It may also address issues of being a PhD student in public health sciences. Find more information here: https://ssphplus.ch/en/teaching-training/yre/.

Pursuing a PhD in Africa

Students interested in PhD studies in Africa may consider the highly competitive and successful African CARTA PhD program. CARTA provides full-term fellowships to do a PhD at one of the CARTA Universities (only for those who have a contract as an employee at the respective university). CARTA also offers courses for its students, which are also open for PhD students from elsewhere. Swiss TPH chairs the Non-African Partners of the CARTA network (Nino Künzli) and contributes to some of its courses. For questions please contact barbara.buerkin@swisstph.ch

Part-time jobs during PhD studies

Some PhD students work part-time to make some extra income. As this may compete with the time¬ly advancement of the PhD, it is important to discuss this and agree with the supervisor. For foreign students, working permissions may be restricted, e.g. those foreign students with Cantonal or Federal fellowships are usually allowed to work up to 20% (15 hours per week) although exceptions may apply.

Some may find job opportunities within Swiss TPH. In those cases, salaries need to be clarified with the supervisor of the related job. Depending on the duration of the work and the tasks (job description), PhD students may be hired on an hourly basis with a flat hourly salary or on some fixed contract (e.g. as 20% research assistant).

Please note that the contribution of up to 20% of the PhD time to general needs of Swiss TPH does not count as “job” nor is it paid but considered a “volunteering” contribution to the institution. Working though as a “project assistant” on studies or projects (that are not led by your PhD supervisor) does not qualify as “volunteering institutional contribution” but as a paid part-time job. In case of uncertainties discuss it with your supervisor or the Head of ET.

58 – Guidelines for Doctoral Studies at Swiss TPH

Students’ Rights and Obligations Students at the University of Basel and the Swiss TPH have rights as well as obligations.

Students have the right to: • Be treated in a respectful and responsible way by the supervisor and all other staff members • Regular supervision • Adequate representation in the different bodies of Swiss TPH • Adequate working space – for PhD students this means lab and / or office space; for MSc-students, working space is available in the library • Adequate equipment and supplies for work • Computer access • Be introduced to the security guidelines (both for offices and labs) by his/her supervisor, in association with the Swiss TPH Security Officer

General information – 59

Students are obliged to: • Respect the rules and regulations of Swiss TPH and the University of Basel, and those of scientific and personal conduct at all times • Read all emails that are sent to their Swiss TPH and unibas account • Actively participate in Swiss TPH academic life, including attending weekly department seminars, presentations, and student meetings, especially the biannual student meetings (Mai & October) • Contribute to the Swiss TPH community by assisting new students or visitors, supporting fellow students, supervising exams, carrying out other Swiss TPH related tasks when requested (up to 20% of full-time studies) • Maintain adequate health and travel insurance during their time in Basel Before leaving the institute, students are obliged to: • Provide copies of laboratory notebooks and data sets (along with the documentation) and the programming codes they have used to their supervisor and the Swiss TPH data repository (see more information on intellectual property and data protection on page XX • International students must: –– inform the Migration Office in Basel or the relevant community about their departure date (to avoid taxation). Bring a copy of this information to ET –– clear their Swiss bank account(s) and terminate mobile phone contracts after their studies and before leaving Switzerland

Resolution of conflicts

In case of problems or conflicts between the student and staff of Swiss TPH (his/her supervisor, other staff, fellow students) or in case of serious personal problems, students are advised to consult the following people (in this order): 1. Supervisor 2. Head of Department 3. Head of Bachelor-Master-Doctorate unit (Nino Künzli) 4. Director of Swiss TPH 5. Dean of the Faculty of Science or Faculty of Medicine Additionally, student representation at the institute (Master and PhD Student Representatives) and university level can offer support in case of problems or conflicts: • Skuba: “Studentische Körperschaft der Universität Basel” as the official body representing the interests of Bachelor and Master students.

• Avuba: “Assistierendenvereinigung der Universität Basel”, the assistants association of the University of Basel representing the interests of doctoral and postdoctoral researchers.

In case of conflict there are also two persons of trust available at the Institute: Barbara Bürkin and Dr. Nicolas Brancucci. You can find their contact details on the Intranet.

In a case of serious student misconduct, the same people should be consulted. For the most serious cases, the University discipline commission (Disziplinarkommission) will be consulted.

60 – General information

Sexual harassment Sexual harassment is illegal according to Article 4 of the Swiss Equality Law (GIG) of 24 March 1995.

That law prohibits any harassing behaviour of a sexual nature or other behaviours of sexual orientation which compromises the dignity of men and women in the workplace. Sexual harassment consists of any action with a sexual reference which is undesired by one party, and may range from offensive and distressing observations, sexist remarks, demonstration or display of pornographic material, undesired bodily contact and sexual advances.

Sexual harassment is not tolerated within the Swiss TPH and individuals found guilty of harassment shall face sanctions, including exclusion from the Swiss TPH and the University of Basel, and in serious cases legal measures will be taken. The complainant shall not suffer any disadvantages as a result of making such a case known.

The Institute expects all employees and students to respect the personal limits claimed by their colleagues for interpersonal contact. Students who feel sexually harassed are encouraged to inform one of the persons of trust mentioned above.

Swiss TPH students are expected to attend: • Team / student meetings: All units and departments organise regular meetings. Master and PhD students are required to take part in the meetings of their particular unit and department.

• EPH meetings: Take place on Mondays at 10:00. This meeting is an opportunity to discuss administrative matters, give departmental updates, introduce new staff members and ensure that everyone knows what is happening in the department and at Swiss TPH. • MPI meetings: Taking place on Wednesdays, these meetings are intended to ensure that departmental staff and students are kept informed of current issues of the department, Swiss TPH and in the field of MPI. • Academic student meetings: Take place on Mondays from 11:00-12:00 for EPH. This meeting is organised by one or two students who take turns arranging a program according to proposed topics and chair the meetings. It is intended to provide a forum for students to present their work (either finished or in progress) to their peers, gain presentation experience, discuss specific topics of interest, invite guest speakers, etc. One or more academic staff members attend each session, but the students run the meetings. It is compulsory for all students to present at least once in this meeting during their studies (MSc or PhD).

Academic student meetings are held separately for EPH and MPI. • MPI and EPH research seminars: This departmental seminar series takes place every Thursday.

Sessions are dedicated to either a MPI- or EPH-relevant research topic. The research seminars serve as a platform for students and staff to share and discuss the results of their on-going research projects. Local, national or international senior scientists are also invited to present their work. These seminars are mandatory for EPH and MPI PhD students.

General information – 61

Student Representative’s Roles and Responsibilities Each research department should have a student representative (PhD and Master) that is either: chosen by their peers, chosen by the Swiss TPH departments or a volunteer.

Student Representatives (Student Reps) are a critical component of effective communication between students, the department of Education and Training (ET) as the leading department of student affairs, the Institute administration, their departments, and the directorate. The main focus for Sudent Reps is academic representation. They represent the interests of the student body. In this function they are the primary contact for the students and for institutional bodies with respect to students’ concerns.

The Student Representative Committee (SRC) at Swiss TPH comprises 8-9 students: 5 PhD Student Representatives (across the departments) and 3-4 Master Student Representatives (ideally, 2 of each program). The SRC acts in close collaboration with the Head of ET. The SRC is involved in the National Union of Students (NUS), the top representative body of all tertiary students in Switzerland that works to protect the rights of all students. This is achieved via connection with avuba “Assistierendenvereinigung der Universität Basel”, the assistants association of the University of Basel. Information on NUS activities can be accessed via http://vss-unes.ch.

Selection process of Student Reps For a new academic year all enrolled students are invited to volunteer as Student Rep candidates. Nominations will be called for by the acting Student Reps. It should be avoided that all Student Reps are changing at the same time to ensure continuance. For the PhD level, the term lasts for 1 year and 2-3 Student Reps should be replaced during the summer, and during the winter, academic break.

Criteria for Student Reps • • • • •

Good communication and interpersonal skills Organisational and planning skills Reasoning and problem-solving skills Ability to negotiate, make constructive suggestions and find appropriate solutions Commitment to: –– participate in meetings scheduled over 12 months –– work with other students, administrators and project leaders to implement initiatives and solutions –– create connections between students as well as students and working professionals by planning social and professional events –– devote about 20 hours a month to the SR role

Why become a Student Rep? The role enables Student Reps to develop and/or strengthen leadership skills, and connect with various units and departments and their leaders. The responsibility of assisting student peers in having their voice heard, knowing about and contributing to strategic decisions is of mutual benefit for both, students and Student Reps.

Master Student Reps: The 3-4 Master Student Reps represent all the students in the Infection Biology Master course and the Epidemiology Master Course. At least one representative is elected from each.

62 – General information

Responsibilities of Master Student Reps: 1. Be the central contact point for students, PhD representatives and Institute faculty / directorate / administration and ensure optimal flow of information 2. Promote student communication and team spirit in the master's class, e.g., by organizing social events 3. Welcome the next master student class; introduce them into the course and Institute 4. Promote scientific and social exchange with master students from other institutions and other master courses, e.g., African studies, Biozentrum, by liaising with their respective representatives (information about lecture series, etc.)

The Master Student Reps will work independently but in close collaboration with the PhD student representatives. They will be introduced into their role and responsibilities by the previous year's Master Student Reps.

PhD Student Reps: 5 PhD Student Reps will represent all PhD students from Swiss TPH, at least one from EPH and MPI. Ask fellow students or your supervisor for the name of your current PhD Student Rep. PhD Student Reps are responsible for organising student meetings, the coordination of the “volunteer” work (VOLO tasks), assigning PhD defense assistants, and the management of the office workspaces of PhD students in their department. PhD Student Reps should be contacted by Supervisors before arrival of new students so that work spaces can be planned and allocated. Please also let your PhD Student Reps know when you leave the Institute for an extended period of time, e.g., for fieldwork, so that work spaces can be adequately used. Do not hesitate to contact the PhD Student Reps to discuss any questions, concerns or suggestions.

Responsibilities of PhD Student Reps 1. Establish yourself as a central point for information and guidance: The Student Reps are the contacts for all students on administrative and study related issues. This might include problems related to campus life, their supervisors, other students, colleagues in their offices, etc. The role of the PhD Student Rep is to suggest, develop and implement solutions to these problems, acting as a moderator if the situation requires. This does not include being involved with the students’ personal problems, academic difficulties and individual student allegations of unfair or inappropriate treatment. If a student comes to you with such a problem, recognise that they have identified you as a source of information and encourage / support them to talk to their direct unit superior or to come to the Students’ Union Advice Centre. The Advice Centre staff can provide support and guidance on academic, international and personal issues.

Confidentiality is imperative when dealing with student issues. If the Student Rep would like to discuss a student’s situation with a third person, they must first obtain consent from the student beforehand.

2. Provide feedback to the student community from high-level meetings: Briefings from meetings (e.g., annual retreat at the Swiss TPH) should not only be done with a written summary sent by e-mail, but the Student Reps must create an atmosphere for students to ask questions and comment freely. It is recommended to schedule a meeting, in addition to sending a written summary of the meeting minutes by e-mail to all the PhD students. It is important to remember that the role of Student Rep does not end with attending high-level meetings but must be combined with strong feedback to the student community, both in Basel and in the field.

General information – 63

3. Organize work space for PhD candidates: An essential task of the Student Reps is to organise work spaces for the PhD students. This is a very challenging task, especially in autumn when many external students are in Basel for course work. Seating places for PhD students are located in Eulerstrasse 54 and Socinstrasse 55 / 59. It is very important to keep regular contact with the room management coordinators to organize the work spaces for all PhD students and to maintain up-to-date information every semester.

–– EPH, SCIH, MED, ET Student Reps coordinate Eulerstrasse 54 –– Nora Bauer coordinates the space of EPH staff (not PhD students), including the 3rd floor in Socinstrasse 57 which occasionally may offer space to PhD students.

4. Welcoming new PhD candidates: The Student Rep should welcome and properly organize the working spaces for all new PhD students at the Swiss TPH, once they have received the welcoming package and instructions from Christine Mensch.

Christine Mensch, ET Department, informs the Student Reps of the new arrivals, in addition to the respective supervisors and Department secretariats. Then the Student Rep will show the new students their offices and inform students about rules and other logistics like printers, kitchen usage, internet and student volunteer work. Please make sure that new students receive a copy of the Student Handbook which is available on the intranet (Alfresco) and the Swiss TPH website (e.g. Study with Us -> Doctorate and PhD Programmes). The introduction of new students to all relevant people at Swiss TPH is usually done by the student’s direct supervisor or their group colleagues and is not the responsibility of the Student Rep. However, this responsibility can be delegated to the Student Rep in particular situations (e.g., supervisor not present). All new staff (including PhD candidates) are also invited by HR to Welcome Days, usually offered 2-3 times per year.

5. Relay key messages from the administration to the student body: Find volunteers! Various project leaders and colleagues might be looking for volunteers for specific tasks. Those requests, mainly via e-mail, include: –– Supervise exams (presence) –– Correct exams and evaluation forms –– Assist with cocktail hours or coffee breaks –– Assist with the organisation of conferences or workshops –– Technical support (data cleaning and analysis, teaching, Master student's support, etc.)

–– Assist the administration team 6. Facilitate events to bring students together! Within a big institution such as Swiss TPH it is challenging to know everyone. Bringing together all students of the Institute during free time, evening events or excursions should be organized to overcome this challenge. Usually, PhD students take the initiative themselves to plan such events. The role of the Student Rep is to encourage and support the organization of these activities. Student Reps may ask for financial support from the Head of ET department if needed. Examples for those activities are: –– Winter event (e.g. skiing, sledging) –– Summer event (e.g. hiking) –– Student "end of the year” party (Christmas), and beginning autumn semester party 7. Liaising with other Student Reps and institutional leaders for support and ideas: It is fundamental to keep in regular contact with the SRC to exchange information and collaborate on creating solutions for arising issues. The Student Reps organize at least two meetings per year with the Head of ET (see below). If necessary, short sessions with other institutional leaders (Director and department heads) may be initiated to provide a channel for dialogue and discussion among students and direct leaders.

64 – General information

8. Represent fellow students at the following meetings: Student Rep Meeting with Head of ET Purpose: Discuss state of work, needs, strategies or upcoming events to get feedback and support and decide on next steps.

Student Reps Role: Communicate all major issues / concerns / needs with department head, who will bring issues to Directorate Board if needed. Take notes of the issues raised and write the decision minutes in a timely fashion to report back to students.

In attendance: Student Rep, Head of ET; others if agreed upon in advance.

When: Student Rep initiate scheduling at least twice a year (usually prior to a new semesters).

Meetings with Research Commission (RC) Purpose: Discuss reviews of student's PhD proposals and strategic issues related to academic requirements of the programs.

Student Reps Role: Solicit and read agenda items (summary of proposals to be submitted and their reviews). Speak on behalf of the students to explain their issues / concerns and / or suggest ideas for improvement.

In Attendance: Student Rep and RC members.

When: 3–4 times per year Meetings with the department project leaders (exclusive for EPH) Purpose: Discuss strategic, high-level issues with the departmental project leaders.

Student Reps role: Solicit and submit agenda items. Speak on behalf of the students to explain their issues / concerns and / or suggest ideas for improvement.

In attendance: Student Rep and project leaders When: Every first Monday of a month Meeting with senior management (Swiss TPH retreat) Purpose: Discuss strategic, high-level issues with the Institute Senior managers.

Student Reps role: Solicit and participate in agenda activities. The content of the retreat is drafted in advance during pre-meetings. Speak on behalf of the students to explain their issues / concerns and / or suggest ideas for improvement.

In attendance: Student Rep and senior managers When: Schedule developed annually. Usually takes place in the Spring, over two-days, and upon invitation from the Director.

ET Meetings Purpose: Discuss strategic issues related to PhD studies with ET team.

Student Reps role: Solicit and submit agenda items. Speak on behalf of the students to explain their issues / concerns and / or suggest ideas for improvement.

In attendance: Student Rep and ET team members When: Schedule developed annually, usually takes place every month.

General information – 65

Overview of Courses Offered by Swiss TPH www.vorlesungsverzeichnis.unibas.ch/en/home Registering for Courses All Master and PhD students of the University of Basel must register for every semester at the university (even if they are not spending the semester in Switzerland) and register for all courses online via www. unibas.ch/en/Studies/My-Studies/Course-Registration.html within the first four weeks (please see the relevant deadlines).

Courses University of Basel courses that are offered under the lead of Swiss TPH are open to all students registered at the University of Basel. Each course can be found by entering the course title or name of the lecturer under the following link: www.vorlesungsverzeichnis.unibas.ch/en/home. Course descriptions include information about the location, dates and times, content and number of ECTS credit points associated with the course.

Additional information for individual courses (e.g. handouts, zoom-links for online sessions etc) are available on the respective ADAM-workspaces (you will automatically receive access as soon as you register for a course).

All lectures are held in English. The lecture location may change on short notice. If so, the lecturer will notify you.

On the following pages, there is an overview of all the lectures, as well as the relevant timetables.

Students may register to other courses offered by University of Basel. Please clarify your plans with the supervisor.

66 – General information

Specialised Master in Infection Biology Addendum Master in Infection Biology Specialised Master in Infection Biology

Mandatory

Lecture

2021/2022 Semester

CP

Responsible

Biostatistics (lecture)

AS

2

M. Kwiatkowski

Concepts in Molecular Epidemiology

AS1

2

S. Gagneux

Drug Discovery and Development for Parasitic Diseases

AS1

2

J. Keiser

Evolution of host-parasite interactions

AS1

2

D. Ebert

Immunology of Infection

AS1

2

C. Daubenberger / D. Portevin

Interdisciplinary Research in Epidemiology and Infection Biology

AS2

1

J. Utzinger / J. Keiser

Introduction to Bioinformatics

AS1

2

P. Mäser / D. Brites

Molecular Infection Biology

AS1

2

T. Voss / N. Brancucci et al

Topics in Host-Pathogen Interactions

SS

2

T. Voss / S. Gagneux

Transferable skills

AS1

1

T. Voss / P. Mäser

TOTAL Advanced Immunology of Infection

SS

2

C. Daubenberger

Exercise: Immunology of Infection

AS1

2

C. Daubenberger

Advanced one health methods

SS

2

J. Zinsstag / N. Chitnis

AS/SS

1

J. Utzinger

Epidemiological concepts

AS

3

Ch. Lengeler

Epidemiological methods

AS

4

D. Mäusezahl

Essentials in drug development and clinical trials

SS

2

Ch. Burri

Key issues in public and international health

AS

2

P. Steinmann

Malaria epidemiology and control

SS

2

N. Chitnis / M. Penny

Mathematical modelling of infectious diseases

SS

2

M. Penny / N. Chitnis

Medical parasitology and neglected tropical diseases (lecture)

AS

2

P. Odermatt

Medical entomology

SS

2

P. Müller

Qualitative and mixed methods

AS

2

S. Merten

Techniques in Molecular Parasitology; Lab Training for MSc Students

AS1

4

T. Voss

Biostatistics (exercise)

AS1

1

M. Kwiatkowski

Advances in infection biology, epidemiology and global public health

Optional

18

TOTAL

33

All lectures offered by Swiss TPH (also lectures from Master in Epidemiology) and Additional lectures from other fields within the University of Basel in agreement with the supervisor and approval by Till Voss Credit points from other Universities must be approved by the faculty teaching commission prior to course Options registration and will only be granted if at least 3 CP. AS: autumn semester / SS: spring semester / CP: credit points

12.08.2021

General information – 67

Timetable Master in Infection Biology

Master in Infection Biology - Autumn Semester 2021 08:1509:00

09:1510:00

11:1512:00

12384 Molecular infection biology (online)

Monday Tuesday Wednesday

10:1511:00

EPH meeting

11911 Introduction to One Health (Lhotse/hybrid)

Student meeting

12:1513:00

13:1514:00

14:1515:00

15:1516:00

16:1517:00

17:1518:00

18:1519:00

19:1520:00

62484 Fundamentals of 28892 Key issues in Advances public and international in Infection Public Health 62177 health (weeks 2-8) Biology, Qualitative (online) (Borromäum, tbc) Epidemiolo Research gy and Journal 51775 Transferable Global Club skills 28872 Concepts in Public (Lhotse) (8 dates, see course molecular epidemiology Health directory) (Lhotse) (online) (Lhotse)

11650 Immunology of infection (Biozentrum Neubau, Seminarraum U1.197)

28893 Biostatistics week 1 - 7 (Pathologie, Unterer Hörsaal)

48608 Public health across the life course (Lhotse or online)

58921 Basic statistical modelling week 8 - 14 (Universitätsstpital, Klinikum 1, Hörsaal 1)

English for global and public health (17h30 - 19:00) (Lhotse or online) (registration via Sprachenzentrum Unibas)

34889 Medical parasitology and Neglected Tropical Diseases (Kilimanjaro)

11655 Epidemiological concepts (Pathologie, Unterer Hörsaal)

MPI Research Seminar / Swiss TPH Seminar (Lhotse)

28885 Environmental epidemiology week 8 - 14 (Matterhorn / hybrid)

62165 Health interventions (online)

28887 Statistical modelling (Lhotse) 11652 Drug discovery and development for parasitic diseases (Borromäum, tbc)

Friday

Thursday

11654 Epidemiological methods (Borromäum, tbc)

28394 Evolution of HostParasite Interactions (online tbc)

11647 55047 Biostatistics Interdisc. 58921 Basic statistical (practicals) modelling Research week 1 - 7 week 8-14 in Epi and (Biozentrum Neubau, (Universitätsspital, IB Seminarraum U1.191 & (Borromäu Klinikum 1, Hörsaal 1) Hörsaal U1.141) m, tbc) 28871 Chronic disease and molecular epidemiology week 1 - 7 (Matterhorn / hybrid)

44722 Qualitative and mixed methods weeks 1 - 7 (online) 18423 Health systems weeks 8 - 14 (Lhotse & online - mixed format)

28880 Introduction to Bioinformatics (online) 11718 Current ecological and health issues in Africa (Lhotse) 30.08.2021

Techniques in Molecular Parasitology: January 2022

= mandatory courses

62484 Fundamentals of Public Health: 25.10.: online 11654 Epidemiological methods: 23.9. & 2.12.: Lhotse/hybrid 11647 Interdisc. Research in Epi and IB: 2.12.: online 11652 Drug discovery and development for parasitic diseases: 2.12.: online 18423 Health Systems: 12.11., 3. & 10.12: 09:15-13:00 ! Please check the course directory or ADAM for updates on rooms !

68 – General information

Specialised Master in Epidemiology Addendum Epidemiology SpecialisedMaster Master ininEpidemiology Module a)

MANDATORY COURSES

Module b)

Module c)

Module d)

OPTIONAL COURSES

Module e)

Additional Options

Lecture Foundations in epidemiology Epidemiological concepts Epidemiological methods Chronic diseases epidemiology Environmental epidemiology Qualitative and mixed methods Producing, interpreting and using evidence in health care GIS in health and exposure sciences Biostatistics and computing Biostatistics (lecture) Biostatistics (exercise) Basic statistical modelling (OR Statistical modelling) Statistical modelling (OR Basic statistical modelling) Data analysis in epidemiology Demography for Health Statistical methods in trial design Research Data Management Global public health Public health across the life course Adv. in infection biology, epidemiology and global public health Key issues in public and international health Interdisciplinary research in epidemiology and infection biology Health systems Health financing and economic evaluation Fundamentals of Public Health

2021/2022 Semester

CP

Responsible

AS1 AS1 AS1 AS1 AS1 SS1 SS1

3 4 1 1 2 2 2

Ch. Lengeler D. Mäusezahl N. Probst Hensch M. Röösli S. Merten X. Bosch Capblanch D. Vienneau / K. de Hoogh

AS1 AS1 AS1 AS1 SS1 SS1 SS1 SS1

2 1

M. Kwiatkowski M. Kwiatkowski F. Vanobberghen / A. Farnham P. Vounatsou A. Ross G. Fink T. Glass M. Hetzel

AS1 AS/SS AS1 AS AS1 SS1 AS1

2 1 2 1 2 1 1 40

3 3 2 2 2

J. Dratva J. Utzinger P. Steinmann J. Utzinger K. Wyss P. Hanlon J. Bohlius

SUBTOTAL Transferable skills and competences (5 CP to choose, incl. the two compulsory courses) Good scientific conduct in health sciences SS1 1 Ch. Lengeler Application to an ethics committee SS1 1 Ch. Burri Scientific writing SS1 2 R. Paola Project management SS 2 A. Hoffmann Effective presentation skils SS 1 M. Winkler Meet the Epidemiology professionals SS 1 K. Boutsika SUBTOTAL 8 Advances in epidemiology, statistics and public health: students must choose 15 CP Mathematical modelling of infectious diseases SS 2 M. Penny / N. Chitnis Introduction to One Health AS 3 J. Zinsstag Advanced one health methods SS 2 J. Zinsstag / N. Chitnis Current ecological and health issues in Africa AS 2 J. Utzinger Essentials in drug development and clinical trials SS 2 Ch. Burri Drug discovery and development for parasitic diseases AS 2 J. Keiser Malaria epidemiology and control SS 2 N. Chitnis / M. Penny Medical parasitology and neglected tropical diseases AS 3 P. Odermatt Bayesian biostatistics and exercises SS 5 P. Vounatsou Biostatistics (Journal Club) AS/SS 1 P. Vounatsou Programming in STATA SS 1 J. Hattendorf Medical entomology SS 2 P. Müller Health impact assessment SS 3 ETH ZH (M. Winkler) Climate change and health SS 1 G. Cissé Introduction to R for epidemiological data analysis SS 1 J. Hattendorf Current topics in epidemiology * AS/SS 2 S. Knopp Health interventions (Journal Club) AS 1 M. Hetzel Introduction to bioinformatics AS2 2 P. Mäser Qualititive Research (Journal Club) AS/SS 1 S. Merten Co-Producing Knowledge in Transdisciplinary Research Projects AS 3 Hofmänner Hands on causal inference with R AS 1 G. Moffa / T. Glass SUBTOTAL 42 All lectures offered by Swiss TPH (also lectures from Master in Infection Biology) AND lectures from other fields within the University of Basel in agreement with the supervisor/Swiss TPH

12.08.2021

AS: autumn semester / SS: spring semester / CP: credit points

Non-mandatory surplus CP from modules c) Global & Public Health and d) Transferable Skills and Competences may count towards module e) Advances in Epidemiology, Statistics and Global & Public Health .

But be aware that credit points from one lecture cannot be split between two modules.

In module b) Biostatistics and computing only 'Basic statistic modelling' OR 'Statistical Modelling' is mandatory, not both.

In module e) Advances in Epidemiology, Statistics and Global & Public Health credit points from other study programmes of the University Basel may be used in agreement with Swiss TPH supervisor and approval by Christian Lengeler.

Credit points from other Universities must be approved by the faculty teaching commission prior to course registration and will only be granted if at least 3 CP.

General information – 69

* not available for MSc IB und Epi in the same semester as 'Advances in infection biology, epidemiology and global public health'

Timetable Master in Epidemiology Biology

Master in Epidemiology - Autumn Semester 2021 08:1509:00

09:1510:00

11:1512:00

12:1513:00

11650 Immunology of infection (Biozentrum Neubau, Seminarraum U1.197) 11911 Introduction to One Health (Lhotse, hybrid)

48608 Public health across the life course (Lhotse or online) 62166 Biostatistics journal club (Alpamayo)

Wednesday

13:1514:00

14:1515:00

15:1516:00

16:1517:00

17:1518:00

18:1519:00

19:1520:00

12384 Molecular 28892 Key issues in 62167 infection biology public and international 62177 Advances in (Biozentrum Neubau, health Qualitative 62484 Fundamentals of infection (online) Seminarraum U1.193) Research Public Health biology, Journal (weeks 2-8) epidemiology 28872 Concepts in Club (Borromäum, tbc) and global EPH Student molecular epidemiology public health (Lhotse) meeting meeting (Lhotse) (online)

Monday Tuesday

10:1511:00

11655 Epidemiological concepts (Pathologie, Unterer Hörsaal)

MPI Research Seminar / Swiss TPH Seminar (Lhotse)

28893 Biostatistics week 1 - 7 (Pathologie, Unterer Hörsaal)

English for global and public health (17h30 - 19:00) (Lhotse) (registration via Sprachenzentrum Unibas)

58921 Basic statistical modelling * week 8 - 14 (Universitätsspital, Klinikum 1, Hörsaal 1)

34889 Medical parasitology and Neglected Tropical Diseases (Kilimanjaro) 62165 Health interventions (online)

28885 Environmental epidemiology week 8 - 14 (Matterhorn / hybrid) 28887 Statistical modelling * (Lhotse)

Friday

Thursday

11652 Drug discovery and development for parasitic diseases (Borromäum, tbc)

11654 Epidemiological methods (Borromäum, tbc)

44722 Qualitative and mixed methods weeks 1 - 7 (online) 18423 Health systems weeks 8 - 14 (Lhotse/hybrid & online - mixed format)

11647 Interdisc. 58921 Basic statistical modelling * Research week 8-14 in Epi and (Universitätsspital, IB (Borromäu Klinikum 1, Hörsaal 1) m, tbc) 28871 Chronic disease and molecular epidemiology week 1 - 7 (Matterhorn / hybrid) 11718 Current ecological and health issues in Africa (Lhotse)

55047 Biostatistics (practicals) week 1 - 7 (Biozentrum Neubau, Seminarraum U1.191 & Hörsaal U1.141)

28880 Introduction to Bioinformatics (online) 30.08.2021

= mandatory courses * mandatory: either Basic statistical modelling (58921) OR Statistical modelling (28887) 11647 Interdisc. Research in Epi and IB: 2.12.: online 11652 Drug discovery and development for parasitic diseases: 2.12.: online 11654 Epidemiological methods: 23.9. & 2.12.: Lhotse/hybrid 18423 Health Systems: 12.11., 3. & 10.12: 09:15-13:00 62166 Biostatistics journal club: 21. & 28.9.: Olympus 62484 Fundamentals of Public Health: 25.10.: online ! Please check the course directory or ADAM for updates on rooms !

70 – General information

Appendices

Writing a MSc thesis proposal The thesis proposal helps you to – Focus your ideas – Make clear what it is you aim to achieve – Create a document to share with potential collaborators and – Provide documentation for ethical and scientific clearance if required.

The thesis proposal should be 10-15 pages long and should include: 1.

Title: A short statement of the research topic, including geographic location of work e.g.

Incidence of intestinal parasites in school children in Timbuktu.

2.

Author: Your name.

3.

Address: Your address, phone numbers and e-mail address.

4.

Supervision: Name of your Supervisor and co-Supervisor (if any) along with their e-mail addresses.

5.

Specialisation: Master in epidemiology or infection biology.

6.

Summary: Not more than 200 words containing background, aim, approach and expected outcome of the research.

7.

Introduction: Summary of what is known about the subject (1-2 pages). Do not waste space with extended descriptions; try to be to the point. Provide the reason(s) and rationale for the thesis.

8.

Aim and objectives: State the aim of your thesis, e.g. identify highly variable micro- satellites of M.ulcerans. Objectives are steps or smaller goals on the way to achieving your aim. In this section you can also formulate your hypotheses, e.g. Adults have a higher burden of Schistosoma than school children, or research question, e.g. what are the dynamics of acquired immunity against nematodes in cattle?

9.

Approach: Describe your proposed research activities (2-3 pages) and give a detailed description of your methods. If you intend to do a field study, start with a short description of the study population, study type (cross-sectional, case-control), sample size considerations, data collection, questionnaire design and validation, interventions, data analysis. If you intend to do a laboratory study, describe the source of the samples, the sample material you will use (worm eggs, DNA, serum samples, etc.), the methods of analysis, experiments, and evaluation of results.

10.

Expected outcomes: Imagine the results you expect from your work and try to describe them, e.g. knowledge on the prevalence of P. falciparum in women.

11.

Ethical statement: Identify and discuss with your Supervisor ethical concerns that may arise during your research and describe them (half page). For example, every child excreting worm eggs will receive mebendazole treatment. If you intend to work on human subjects, you require an ethics clearance. Discuss this with your Supervisor ahead of fieldwork. If ethical clearance is deemed necessary please see also section 3A "Ethical Clearance" before starting the writing process.

Appendix - 71

Page 2

12.

Institutional setup and collaborations: Describe briefly (half page) the department and research unit in which you will do your work. If your research will be done abroad, describe the partner institutions, department and working group. Describe possible collaboration with other students and demarcate the objectives of each project. Show how you will complement each other’s work.

13.

Time frame: Make a timeline for research progress, as shown below, giving a few details about each step.

Month 1

2

3

4

5

6

7

8

9

10

11

12

Study protocol Planning of field work Field data collection Data entry Data analysis Interpretation and write up of manuscript Handing in Thesis 14.

Budget: Estimate the cost of your project, accounting for personnel, international and local travel, equipment, consumables, communication and administrative costs. Discuss with your Supervisor.

15.

When preparing your documents, please consider “good documentary practice” for the proposal and all ancillary documents. The following details should appear on each side in the header: -

16.

Short running title Version-number and date of proposal (e.g. Proposal v1.1/15.04.2014) - (use 0.x for drafts; submit v1.0 to the first ethics committee)

The following details should appear on each side in the footer: Clear page numbering e.g. X of Y or X/Y For study-related documents which have their own version-no and date, the version-no and date of the proposal have to be added; e.g. for the “Patient Information and Consent” – document: PIC, v1.1/14.04.2014 referring to proposal v1.2/30.03.2014

17.

Add a signature page at the beginning of your proposal (Principal investigator and/or supervisor, student, statistician, if applicable other key persons to the project. Only collect the signatures on the final document version.

72 - Appendix

MSc Thesis Structure Student research activities should result in a final, comprehensive, consistent and clear thesis report.

You should write your thesis as if it were a scientific article for publication, but with rather more detail in the introduction and methods sections. The thesis should be understandable for a non-specialist.

The thesis is not restricted by any fixed length requirements, but as a general rule, the thesis should consist of 40 - 80 pages, excluding annexes. A good thesis is not necessarily a long thesis!

A good thesis: – Should be clearly written and presented.

– Should be concise.

– Should be consistent in style and logic.

Thesis structure Title Table of contents: The table of contents gives an overview of the thesis’ chapter structure and its page numbers. It should also include the summary and any annexes.

List of tables and figures: The outline is followed by a list of the tables and figures appearing in the text, including their (short) titles and respective page numbers.

Summary: Provide a short (one page), complete summary of all chapters, including comments and/or recommendations.

Acknowledgment: Additional help must be mentioned, such as field workers’ activities or active support and practical help from technicians and colleagues. Similarly, any official financial support given to you or the project must be mentioned here. You could also acknowledge others who supported you or your thesis in other ways.

Introduction and Rationale: The introduction includes relevant background information or a brief overview of the field, including a review of the literature and the theoretical concepts you plan to use.

This is the basis from which you formulate the problem statement and your hypothesis leading to a statement of your research questions and objectives.

You can also give a characterisation of the type of work carried out and a short outline of the chapters that follow. During your research, you may have come up with additional questions. These should also be mentioned here, but it should be clear that these questions were not originally planned.

Goals and Objectives: This part states the overall goal of the project. It also contains a number of specific objectives, usually 2-4, which can later form chapters of the thesis or be converted into manuscripts for publication.

Material and Methods: This part reports on the information sources used, the methods applied, and the materials used for lab work or data collection, and for data analysis. You should present what was actually done, and reference any problems encountered. In the case of fieldwork, you should describe the area and sites at which the research was carried out. For experimental work, you should give all

Appendix - 73

Page 2

relevant details of the procedures followed. If relevant, the process for ethical clearance should also be mentioned.

Results: Results should be presented in the most comprehensive and yet succinct manner. Mixing results with interpretation and discussion should be avoided, unless the work is very descriptive. Where appropriate, the findings should be illustrated or summarised with tables and figures. Tables and figures must be drawn in such a way that they can be read on their own, independently of the main text. Avoid showing the same data in figures and tables. Do not forget to include measurement units and explanations of abbreviations. References to tables and figures should be made in the text (e.g., see table 1; as shown in figure 2).

Discussion: The discussion section should always start with a discussion of the methodology or approach chosen, and its limitations. Next, link your own findings, as presented in the results section, with those of other researchers. What do your results mean and imply? The challenge here is to argue for and against the findings and the related theoretical concepts. Literature references are therefore required and you must discuss your findings in the context of both the scientific objectives and the research questions laid out in the introduction. An internal and external validation of your results is also required. The discussion should not simply be a summary of the results!

Conclusions: This section brings together the most important consequences of your research, normally referring to: 1. The scientific objective and the research questions (results); 2. Suggestions for future research on this topic 3. Practical implications of the findings References: It is very important that you give proper references when making statements from the literature. References acknowledge the work of others, and provide the reader with information on the sources that you used. You can use either the system of giving the author’s surname, and year of publication, with an alphabetical list of references at the end of the thesis, or you can number your references in the text and include a numbered list of references at the end. We recommend that you use a reference management software.

Annex or Appendix: An annex or appendix should be added to incorporate any information, which is too long or detailed to be included in the main body text, but is relevant for understanding the research or important steps taken. This could mean for example: providing original data, detailed statistical analysis, etc.

Font: Font should be Helvetica, Times New Roman, or comparable (Universal, Arial). Font size is normally 11. Do not use very small fonts. Line spacing should be at least 1.5 to allow for hand written corrections by the supervisor.

Figures and tables: Figures and tables complement and clarify text. All tables and figures should be referred to in the text. Figures and tables should be clear, avoiding unnecessary lines and frames.

Avoid vertical lines in tables. Similarly, coloured or grey backgrounds for figures should be removed if these do not add to comprehension. Each figure and table should have a legend that allows the table or figure to be understood without reading the text.

74 - Appendix

Swiss TPH Academic Teaching Staff List Possible roles and responsibilities of Swiss TPH academic staff in PhD student supervisions and committees For supervisions of Master theses (at least) one supervisor has to be a member of the Science Faculty (Group I or II) at the University of Basel.

Table 2A: Swiss TPH academic staff, Academic status **), faculty group and faculty affiliation of all Swiss TPH University of Basel academics and related roles and responsibilities in PhD thesis committees.

Staff not listed below need a special request from the Group I PhD (co-)supervisor made to the respective faculty to ask for permission to act as (First or Second) supervisor (Prof. emeriti – not listed below cannot take up new PhD supervisions but might still be on the committee of previously enrolled PhD students up to three years after retirement).

IMPORTANT EXCEPTIONS: Several Swiss TPH scientists who are not Group I members and / or not in the Science Faculty or the Medical Faculty, respectively, have received the permission to act in Swiss TPH PhD student committees in the role of a “Group I” First or Second supervisor in both faculties. Table 2A below provides all the details (according to the decision of the Faculty of Science Dean’s office, June 2016 and the Faculty of Medicine decision, June 2018).

Name Swiss TPH

Academic

Faculty

Uni

Scientist

status

Group

Basel

(professor

2)

Faculty

level)

3)

1)

PhD Faculty of Science

PhD Faculty of

MD (Dr.med.) 1-yr Thesis, Med

Medicine

Faculty

First or Second

Chair

First or

Chair

Dissertatio

supervisor

thesis

Second

thesis de-

nsleitung

Dissertationsbetreuung

(1st and 2nd

defence

supervisor

fence 4)

(lead)

(supervisor)

supervisor must not be in the same research group) Blum Johannes Bohlius Julia Bosch-Capblanch Xavier

Titulary

II

Med

Yes if 7)

No

Yes if 6)

No

Yes

Yes

Associate

n/a

Uni Bern

No

No

Yes if 6)

No

No

Yes

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes Yes

Brancucci Nicolas

Assistant

I

Sci

Yes

No

Yes if 6)

No

No

Burri Christian* ^

Titulary

II

Sci

Yes

Yes

yes

No

No

Yes

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Cissé Guéladio

Professor

n/a

Burkina Faso Upon request to Dean

No

Yes if 6)

No

No

No

D’Acremont Valérie

Associate

n/a

Med Lausanne

No

No

Yes if 6)

No

No

Yes

Titulary

II

Sci

Yes

Yes

Yes if 6)

No

No

Yes

De Hoogh Kees

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Eeftens Marloes

ERC Förderprof

I

Sci

Yes

No

Yes if 6)

No

No

Yes Yes

Chitnis Nakul

Daubenberger Claudia*

Fink Günther ^

Associate

I

Sci/ Econ

Yes

Yes

Yes if 6)

No

No

Gagneux Sébastien ^

Associate

I

Sci

Yes

Yes

Yes

No

No

Yes

Glass Tracy

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Hattendorf Jan

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Hetzel Manuel

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Keiser Jennifer

Associate

I

Sci

Yes

Yes

Yes if 6)

No

No

Yes

Knopp Stefanie

Assistant

II

Sci

Yes if 5)

No

Yes (if 6)

No

No

Yes

Full

I

Med

Yes

No

Yes

Yes

Yes

Yes

Assistant

I

Med

Yes

No

Yes

No

Yes

Yes

Titulary

II

Sci

Yes

Yes

Yes

No

No

Yes

Associate

I

Sci

Yes

Yes

Yes

No

No

Yes

Mäusezahl Daniel

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Merten Sonja

PD

II

Med

Yes if 7)

No

Yes if 6)

No

Yes

Yes

Moore Sarah

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Mueller Pie

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Neumayr Andreas

PD

II

Med

Yes if 5)

No

Yes if 6)

No

No

Yes

Odermatt Peter * ^

Titulary

II

Sci

Yes

Yes

Yes if 6)

No

No

Yes

Associate

I

Med

Yes if 5)

No

Yes

Yes

Yes

Yes

SNF Förderprof

I

Sci

Yes

No

Yes if 6)

No

No

Yes

Künzli Nino * Labhardt Niklaus Lengeler Christian * ^ Mäser Pascal ^

Paris Daniel Penny Melissa

Appendix - 75

Page 2

Probst-Hensch Nicole *

Full

I

Med

Yes

No

Yes

Yes

Yes

Yes

Associate

I

Sci

Yes

Yes

Yes

No

No

Yes

Ross Amanda

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Steinmann Peter

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Tediosi Fabrizio

Titulary

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Utzinger Jürg ^

Full

I

Sci

Yes

Yes

Yes

No

No

Yes

Van Eeuwijk Piet

PD

II

Hum

Upon request to Dean

No

Yes if 6)

No

No

No

Vienneau Danielle

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

I

Sci

Yes

No

Yes if 6)

No

No

Yes Yes

Röösli Martin ^

Vonaesch Pascale

SNF Förderprof

Voss Till ^

Associate

I

Sci

Yes

Yes

Yes

No

No

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Titulary

II

Med

Yes if 7)

No

Yes if 6)

No

Yes

Yes

Vounatsou Penelope Weisser Rohacek Maja Winkler Mirko

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Wittlin Sergio

PD

II

Sci

Yes if 5)

No

Yes if 6)

No

No

Yes

Wyss Kaspar * ^

Titulary

II

Sci

Yes

Yes

Yes

No

No

Yes

Zemp Elisabeth

Titulary

II

Med

Yes if 8)

No

Yes if 6)

No

Yes

Yes

Zinsstag Jakob * ^

Titulary

II

Sci

Yes

Yes

Yes

No

No

Yes

∗ These professors qualify to act in PhD committees like a “Group I Science Faculty member” (5 year permission) ∧ These Science Faculty professors qualify to act in PhD committees like a “Group I Medical Faculty member” (decision of the Med Faculty from 2017 and 2018; valid for 5 years) 1.

2.

3.

4.

Titles are provided by University Basel Full and Associate Professors (and SNSF Förderprofessors) are Group I; all others Group II Faculties: Faculties of Science (Sci), Medicine (Med), Humanities (Hum) In the Medical Faculty, it is the PhD Faculty commission who chooses the Chair (most often a member of that commission, but all Group I Medical Faculty professors would qualify) 5. “Yes if 5” = Staff qualifies as First or Second supervisor if the other supervisor qualifies as supervisor (Group I) in the Science Faculty 6. “Yes if 6” = Staff qualifies as First or Second supervisor if the other supervisor fully qualifies as supervisor (Group I) in the Medical Faculty 7. “Yes if 7” = Staff qualifies as First supervisor if the Second supervisor fully qualifies as supervisor (Group I) in the Science Faculty

**) Academic positions are PD (Habilitation), Assistentprofessor / Förderprofessor and similar, Titulary Professor, and Associate and Full Professors. The latter two are the only positions for which University assigns “core funding”; the two are meanwhile considered to be “equal”, but the terms still appear.

Usually, full professors may have the responsibility to represent a specific field for which Uni Basel (i.e. the faculties) decided to hold “structured positions” (Ordinariat) which, upon retirement, are usually replaced through new recruitments). Occasionally, even those positions are “ad personam”, thus, retirement does not call for replacement. All other positions are “ad personam” as well, with neither a University “budget line” nor a replacement. NOTE: These are the University rules; as an associate institute, Swiss TPH has its own core funding model and contract with the university. But in terms of academic functions, all university rules equally apply to the Swiss TPH academics.

76 - Appendix

Competences in Medical Parasitology and Infection Biology (MPI) Fundamentals of MPI (includes microbiology and cell biology) PhD students in MPI need to master the fundamental concepts of Infection Biology with an emphasis on neglected infectious diseases of importance to public health. These include: – Disease systems Life cycle and biology of infectious agents; working techniques in modern biology (biochemistry, genetics, immunology, molecular and cellular biology); tools for diagnosis and interventions (drugs and vaccines).

– Basic epidemiological concepts Epidemiological study design; risk factor concepts; basic statistical analysis skills; understanding problems in the national health programmes of countries with limited resources.

While it is not possible to acquire in-depth knowledge in all of these areas during the course of PhD studies, training should target acquisition of specialist-level knowledge in the disease(s) relevant to the research project and basic knowledge in understanding infectious diseases in resource restricted countries.

Research skills Students need to be: – Trained in general research skills for laboratory and field work (including safety guidelines).

– Able to interpret and critically review data, and pose innovative and relevant research questions.

– Informed by a systematic and timely review of the literature, to deduce from it further relevant theoretical and conceptual models, and to select an appropriate research approach to address the research question.

– Equipped to work in a research team, apply resources responsibly, ensure ethical and responsible professional conduct, and effectively communicate the findings and implications of their research to a broader research community (through scientific publications, presentations, teaching), as well as to non-specialists.

Personal and management skills Many practical skills are acquired during the research work. As the project progresses, the student should gradually take over more tasks related to project management and leadership and thus develop these skills.

Scientific writing skills for production of papers, grant applications, and reports are also important.

Training in presentations skills and ethical conduct is another essential part of doctoral training.

Appendix - 77

Competences in Epidemiology and Public Health Fundamentals of Epidemiology and Public Health PhD students in Epidemiology and Public Health need to master the fundamental concepts of public health. These include: – Epidemiology Determinants of health and illness; epidemiological study designs and measurements; sources of errors and bias; risk factor and causality concepts; statistical concepts to analyse and interpret data.

– Social and behavioural science in health research Addressing inequities in health; psychosocial factors affecting health behaviour; strategies for health promotion and disease prevention.

– Health system research Effectiveness, efficiency and equity of health care systems; outcome research; basic knowledge of health economics and health policy.

– Exposure science Basic concepts on how to measure and characterise exposure to environmental causes of diseases.

Research skills Students need to be: – Trained in general research skills including writing scientific manuscripts and grant applications, and advanced methodological skills in the specific area of research.

– Able to pose innovative and important research questions informed by a systematic review of the literature, stakeholder needs, and relevant theoretical and conceptual models, and to select an appropriate study design to address the research question.

– Equipped to work in a multi-disciplinary team, ensure ethical professional conduct and effectively communicate research findings and implications to technical and non-specialist audiences (through publications, presentations, teaching).

– Able to show the policy implications of their research and express these to a broad audience.

Personal and management skills Many practical skills are acquired during the research work. As the project progresses, the student should gradually take over tasks related to project management and leadership and thus develop these skills.

78 - Appendix

Guidelines for writing a PhD proposal Please use the PhD proposal template provided on Alfresco (do not use older proposals as a template as details might have changed): https://team.swisstph.ch/s/TrB0dISEQqKXr2BWq18EIw and be aware of the following: 1. The proposal should not exceed 15 pages (excluding references) 2. For the main text, use font size 11, and single spacing (references can be smaller).

3. Prior to submission to reviewers and the Research Commission, your supervisor must read and agree with the submission.

The proposal should include: Topic

Comments

Front page

Title of project; PhD subject; student’s name, e-mail address and address; first & second supervisor’s names, date of submission; Institution name & address; co-institution (if applicable); first & second supervisor’s titles, positions, departments, e-mail address

Contacts Acronyms/Abbreviations Table of contents Abstract Introduction and background Objectives and research aim

Research plan and methods

Maximum 400 words summarising introduction, background, objectives, methods, and relevance of thesis Explain what research question(s) you will be addressing and why it is important.

Explain objectives, hypotheses, specific aims, and relevance/benefits of the thesis. Clearly describe rationales for each research question. It may be useful to structure this section according to the manuscripts that will come out of the thesis research.

Describe in detail how you will answer your research question(s), by addressing the following aspects, as applicable: • Study type • Study population and inclusion/exclusion criteria • Sampling / recruitment plan • Exams / instruments / measurements • Statistical analysis plan, including when relevant: o Statement of the null and alternative hypotheses o Precise definition of all outcome and exposure (treatment) variables o Statistical method(s) that you plan to apply o Strategy to minimise confounding o Specification of effect modifiers or subgroups that you intend to analyse o Method to account for non-independence of data (clustering) o Strategy for handling missing data and loss to follow-up o Statistical software that you plan to use • Sample size calculation / justification Appendix - 79

Page 2

Contact statistical support (coordinated by Marek Kwiatkowski) at an early stage for feedback on your research plan and methods.

Ethical issues

If your research involves people, please assure that the methods / data collection / sampling described here are identical with those described in the questionnaire / case report form and the participant information / informed consent.

All research projects involving people need ethical clearance; if the project is carried out in a low resource country, ethical clearance must be obtained from Ethikkommission Nordwest- und Zentralschweiz (EKNZ) and the dedicated local ethics committee (best practice rule). Please contact the Swiss TPH Human Subject Research Desk (HSR Desk) (hsr-desk@swisstph.ch) for advice during the preparation of your proposal.

Clinical trials may in addition need regulatory authority clearance and a study specific insurance.

Research involving animals may need authority clearance

Time plane with milestones List of tentative titles of manuscripts indicating student’s author position Collaboration and support

PhD Committee Short CV Professional training to be undertaken Budget plan Reference list Appendix

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Essentially, all the people and institutions with whom you expect to work. You may have a limited number of external collaborators.

Describe the collaboration with internal and external sources in 1-3 paragraphs List the names and roles of PhD committee members, at least first supervisor and second supervisor at the time of submission.

One-page curriculum vitae so reviewers can understand the proposed learning agreement.

Include assessment of total ECTS credit points needed and detail of planned lecture work, conferences, etc. as far as already known.

Include details about the funding agency and funding concept for the part relevant to the thesis itself (student salary, publications, travel, etc.).

Restrict to most important references (some 30-50 is usually sufficient).

Only if needed; appendices counts towards the 15-page length limit.

Guidelines for the internal PhD proposal evaluation process Swiss TPH Research commission (RC) – version 2021 PhD supervisor Immediately after registration of the new PhD project with the University of Basel/Swiss TPH, the PhD supervisor: 1. suggests and finds two Swiss TPH colleagues (project leaders who are not directly involved in the project) who agree on reviewing the PhD proposal, plus a statistical reviewer (contact Marek Kwiatkowski). The PhD supervisor conveys this information to Marco Waser / the research commission 2. decides (together with Marco Waser) at which forthcoming RC meeting the research proposal will be discussed (this has to occur within three to six months after registration of the PhD student) 3. determines the composition of the PhD committee

PhD candidate 1. writes his/her research proposal according to the guidelines (https://team.swisstph.ch/s/MapGAgp7QRusIh7icCAG0w) 2. submits the complete document to both reviewers four weeks before the scheduled RC meeting at the latest, and uploads all file to his/her designated Alfresco folder 3. schedules a meeting (no later than two weeks before the scheduled RC meeting) to discuss the proposal with both reviewers and the PhD supervisor 4. resubmits the revised proposal (in which all issues have been adequately addressed) to both reviewers (no later than one week before the scheduled RC meeting) 5. submits the final proposal including a concise abstract of their PhD project to the research commission.

6. prepares a short presentation to introduce his/her PhD project to the RC audience (see below ‘Proposed Structure of PhD Project presentation at the Research Commission meeting’)

Reviewers The evaluation process consists of three phases: Phase 1: Within two weeks after receiving the first version of the proposal, the reviewers: 1. evaluate the proposal and use the PhD proposal evaluation form as a tool to assess all relevant criteria 2. discuss the outcome of their evaluation with the PhD candidate and supervisor in a meeting organised by the PhD candidate (if meeting in person is impossible, this exchange has to take place by other means) 3. Statistical review: no need for an evaluation form, as each PhD work has its individual method challenges Phase 2: Within one week after meeting with the PhD candidate and supervisor, the reviewers receive the final, revised proposal from the PhD candidate 1. The reviewers fill out the evaluation form a second time. Criteria that are sound may simply be check-marked and commented by a single phrase if necessary. Only those issues that remain to be solved in the revised version need specific but concise comments. The reviewer also recommends the final proposal for approval, minor or major revision. However, the whole idea behind this streamlined evaluation process is that final proposals can be approved in principle by the research commission Appendix - 81

Phase 3: Presentation at the FK Meeting 1. The reviewer and supervisor briefly comment on the proposal after the presentation by the PhD candidate 2. Major issues may be discussed in the plenary again before the chair decides on further steps if necessary.

Proposed Structure of PhD Project Presentation at the Research Commission Meeting – Presentation should not exceed five to seven minutes!

– Limit presentation to five slides and a Title page.

– Use the ppt template available from the communications intranet page (https://intranet.swisstph.ch/en/aoc/communications/templates/) – Send the slides one day before the meeting to the research commission or upload them to your Alfresco folder.

– Be prepared for questions from the plenary after the presentation.

Suggested Slides: Title page: Title of PhD proposal, your name and affiliation, members of doctoral committee and their function (Primary Supervisor, Secondary Supervisor, additional experts, external expert (as far as known already)) 1 Give some information on who you are (background training) 2 Short background of project. Is it part of a larger research activity, SNF / EU funded?

3 What are the research questions / hypothesis?

4 Methods and expected outcomes 5 Time plan, planned training during PhD

82 - Appendix

PhD thesis structure A typical structure includes: – – – – – – – – – –

Table of contents Acknowledgements Summary (in English) Introduction Chapters made up of manuscripts, either published or ready for publication. Each chapter should be formatted in a unified style. Additional chapters can be added as “working papers” if these will not lead to publication.

Discussion providing a unifying theme through the work and touching upon points not found in the chapter discussions.

Conclusions List of references* (references can also be included at the end of each chapter) Appendices A brief curriculum vitae

Look at recent examples of Swiss TPH theses in the Institute’s library.

*Towards more unified bibliometric referencing in Swiss TPH MSc and PhD theses Using reference manager software (e.g. Zotero, EndNote, etc) allows for one single list of all cited references at the end of the thesis (not each chapter) and thus avoids much redundancy from repeating references common across many chapters and saves pages in the final print versions.

The preferred referencing style of in text citations is Harvard Style, which names first authors and the year in the text, and lists all bibliographic references in alphabetic order in a single list at the end of the thesis including all authors (no et al). This makes it easier for examiners to appreciate whether appropriate literature has been cited in the appropriate places without constantly checking numbered lists in the manuscript into different bibliographies in the thesis.

For reference managers to assemble a single bibliography at the end of the thesis requires a single manuscript of the thesis. Ideally the MSc and PhD dissertation manuscript should apply internally consistent and continuous page numbering and chapter numbering linked to a detailed Table of Contents. This is easiest done using the original manuscripts of the chapters or published papers concatenated into a single word processed document using section breaks for chapters and unique chapter headers. For the PhD dissertation where some chapters will have been already published as papers, this could include the final word processed manuscript as submitted but also incorporate where advantageous any professional graphics from any of the published versions. This allows the automated Table of Contents and Table of Figures to be complete. Such chapters have a facing page indicating the citation of the published paper.

Appendix - 83

Ethical Clearance for Swiss TPH Projects Principle: Any project involving humans requires an ethical clearance.

General info The Swiss TPH Human Subject Research Desk (HSR Desk) (hsr-desk@swisstph.ch) has the mandate to support Swiss TPH researchers with applications to Ethics Committees and Authorities and in the related processes, and with this to ensure a consistent quality of Swiss TPH documents submitted worldwide.

The service is free for Swiss TPH staff and students. The HSR Desk has to be mandatorily contacted during the preparation of any study involving humans including the collection of human health data and samples. HSR Desk provides information on documents needed depending on the study type, and the format and content of such documents.

All documents necessary for submission have to be reviewed by the HSR Desk prior to submission (see Swiss TPH intranet (https://intranet.swisstph.ch/en/information-resources/human-subject-researchdesk/). Please note: the earlier HSR Desk is contacted during the project preparation the more efficiently the service may be provided. Turnover time by HSR Desk for requests and reviews is normally five working days per cycle.

Ethical clearance The general policy of Swiss TPH is to follow the best practice rule for ethical clearance and in accordance with this all research we conduct in the Low and Middle Income Countries and in which we have a major role (Sponsor, PI, MSc / PhD supervisor or similar) has to get double clearance from Switzerland (i.e. EKNZ by law for Swiss TPH) plus the country where the research is being performed (including potentially a local institutional review board).

As an exception, no submission to a Swiss ethics committee is required if there is another official Northern Ethics Committee which has given a written positive opinion for the comprehensive project, e.g. WHO, MSF, US IRB). Local clearance by the responsible Ethics Committee is mandatory in all cases and independent of an existing Northern approval.

Drug authority authorization In addition to ethical approval which has to be obtained for each project involving humans including the collection of human health data and samples, clinical trials also need the approval of the respective National Authority (Drug Regulatory Authority, Ministry depending on the country). The necessary process needs to be clarified in advance with the local partner.

Research Clearance Certain countries require a research clearance for expatriate and/or visiting scientists. If such clearance is required in a country, researchers have the obligation to assure such approval is obtained in a timely manner from the respective national authorities.

Study Insurance Depending on the type of research and the local regulations, a special study insurance covering any harm to the participant may be necessary; HSR Desk can provide support.

Please note • For existing biospecimens, e.g. those stored at Swiss TPH, that may be re-evaluated or used in a new study, current international guidelines and literature require acquisition of a new ethical clearance and consent from the participant (certain exceptions may exist).

84 - Appendix

•

Current international guidelines and literature require the destruction of samples after the completion of a study. The time point of destruction should be defined in the study protocol and be mentioned in the patient information – from a pragmatic point of view we suggest publication of the final study report or the major publication of the respective project as an optimal time point for sample destruction. We further suggest to consider in each project to integrate a separate general research consent allowing the future use of collected samples.

•

In Switzerland, Ethics Committees are organized by region; the responsible Ethics Committee is defined by the domicile of the investigator. In case of a multicenter-study, the Lead Ethics Committee (where the Principle Investigator is domiciled) informs the other Ethics Committees where the study will be conducted, so only one submission is necessary.

•

When preparing your documents, please consider “good documentation practice” for the proposal and all ancillary documents. The following details should appear on each page (e.g .) in the header: o Short running study title (Study Acronym) o Version-nr and date of protocol (e.g. Protocol v1.0_15.04.2019 => use 0.x for drafts; use Ver 1.0 for the first submission to ethics committee The following details should appear on each page (e.g. in the footer): o Clear page numbering e.g. X of Y or X/Y o For study-related documents which have their own version-nr and date, the version-nr. and date of the protocol have to be added; ex am p l e : for the “Patient Information and Consent (PIC)” – document:

PIC, v1.0/1.04.2019 referring to protocol v1.0/15.04.2019

•

For studies involving humans, add the copy of your signed PhD / Master Proposal Cover Page at the beginning of your proposal (Principal investigator and/or supervisor, student, statistician, if applicable other key persons to the project. Only collect the signatures on the final document version (i.e. after FK clearance for PhD students)

•

Before submitting your dossier via the BASEC platform (Swiss ethics electronic submission platform) to the corresponding Swiss Ethics Committee (in general EKNZ) your cover letter attached to your submission dossier must be signed by: • Your supervisor • and co-signed by Prof. Daniel Paris, Medical Director at Swiss TPH (clinical trials) OR Prof. Christian Burri, Head HSR Desk at Swiss TPH (studies other than clinical trials) • Please use the correct Swiss TPH letter template (from intranet) with the contact details of your supervisor (but not your private address) • Indicate the Swiss TPH invoice address and recipient in the letter

•

Please list your project in the Swiss TPH project database accessible through Swiss TPH intranet (responsibility of the Project Leader / Supervisor)

•

International registration is mandatory for clinical trials: Swiss TPH has an account with

clinicaltrials.gov for registration of clinical trials. Prof. Christian Burri is the Swiss TPH administrator; please contact him to obtain access for study registration (prior recruitment of 1st participant). Other official registries may be chosen if needed.

•

The Swiss TPH has a US OHRP registration number, which is available at the HSR Desk if required (e.g. NIH grants, Bill & Melinda Gates Grants, US FDA registrations).

Appendix - 85

Swiss TPH Human Subject Research – Desk (HSR-Desk) & Ethical Submission Procedure in Switzerland Action

Responsible

Details

First contact with Swiss TPH HSRDesk (hsr-desk@swisstph.ch)

Project Leader or Student

Describe your request/study idea and attach your project proposal or synopsis if already available

~ 5 working days

Feedback on “risk category” of project and instructions on the documents to be prepared (according to BASEC Document Matrix)

Preparation of documents, sending them to HSR-Desk for review

HSR-Desk Team

Project Leader or Student

HSR-Desk Team (+ Medical Director for clinical trials)

Check of documents

Documents ok

• Is an ethical clearance necessary or an “ethical exemption” sufficient?

• Definition of risk category • Which documents have to be prepared?

Feedback to Project Leader or Student, ≤ 5 working days

Documents not yet ok Revision of documents according to feedback of HSR-Desk

Project Leader or Student

Ready for submission

Create an account on BASEC platform https://submissions.swissethics.ch/en/ user/login

Project Leader or Student

Upload HSR Desk approved documents

If documents ok for submission: • Get cover letter signed by Prof.

Daniel Paris (Medical Director) for clinical trials / Prof. Christian Burri (Head HSR-Desk) for all other studies • PL signs cover letter (not student) • HSR-Desk sends detailed instructions uploading of documents on BASEC platform • Create an account in BASEC and upload your documents • You will receive an automatic confirmation of your uploaded dossier by email

(e.g. Feedback from EKNZ ~ 4 weeks after submission date)

EC Approval or request for changes and invoice will be sent to HSR-Desk that will forward documents to Project Leader

Ethics Committee(s) Approval

Forward Ethics Committee(s) approval to Project Leader

HSR-Desk Team

Please note: The HSR-Desk is provided by Swiss TPH / Department of Medicine Contact info: T: 061 284 89 60 (Monique Vogel) / Email: hsr-desk@swisstph.ch

86 - Appendix

V09/23.07.2019

Plagiarism Swiss TPH considers plagiarism to be a serious academic offence. For the University of Basel’s official rules (Faculty of Sciences) on plagiarism, please visit: https://philnat.unibas.ch/de/studium/ (Informationen & Downloads).

What Is Plagiarism?* Plagiarism is copying or paraphrasing text that is not your own and using other people's ideas without giving due credit (i.e. giving the impression that the ideas are your own). Using material for which you have already received credit points and failing to acknowledge assistance you have received also constitutes plagiarism Avoiding Plagiarism* Document your source whenever you use a phrase, text or idea put forward by someone else. Make sure that you do this thoroughly, correctly and consistently. When taking notes, carefully distinguish between your own thoughts and material you have found elsewhere. In a publication, indicate the source of ideas that are not your own, both in the body text (with in-text citations) and in the list of references.

If you use material and ideas that you have used before, indicate this in the Acknowledgements section. If you are actually quoting yourself, quote yourself explicitly.

In addition, include an Acknowledgements section at the beginning of your paper. If you have received assistance, for example, with statistical analysis or English language correction, give a fair account of this in your "Acknowledgements" section. If you are in doubt about how to acknowledge the help you have received, choose the more explicit version. Those who have helped you will appreciate your generosity. *Adapted from the document On Good Academic Practice/Plagiarism produced by the Department of English at the University of Basel.

Appendix - 87

Corporate Identity It’s crucial that Swiss TPH CI/CD is used by all employees and students to ensure that we speak with one voice as an Institute, to both the internal and external population. By sharing a consistent, cohesive image and culture, it positions us as a leader in global health. Therefore, we depend upon our staff and students to consistently use the following Swiss TPH corporate identity information and materials

Official Names Swiss Tropical and Public Health Institute Schweizerisches Tropen- und Public Health-Institut Institut Tropical et de Santé Publique Suisse

Abbreviation Swiss TPH as written in the logo, is our official abbreviation for all languages. Abbreviations like 'STPH' and 'ITSP' should not be used. This is especially important due to today's full text index searches, e.g., Google.

Resources available on the Swiss TPH Intranet (https://intranet.swisstph.ch/en/aoc/communications/corporate-identity/) Corporate Identity and Design materials and guidelines Media Relations guidelines MS Office Templates Swiss TPH Publications Institute Vision, Mandate and Goals Additional Resources: Proof readers, editors, translators, event materials

88 - Appendix

Accommodation for students Please check the following resources: General information/list of student accommodation: https://www.unibas.ch/en/Studies/Student-Life/Accommodation.html Uni-Markt: https://markt.unibas.ch/category/wohnen-angebot Verein für Studentisches Wohnen WoVe Petersgraben 52 CH-4051 Basel Tel: +41 61 260 24 30 E-mail: info@wove.ch www.wove.ch

Appendix - 89

90 - Appendix

Swiss TPH

Biozentrum

URZ

Institute For Med. Mic. Bio

University Library

University Main Building

KUG

NL

Map of Basel

Swiss Tropical and Public Health Institute Socinstrasse 57 P.O. Box 4002 Basel Switzerland Telephone +41 (0)61 284 81 11 www.swisstph.ch

Last update: August 2021