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Leiden Academic Centre for Drug Research

PhD Portal

The objective of the PhD Education and Supervision program is to educate PhD candidates in becoming professionals who are competent to conduct scientific research in the field of the pharmaceutical sciences independently. The program constitutes the basis for guiding PhD candidates in their research ultimately leading to a successful defense of their PhD dissertation within the set period. As part of this program, PhD candidates will be advised by an individual “PhD Advisory Committee” (PAC). In addition, a program of courses is offered, providing a basis to acquire a number of personal and professional skills.

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PhD Meetings & Portfolio

You will be advised by a PhD Advisory Committee (PAC) that is appointed especially for you. Typically the members of the PAC are: the LACDR Scientific Director, your promotor(s), if applicable, your co-promotor(s) and an external advisor.

The external advisor is often a senior LACDR staff member, e.g. an assistant -, an associate - or a full professor. The advisor is selected by your promotor in consultation with you. The advisor cannot be a staff member from the LACDR research division where you conduct your research. In some cases the advisor is from another institute outside LACDR.


Your PhD meetings

You will meet with the PAC on at least four occasions during your contract. In these meetings the focus is on the planning and the progress of your research. Each meeting will last approximately one hour. The PhD program office arranges the meetings with the PAC and issues the invitations.


At a minimum of one week prior to the PAC meeting, you are required to submit a progress report and a PowerPoint presentation with a maximum of 10 slides summarizing the progress in your research. For the progress report a template is available which you can download from the bottom of this webpage.

The completed form and a powerpoint presentation must be sent to the PhD program officer (Ivonne Koomen) at least one week prior to  the meeting.

A.      Start Up meeting - after two months

At the start-up meeting you will present your research plan with milestones and timelines, a proposal for education and a description of your contributions to teaching.

If applicable,  a decision is taken with regard to the selection of a second promotor and/or 1-2 co-promotor(s).

At the start you sign a declaration in which you declare to maintain and promote proper scientific conduct and to adhere to the rules of the Leiden University Code of Conduct.

B.      Admission meeting - after 9 months

At this meeting a decision is taken with regard to your admission to the second phase of the PhD program, which lasts three years.

Furthermore at this meeting you will present the progress in your research and the plans for the upcoming three years with milestones and timelines. In addition the progress with regard to education and teaching is reviewed, and after approval, the data management plan is adopted.

C.      Progress Evaluation meeting - after two years

On this occasion you will present the research progress during the past two years, your plans for the next two years, any updates of the data management plan and the progress with regard to education and teaching. Any bottlenecks will be addressed during this meeting.

D.     Finalization meeting - after three years

At this occasion you will present your research progress during the past 3 years, your planning for the last (writing) year, updates of the data management plan and the progress with regard to education and teaching.

Special attention will be paid to the timely completion of your PhD thesis and any measures that need to be taken to ensure this.  In addition, your ambitions with regard to the continuation of your career will be addressed. A timely orientation on the job market will be emphasized.

Finally a press release on your research will be discussed and approved.


You and the PAC will sign the corresponding PhD Education & Supervision Plan form. The signed documents can be included in your overall PhD Education & Supervision Plan and Portfolio.

To file all important documents on your PhD, you will obtain a LACDR PhD Portfolio binder from the PhD program office.

Performance & Development

The meetings are planned in conjunction with the annual Performance & Development interviews and cycle. You will receive an invitation by e-mail from your promotor to fill in the Performance & Development form. You can upload the signed PhD forms in the Performance & Development form via self-service, to avoid duplications.

Teamsite LACDR PhD group

Every LACDR PhD candidate has access to the SharePoint teamsite of the LACDR PhD group. This site is specially and only for PhD candidates of the LACDR. We strive to collect here all relevant PhD information and to stimulate the collaboration and communication in the LACDR PhD community.

The site contents several topics:

  • PhD templates
  • Important documents
  • Useful links
  • Lists with recommended courses and conferences
  • Available equipment
  • PhD calendar and news
  • Discussion forums

For the teamsite go to: https://intranet.universiteitleiden.nl/sites/lacdr/phd-lacdr

Scientific Output

The ultimate goal of the PhD program is the preparation and successful defense of a PhD dissertation. Typically a PhD dissertation consists of an introduction, 4 chapters on experimental research and 1 chapter with conclusions and perspectives.

In addition to a PhD dissertation, you are expected to present your scientific results in the form of posters and/or oral communications at national and international conferences, symposia and workshops. Ultimately the results of your research will be published in international scientific journals. Typically the results from the 4 experimental chapters of the dissertation will be published as full papers, while an adapted version of the introduction may be published as a review.


The purpose of PhD education is to provide you with personal skills and skills related to your professional discipline. The education program for each PhD candidate comprises a mandatory part and an optional part.

1. Courses on personal skills - your mandatory part:

2. Courses on professional skills - your optional part: 


EC points

You have to collect a minimum of 10 EC points for education during four years. One EC point refers to 28 hours of education. This number of EC points is divided into 5 EC (140h) points for courses in personal skills and 5 EC points (140h) for skills related to professional discipline.

The total program of courses needs approval from the individual PhD Advisory Committee (PAC).  You are responsible for keeping a record of the courses you have successfully completed.

Related Links


As part of your assignment you are required to contribute to teaching in the Bachelor and the Master programs in Bio-Pharmaceutical Sciences of Leiden University.

Teaching & Supervision Course

All LACDR PhD candidates receive training in teaching and supervision. As part of this program you follow the course “Introduction to Teaching & Supervision for PhD candidates” in your first year, which is designed for you. The course is presented by education specialists of the Leiden University Graduate School of Teaching (ICLON).

This course aims at the formulation of learning goals, choosing the format for teaching and learning activities, student motivation and, of course, at teaching and supervision of students.


The curriculum is as follows:

  1. Self-study (10 hours)
  2. Workshop Introduction to Teaching & Supervision for PhD candidates (4 hours)
  3. Preparing two self-evaluations (2x 5 hours)
  4. Feedback meeting (4 hours including preparations)

You will be invited to participate in the course by the LACDR PhD program office. This course will give you 1 EC point (28 hours) in total.


After studying the materials made available through the ICLON and participating in the workshop you are required to prepare two self-evaluations on:

  1.  Teaching Assignment in a classroom/ laboratory setting
  2.  Supervision Assignment of a bachelor and/ or master research project

Templates for the self-evaluations can be found on the Teamsite LACDR PhD group. The self-evaluations will be presented and discussed during a feedback meeting. Generally the presentation of the self-evaluations will be in year 2 or 3 of your PhD program.


Data Management

LACDR adheres to strict data management rules, with the aim to make our data findable, accessible, interoperable and re-usable. For this reason all LACDR PhD candidates are required to prepare a data management plan and to implement data management rules accordingly. All PhD candidates follow a data management course in the first year.

Learning objectives

Participants will be aware of the importance of sound data management; they learn about requirements set and are able to manage their own data according to standard procedures and best practices for responsible data curation common in their field of research.

Furthermore, understanding the need for Good Academic Practice Procedures- being able to shortly summarize the key points in GARP. Understanding the importance of having a consistent and structured way of naming files and folders. Being able to make a folder tree with names, and coding for components of research that can be part of filenames. In addition the participants will be aware of the possibilities and global procedures of the Electronic Notebook.

Course program

The data management course will give you 0.5 EC points (14 hours) in total. You will be invited for this course by the LACDR PhD program office. The course consists of the following parts:

a.       Preliminary assignment

In preparation for the Data Management course you will receive a preliminary assignment two weeks before the start of the course.

b.    Data Management course - part 1 and 2

Introduction in data management presented by Leiden University Librarians and three LACDR data management trainers. 

The following subjects will be discussed:

  • Policy issues for LACDR, Faculty of Science, University and funding organizations
  • Public Database Search and Use
  • Data management and good academic practice issues in science
  • Research data life cycle considerations: steps from collecting data to publication
  • Electronic lab notebook
  • Relevant standards
  • Ethics & legal compliance

c.     Writing of Data Management plan

Within 2 months after attending the workshop you are required to write your own data management plan. The template for the data management plan can be downloaded from the bottom of this webpage. Two weeks prior to the Data management course – part 3, you have to send your data management plan to the Leiden University Librarians.

d.       Data management course - part 3

During this meeting you will present your data management plan in 10 minutes to your colleagues, the librarians and the LACDR data management trainer. They will provide you with feedback. You are encouraged to pay special attention to your considerations, your challenges, the implementation and expected obstacles.

Implementation & Dissertation

As a PhD candidate you are required to implement data management as proposed in your data management plan. The implementation will be discussed in the meetings with the PAC i.e. the progress evaluation meeting (two years) and finalization meeting (three years).

At the end of your PhD research you must be prepared to give the PhD Committee and the Dean/ Graduate School access to the data underlying the results in your dissertation.


Basic scientific computing for drug discovery

We have developed a LACDR PhD course ‘basic scientific computing for drug discovery’, because data analysis with R and Python are rapidly becoming essential skills for modern scientists. 

The course is split up in two courses:

  • Course: Basic scientific computing for drug discovery
  • Course: Basic scientific computing applications for drug discovery

Both courses are optional for LACDR PhD candidates. The information for the course ‘Basic scientific computing for drug Discovery’ is:

Learning goals

After following this course you will be able to use R and Python in your basic data manipulation and visualization tasks. You will be able to reformat data as needed, calculate summary statistics and you will be able to visualize results in publication ready graphs. Moreover, you will learn the basic structure of the language in such a way that it will become easier to follow more advanced topics such as Bioconductor or more advanced applications.

Basic knowledge

For the course ‘Basic scientific computing for drug discovery’ no prior programming experience is required. This course is mainly intended for experimentalists who need a better understanding what tools to select and how to apply these to analyze their data. For this reason we focus on basic principles and application of tools. After a brief introduction on programming concepts and language syntax the students will work on case studies.

Course program ‘Basic scientific computing for drug discovery’

During this course the following subjects will be treated:

  • R and python syntax
  • R and python data structures
  • R and python objects, methods and functions
  • reading and writing of data files
  • data processing such as reshaping and aggregation
  • making publication ready graphs

Credits - application

The course Basic scientific programming for Drug Discovery will give you 1,7 EC points in total.  This means 48 education hours (of which 32 contact hours). For registration and more information, please go to the teamsite of the LACDR PhD group.

The information for the course ‘Basic scientific computing applications for drug discovery’ will follow later.

PhD Dissertation

Leiden University prescribes no strict regulations with regard to the format and structure of a PhD dissertation. For PhD dissertations at the LACDR the following may serve as a guide:

  1. Typically a PhD dissertation contains six chapters: one chapter with a general introduction, four chapters with results of original research and one chapter with a general discussion, conclusions and perspectives
  2. Generally, a minimum of two chapters should have been published in an international scientific journal or been accepted for publication
  3. The PhD candidate is first author of the majority of the publications
  4. Typically, the publications have been published not longer than four years ago
  5. A chapter can only once be included in a PhD dissertation
  6. The PhD dissertation is presented in book form and written in English

The PhD Doctorate Committee reviews your work. The PhD dissertation is formally defended in front of a PhD Opposition Committee.

Public Defense

LACDR has delegated two roles in the process of reviewing your dissertation in preparations of your public defense:

LACDR Doctorate Secretary role

The doctorate secretary role is the responsibility of a LACDR professor. He/ she coordinates the review process of your dissertation with the appointed Doctorate Committee. Please note that this process can take six weeks (see checklist).

Approval non-scientific part role

The PhD program director will give the final approval for the non-scientific part of your dissertation. Please note that this process can take two weeks.

Please send the following documents to  phd.office@lacdr.leidenuniv.nl:

  • Cover
  • Title pages
  • Propositions
  • Curriculum vitae
  • List of publications
  • Dutch summary
  • Acknowledgements (are not applicable, see for instructions regulations)


On this webpage you find a LACDR checklist describing the steps for the approval of the PhD dissertation and admission to the public defense. Furthermore you can find an hyperlink to the Leiden University PhD regulations 2018 on this webpage.

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