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Leiden University Student Repository

Browse through thousands of student theses

Explore more than 40.000 theses across more than 70 University Bachelor and Master programmes. Search all items

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Student theses at Leiden University

The Student Repository offers an online overview of theses from most Leiden University Bachelor and Master programmes.

Many of these theses are available in full text. Bachelor Theses are by default closed access, unless the author and thesis supervisor have decided to make the thesis available. Master thesis are by default available in open access unless the author and thesis supervisor have decided to put an embargo on the availability of the material.

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Dissertations

Dissertations published at Leiden University. Browse all items via the link in the sidebar.

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LIACS Thesis Repository

These webpages contain theses and reports by students affiliated with the various bachelor and master programmes offered at the Leiden Institute of Advanced Computer Science ( LIACS ), the computer science and artificial intelligence department of Leiden University . Note: this thesis repository might be incomplete for certain programmes.

849 entries found.

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Submitting your PhD dissertation

Practical information on submitting your dissertation

The Beadle’s office

You must submit 2  copies of your thesis and appended propositions to the beadle’s office for the attention of the Doctorate Board no later than  three weeks before the date of your doctoral defence .

Delivery during office hours or send: Bureau Pedel, Rapenburg 73, 2311 GJ Leiden.

PhD Regulations

By decision of the Doctorate Board every PhD candidate at Leiden University is obliged to deliver two  copies of his/her dissertation to the library. He/she also submits the dissertation in digital form to the library for the benefit of the Institutional Repository (IR) of the University. For relevant changes see  PhD Regulations Leiden University .

Candidates are required to fill in both forms below.

• Dissertation Description & Upload Fill out the form with a short summary and metadata of your dissertation. Also, use this form to upload  PDFs of the dissertation, dissertation cover and propositions . If the dissertation contains published articles please fill in the DOIs. In the form you are asked for keywords. If there exists a generally accepted keyword list within your subject it's best to choose keywords from that list. If there's no such list, consult your promotor or mentor. Avoid words that are used in your dissertation's title, and words which have multiple explanations.  
• Appendix B (Licence Agreement, to be filled out and signed digitally and/or printed out and signed ). By signing the licence you grant Leiden University the non-exclusive right to post your dissertation in the digital archive, making it available Open Access worldwide. The university will clearly indicate the author or owner of the publication, and will not make any changes other than allowed by this licence. On this appendix you can also indicate which parts of your thesis should be put under embargo.

Send one  completed and signed copy  of Appendix B, together with  two copies  of your dissertation, to the following address:  University Libraries Leiden - MDA  Van Steenis Building  Einsteinweg 2 2333 CC Leiden 

Compensation for printing costs

PhD candidates receive a financial compensation of €500,-  for the printing costs of the dissertation. This compensation is paid by the UBL after receiving two printed copies of the dissertation, a digital copy of the dissertation and the signed license for the non-exclusive publication of the dissertation in digital form.

File types should be PDF. In most cases candidates will already have a PDF-file that is used for printing purposes. Word files can be turned into PDF by choosing File -> Save as Adobe PDF.  Please submit your dissertation as one single PDF. In case one or more chapters are embargoed please indicate so on Appendix B. Further editing is done by our metadata specialists. Also submit the DOI's from chapters that have already been published as articles. The cover and propositions can be submitted separately.  When you would like to store your research data please contact the data management experts at the Centre for Digital Scholarship .

When you only have files in Word (or other file formats), or have questions on the procedure please contact us by  e-mail  or call us at (071) 527 1525.

It is possible to request an embargo of 6, 12, 18, or 24 months for parts of the thesis in those cases where this is necessary because of arrangements with a publisher or for future publications. This embargo period can be stated in the licence. Doctoral candidates are required to check for themselves if and for how long the embargoes need to be set. In case the embargo period is insufficient, this can be extended within reason by the library as stated in the Ph.D. regulations. Please contact the library in case you need an extension.

Although a thesis might be placed under embargo, a candidate is still obliged to submit his/her disseration. Dissertations under embargo are archived for the long term, but not made available full text. However, the abstract and bibliographical information will be made available.

Publishing at your own website or a publisher

Candidates can publish the pdf of their dissertation on their own website. It is easier though, to put the repository-url of your dissertation on your website instead of the pdf. This url is permanent and will therefore remain unaltered.

If you have already published (articles from) your dissertation through a publisher, or are planning to do so, and also want your dissertation published in Open Access, approval depends on the type of licence you and your publisher have signed. In most cases you will have kept the right to submit your article / dissertation in an institutional repository or most publishers will grant you this right. In these cases you will have no problem submitting your dissertation. Note that some publishers can object to submitting a publisher's pdf. A new pdf will then have to be made. If your licence does not mention submitting your publication to an institutional repository, you may be able to find information about their Open Access policy on the publisher's website. Finally, you can write to the publisher to request permission to submit your publication to the repository. Most publishers are obliging in these cases. An up to date overview of publishers and their policies regarding copyright and online archiving in institutional repositories can be found on  Sherpa Romeo Publisher copyright policies & self-archiving .

If you have any questions on the procedure please contact us by  e-mail , or call us at (071) 527 1525.

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Submitting your dissertation

The PhD regulations explain, among other things, which criteria a dissertation has to meet, the requirements for the non-scientific part of the dissertation, the composition of the doctoral and opposition committee, and so on.

Information about the procedures relating to submitting and defending your dissertation and which forms are required can be found here .

Your dissertation layout must meet certain requirements. Find out here which special rules apply if you have written your dissertation with others or if you are publishing a commercial edition.

More practical information about submitting your dissertation can be found here .

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Master Thesis Lab

The Master Thesis Lab (MTL) of the Faculty of Social and Behavioural Sciences is open to students working on their Master thesis in any of the Institutes in our Faculty, providing both soft services and work tools. You are welcome, when all is going smoothly, when you experience a patch of storm, or somewhere in between. We are looking forward to meeting you!

• 2022-09-13: Room number(s) and directions are added to the contact details below.
• 2022-09-09: The Master Thesis Lab is being updated: we will have a limited number of desktop computers ith specialized software, and several laptop-based desks with external screen and peripherals. During this process the existing access registrations to the computers may be locked. We apologize for the inconvience.
• 2022-09-01: The online booking widget was updated, and now requires both the (short) statistical consultation question, as well as an indiciation of previous contact. The online booking widget is now fully functional.
• 2022-08-28: Our new shortened website is live. Some information is rearranged, or has moved to our Brightspace module. We have added an online meeting scheduler (see below). This module is not fully functional yet. If you do not see any options or advisors on multiple days, please email us directly for meeting/consulstation request.  The Dutch information page is coming soon! 

The MTL offers a quiet and partially supervised office space, with desks available to connect your own laptop to provided external screen, mouse and keyboard. In addition, a limited number of desktop PCs (Windows) is available to host specialized software for (meta) data analysis of qualitative and quantitative data. We provide several laptop desk spaces with external monitors. In addition, there is a limited number of desktop computers, each with all the necessary software (Word, Excel, SPSS and other specialized software). The work spaces have adjustable seats and tables and are especially designed for working comfortably for extended periods of time.

Eating and drinking is not allowed in the Lab and long discussions may distract others. Please use the meeting area for those purposes. We trust you to keep this area clean and tidy! It is not possible to reserve a desk or a computer in advance.

You can ask our expert colleagues for a dialogue regarding the general thesis process, as a sounding board when in doubt about supervisor comments, (statistical) strategy, or when you find yourself in a more general stressful thesis-related situation. Issues regarding ethics, open science, programming, and more can be addressed via our interactive discussion board so that others can also learn from it, or you can contact us individually through the MTL email. For language or literature support we can assist in coordinating appointments with expert colleagues. You can book statistical consultation (by appointment only) with one of our experts directly through the meeting wizard online (see below), in which we show live updates of (limited) availability.

Please be aware that the MTL provides support and advice, but does not and will not take a supervising position at any time. Final responsibility for all substantive communication and synchronization towards the final thesis lies with you and your supervisor. We kindly ask you to use the MTL services, facilities and time respectfully.

What we do and what we don't do

• Give advice on how to structure the time spent on your thesis;
• Give advice on general lay-out;
• Help to think about the consequences of your choices;
• Help you with practical SPSS of R problems;
• Make an appointment with the statistical advisors (e.g. for more advanced SPSS or other statistical problems);
• Make an appointment with the staff members of the Master Thesis Lab who are specialized in qualitative research;
• Give you information on where to find information about various aspects of writing your thesis.
• Read (parts of your) Master Thesis;
• Give advice concerning the specific and specialist content of your thesis;
• Provide critical comments on the content of your thesis;
• Act as a substitute for your thesis supervisor (also not when your supervisor is not available during a longer period);
• Take responsibility for your choices with respect to any part of your thesis. 

When you are writing your Master's thesis, you might want to have a look at some examples. In the Leiden University Repository  there are Master's theses from students from all FSW institutes.

Experts on methodology and statistics from different institutes, are available to you for consultation.

Availability per advisor is limited to 2 hours per week and within fixed hours, usually between 13:00 and 15:00. Due to other (teaching) obligations, consultation time slots may vary per semester or block. 

You can book appointments of 45 minutes via the module below. All statistical consultation are in room 6.C05, in the hallway next to the elevator, or as specified by the advisor.

The statistical consultant provides you with an advice fitting to your research question, timeframe and ability. You are completely free to follow up, ignore or discuss the advice with your thesis supervisor. 

The MTL does not communicate with your thesis supervisor about the (amount of) support or advice given.

You can book a stats consultation meeting directly below. To send a request, an informative description of your questions is required.

Please allow your fellow students to also book a consultation meeting by considering the following:

• book (only) one appointment at a time, to not clog the calendar
• should a followup meeting be needed, please book with the original consultant
• upon required cancellation, do so ahead of time, to allow your fellow student to use the time slot (the booking system currently does not allow for new student bookings if less than 24h in advance!)
• use the consultation time well: fill in your question(s) seriously and prepare for the meeting  

[email protected] . Please note that we will check if you are a registered master thesis student prior to (accepting) a meeting.

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appointment for consultation directly through the online module above.

Physical location: We are located on the 6th floor.

Only the blue-door elevators go here. Take the one on the library side of the building, which takes you direcly to the correct side of the 6th floor.

You can also take the stairs from the 5th floor. These are "hidden"  behind the double white doors in the central hallway on the 5th floor. Taking the stairs, go up to the left; this will take you to the correct side of the 6th floor.

6C02 -> consultation room in the staircase hallway 6C05 -> main MTL (with desks) -> 6c05

You can join the MTL facilities by registering for the "Master Thesis Lab" course in uSis. This will enroll you automatically in the MTL Brightspace module, in which we (start to) collect and provide structured questions and answers from our experience and interactions throughout the years. It also enables you to contact the MTL and connect to fellow thesis students.

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With this algorithm, new medicines can be found more quickly

Did he dare take a gamble with his PhD research? Jeroen Methorst didn’t have to think long about it. It could fail or turn out very well. The latter is the case. Methorst developed a computer system that helps researchers find the protein they need. ‘Our whole group is now using this program.’ Methorst will defend his PhD thesis on 2nd April.

Jeroen Methorst is a nanobiologist and biophysicist, but he didn’t find himself very handy in the lab. He taught himself programming: that turned out to be his forte. ‘My supervisor, Jelger Risselada, asked if I was up for taking a risk and developing something that could fail, but might also turn out very well.’

Methorst completed his PhD at the Leiden Institute of Chemistry on a computer strategy that the scientific community is likely to find very useful. For instance, colleague Niek van Hilten sought a protein capable of detecting and destroying many types of viruses. He achieved this using the strategy developed by Methorst.

The system knows enough about physics

Methorst: ‘Niek’s research started with the idea of developing a small protein, composed of twenty amino acids. It had to be able to recognize and break apart the strongly curved membrane of a small virus sphere.’ Methorst’s system knows enough about physics to assess whether a molecule can do this. It can also virtually simulate evolution to propose a suitable molecule. ‘You put in that you want a protein composed of twenty amino acids, and what it needs to do. A computer program starts with a few hundred randomly generated protein molecules, each twenty amino acids in size.’

An evolutionary algorithm allows the selection to crossbreed

Another program evaluates these molecules based on physics: which ten or twenty molecules are the best at recognizing and breaking apart curved membranes? This selection is then fed back into the evolutionary algorithm. This algorithm virtually breeds them together, akin to natural selection. The molecules essentially have offspring. Like in nature, these offspring resemble their parents but are also different. The selection program then chooses the best ones and feeds them back into the evolution algorithm. This process continues for about twenty or thirty generations, until the researchers are satisfied.

Simulation videos demonstrate the result

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Whether the researchers can be satisfied is made clear to them by a simulation video generated by Methorst’s strategy. ‘The program that selects the best molecules does so by virtually testing all the molecules in simulations.’ The researchers can view (a sample of) these simulations and stop the system when they are satisfied. Niek van Hilten, who was searching for an effective virus killer, stopped after about 25 generations. The subsequent generation didn’t improve upon the previous one. In a German lab was found that the molecule was indeed capable of recognizing and destroying viruses in reality.

Sometimes things go wrong: the ingenious evolutionary biodynamic system also found molecules that could attract cholesterol. ‘Unfortunately, these molecules also strongly attracted each other in the lab. That clustering is undesirable.’ Such mishaps can occur because the system’s knowledge doesn’t encompass all of physics. ‘It lacks quantum mechanics, as that would slow down the selection program.’

A lot of computing power is required

To set Methorst’s system in motion, a vast amount of computing power is required. ‘That’s the bottleneck because supercomputers are scarce. You have to apply for one, much like you would for a research grant.’

The key to completing the system

The next step is making the enormous amount of simulation data usable for other researchers. Student Nino Verwei is working on a self-learning algorithm that predicts how a molecule should be structured to perform its function. ‘That’s the key to completing my system. It saves a lot of computing power, and the likelihood of the molecule working in the lab increases.’ The algorithm is trained using data from numerous simulations from Methorst’s selection program. Based on this knowledge, the algorithm predicts how well a molecule that hasn’t been tested in the lab will work. ‘We’ve now launched a web server where AI predicts how well a molecule works.’ Anyone can use it.

So, the gamble that Methorst took turned out quite positively. ‘Our whole group is now using my programs.’ He himself will remain involved as a postdoc for the time being. ‘Because I wrote the programs, I know exactly how to work with them.’

Text: Rianne Lindhout

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IOE - Faculty of Education and Society

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IOE alumni named winners of the 2024 BERA Master’s Dissertation and Doctoral Thesis awards

27 March 2024

Dr Emily Macleod (PhD) and Kate Fox (Education and International Development MA) have won the British Educational Research Association (BERA) Doctoral and Master’s Thesis prizes respectively.

The awards are given in recognition of academic excellence and research rigour within the field of educational research. 

Emily Macleod won for her thesis, “The status and safety of teaching: A longitudinal study of why some young people in England become teachers, and why others do not.” She investigated young people’s motivations behind pursuing – or not pursuing – the profession amidst the context of national and international teacher shortages. 

She completed her PhD at IOE’s Department of Education, Practice and Society in 2023, and was a co-host on IOE’s podcast series Research for the Real World . She continues on as an honorary postdoctoral fellow. She also worked on the ASPIRES research project studying young people's science and career aspirations, before which she was a secondary school teacher. 

Kate Fox won for her MA dissertation entitled “Building bridges or barriers? A study of home, community, and school literacy practices in rural Tanzania.”

Her dissertation centres the experiences of parents from rural communities within the Tanzanian education system – and the diverse ways families and communities contribute to young children’s literacy learning.

Kate completed her Master’s degree at IOE in 2023. She is now a Research Officer with the IOE Research Development team, and a Research Assistant working on two multi-institutional projects: Climate-U and Equitable research cultures . Her career in education spans 20 years as a teacher, headteacher and teacher trainer in Tanzania and the UK.

Related links

• Read more: BERA announces 2024 Master’s Dissertation and Doctoral Thesis winners
• Emily on ‘Why do people aspire to become teachers?’ RFTRW: S19E03
• More about Kate Fox
• More about Dr Emily Macleod 
• Research for the Real World podcast
• ASPIRES project

Centre for Education and International Development

Emily Macleod (left) and Kate Fox (right).

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