This EMBO Practical course will introduce concepts, methods, and tools for carrying out infectious disease modelling, as well as for developing models further by leveraging the power of genomics. 

Modelling infectious diseases can help to understand the mechanisms of pathogen evolution and predict the development of epidemics. This had an immense impact on the COVID-19 pandemic and is crucial for the general surveillance of pathogens. 

In this course, participants will learn about compartmental models, such as Susceptible-Infectious-Recovered (SIR) models, how to adapt them to a pathogen of their interest, and the differences between stochastic and deterministic models. Taking this further, participants will apply these models to epidemic settings in order to predict changes in case numbers and disease severity. 

Additionally, the participants will learn how to implement and adapt genomics-informed models for pathogen evolution, and they will learn how to make use of genomics to create timed phylogenies and reconstruct ancestral states. 

Finally, bringing together transmission modelling and genomic data, participants will learn about phylodynamic models and how this can help to detect changes in case numbers and pathogenicity earlier and more reliably than with transmission models alone. 

Who is this course for?

This course is aimed at early-stage researchers and others who are working in the fields of infectious diseases or pathogen evolution and will use mathematical modelling, and for professionals who carry out this type of research in policy making, charities or public health settings. 

Basic knowledge of R, command line, and biostatistics will be essential. We recommend to follow these or other similar free tutorials:

• Introduction to the Unix environment – https://swcarpentry.github.io/shell-novice/index.html 
• Introduction to R – https://swcarpentry.github.io/r-novice-inflammation/ 
• Introduction to Biostatistics – https://www.ebi.ac.uk/training/online/courses/biostatistics-introduction/  
   

What will I learn?

Learning outcomes

After the course you should be able to:

• Implement, evaluate and adapt deterministic and stochastic transmission models  
• Apply modelling tools to sequence data from epidemics
• Evaluate model fits and forecasts
• Adapt models for pathogen evolution
• Combine phylogenetics and transmission models into phylodynamic models
• Demonstrate a working knowledge of open access data resources of pathogen (sequence) data and mathematical models

Course content

During this course you will learn about: 

• Introduction to infectious disease modelling
• Stochastic and deterministic compartmental models using using the programming language STAN
• Nowcasting epidemics using EpiNow and EpiEstim
• Models for pathogen evolution using the programming language odin.dust
• Timed phylogenies and ancestral state reconstruction using Beast2
• Introduction to the EBI resources Pathogens Portal and BioModels
• Phylodynamics - combining phylogenetic and transmission models to predict case numbers and pathogenicity  

Trainers

Please read our support page before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59 on 25 May 2025. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 13 June 2025. If you have any questions regarding the application process please contact Barbara Etzi.

Registration fees

The registration fee includes: 

• Catering as detailed on the course programme
• Accommodation for five nights (14, 15, 16, 17, and 18 September 2025)
• Bespoke course handbook with links to the course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Secure virtual machines for practical sessions listed in the programme
• Shuttle bus on the final course day to Cambridge train station

Accommodation 

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Flash talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their poster upon registration. We will print these for you and have them available when you arrive on site.

All posters should:

•          be A2 in size – 420mm x 594 mm
•          be in a portrait orientation
•          include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

Financial assistance

Limited financial assistance is provided by EMBO in the form of registration fee waivers, travel grants and childcare grants. 

Registration fee waiver and travel grant

The travel grant and fee waiver can be used to cover the cost of travel (airfare, train, bus, taxi, accommodation, visa) and/or course registration fees and is provided up to specified caps which are normally as follows:

• up to €500 for any participant travelling to Hinxton to attend the course
• up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to Hinxton to attend the course

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their bursary amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. 

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers, trainers and organisers when attending a course. Eligible costs include (but are not limited to) fees for a babysitter or child-care facility and travel costs for a caregiver. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants. Childcare grant is up to €500.

Accessibility grants

These grants cover additional costs for supporting participants or speakers with access needs, e.g. to adapt the conference environment, or to be accompanied by someone to assist the participants where necessary. Maximally €500 per participant can be allocated.  

Sustainable travels

Limited financial assistance is available to support sustainable travels.

We encourage you to travel by train or other sustainable transport methods where possible. Therefore, if the cost of travelling by sustainable methods is higher than travelling by plane, we will aim to offset the difference in fares between the flight and the more expensive sustainable method of transport. 

Bursaries Terms and Conditions

• Application Process:
  • Apply for the fee waiver and/or travel grant, childcare grant, accessibility grant, or sustainable travel offset alongside your course application.
  • Provide a brief explanation of why you require any of the above and how attending the course will benefit your career.
  • You will be informed of your bursary status at the same time as the outcome of your course application.
• Selection Process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair Consideration: Applying for financial assistance will not impact the outcome of your course application.