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Computational modelling of multicellular systems – Course and Conference Office

EMBO Practical Course

Computational modelling of multicellular systems

Overview

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course overview

This practical course teaches the basics of multicellular modelling to any researcher wishing to enter the field, particularly experimentalists with no prior experience of computational modelling.

It is a “hands-on” course with 60% of the time devoted to students working on laptops performing exercises designed to give a practical familiarity with different types of computational modelling. The course focuses on the dynamics of multicellular systems- from embryos to organoids, covering both the molecular side (how gene regulatory networks perform pattern formation) and also the mechanical side in 2D and 3D (how the movements and activities of many cells together leads to tissue-level morphogenesis and organisation).

A carefully-chosen variety of modelling tools will be introduced, which cover the core approaches of vertex models, finite element models (FEM), and agent-based models (ABM). Attendees will also work through the week in small groups on group projects, which will be presented on the last day to the whole class. Each day will end with a keynote lecture by a prominent researcher in the field, putting the topic of the day into context through an example of relevant biological research.

The week is organised to maximise networking between the students and the teachers and speakers.


This event has been granted the following EMBO sustainability badge:

Grade 1 of 3

Speakers

Speakers, trainers, staff

James Briscoe

The Francis Crick Institute

UK

Javier Buceta

Institute for Integrative Systems Biology (I²SysBio) CSIC-UV

Spain

Alex Fletcher

The University of Sheffield

UK

Jordi Garcia-Ojalvo

Universitat Pompeu Fabra

Spain

Yanlan Mao

MRC Laboratory for Molecular Cell Biology

UK

Berta Verd

University of Oxford

UK

Alexandria Volkening

Purdue University

USA

Scientific organisers

Event organisers

Julia Patricia Nohle

Course and Conference Officer

EMBL Heidelberg

Germany

Preliminary Programme

Day 1 – Saturday 14 June 2025
Time (Barcelona/Europe)SpeakerLocation
14:00 – 15:00Housenotes
Course Overview and Meet & Greet with welcome Drink & nibbles
15:00 – 15:45Bootcamp – Lecture 1
Why modelling biological systems? Basic mathematical concepts that serve to quantify biological processes

James Sharpe – EMBL Barcelona, Spain
Seminar Room
(Aula de Seminari)
15:45 – 16:45Bootcamp – Practical 1
main trainer: James Sharpe – EMBL Barcelona, Spain

– Practical exercises on laptops (introduction to programming): define a function, plot it, compute derivatives, explore Hill functions.
– Software: python code
Seminar Room
(Aula de Seminari)
16:45 – 17:15Coffee break
17:15 – 18:00Bootcamp – Lecture 2
Dynamics of gene regulation through ordinary differential equations (ODEs)
James Sharpe – EMBL Barcelona, Spain
Seminar Room
(Aula de Seminari)
18:00 – 19:00Bootcamp – Practical 2
Practical exercises on laptops:
– Numerically solve ODEs and plot the solutions
– analyse gene regulatory network dynamics
– Software: python code.
Seminar Room
(Aula de Seminari)
19:00 – 21:00DinnerOffsite
Day 2 – Sunday 15 June 2025
Time (Barcelona/Europe)SpeakerLocation
08:50 – 09:00Daily Testing and Welcome, overview of the day
09:00 – 09:45Bootcamp – Lecture 3
– Qualitative interpretation of the dynamics of GRN
– Phase portraits, fixed points and stability
Alejandro Torres-Sánchez – EMBL Barcelona, Spain
Seminar Room
(Aula de Seminari)
09:45 – 10:45Bootcamp – Practical 3
main trainer: Alejandro Torres-Sánchez – EMBL Barcelona, Spain

Practical exercises on laptops:
– Create phase portraits and detect fixed points in gene regulatory models
– Classify their stability
– Trajectories in phase space (connection with previous day)
– Software: python code.
Seminar Room
(Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Bootcamp – Lecture 4
Bifurcations: how phase portraits can qualitatively change leading to different biological behaviours

Alejandro Torres-Sánchez – EMBL Barcelona, Spain
Seminar Room
(Aula de Seminari)
12:00 – 13:00Bootcamp – Practical 4
main trainer: Alejandro Torres-Sánchez – EMBL Barcelona, Spain

Practical exercises on laptops:
– saddle-node & pitchfork bifurcations
– biological examples
– Software: python code.
Seminar Room
(Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Bootcamp – Lecture 5
Modelling oscillations in gene expression. Limit cycles. Hopf bifurcations.

Jordi Garcia-Ojalvo – Universitat Pompeu Fabra, Spain
Seminar Room
(Aula de Seminari)
14:45 – 15:45Bootcamp – Practical 5
main trainer: Jordi Garcia-Ojalvo – Universitat Pompeu Fabra, Spain

Practical exercises on laptops:
– Dynamics of gene regulation through ordinary differential equations (ODEs)
– Software: python code.
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 18:00Bootcamp debrief and discussionBreakout Area
18:00Free evening
Day 3 – Monday 16 June 2025
Time (Barcelona/Europe)SpeakerLocation
08:50 – 09:00Daily Testing and Welcome, overview of the day
09:00 – 09:45Lecture 6:
Spatial systems, partial differential equations, discretized continuum modelling of space / diffusion, different types of gradient formation, interpretation of a gradient – solving the French Flag Problem, scale invariance, positional information.

James Sharpe – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
09:45 – 10:45Practical 6
main trainer: James Sharpe – EMBL Barcelona, Spain
Practical exercises on laptops:
– Dynamics of gene regulation through ordinary differential equations (ODEs)
– Software: Limbnet
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 7:
Main classes of Turing pattern, spots versus stripes, boundary conditions, creating a Pearson plot, travelling waves versus stable patterns

James Sharpe – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
12:00 – 13:00Practical 7
main trainer: James Sharpe – EMBL Barcelona, Spain
Practical exercises on laptops:
– Dynamics of gene regulation through ordinary differential equations (ODEs)
– Software: Limbnet
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture 8:
Controlling self-organised patterns with positional information), how gradients could alter wavelength in 1D, how 2D gradients could alter the spatial patterns, example of limb development.
Limitations of modelling – what it can and cannot do

James Sharpe – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 8
main trainer: James Sharpe – EMBL Barcelona, Spain
Practical exercises on laptops:
– Qualitative interpretation of the dynamics of GRN
– Phase portraits, fixed points and stability
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 19:00Group project session IBreakout Area
19:00 – 20:00Keynote I: Using phase portraits to understand molecular pattern formation
Berta Verd – University of Oxford, United Kingdom
Seminar Room (Aula de Seminari)
20:00 – 22:00DinnerOffsite
Day 4 – Tuesday 17 June 2025
Time (Barcelona/Europe)SpeakerLocation
09:00 – 09:45Lecture 9
More complex spatial systems, Drosophila gap gene patterns, temporal integration, Sonic hedgehog in the neural tube, multiple gradients

Jordi Garcia-Ojalvo – Universitat Pompeu Fabra, Spain
Seminar Room (Aula de Seminari)
09:45 – 10:45Practical 9
main trainer: Jordi Garcia-Ojalvo + 4 assistants
Practical exercises on laptops on Bifurcations: how phase portraits can qualitatively change leading to different biological behaviours
Software: python code.
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 10
Understanding the sources and impact of noise in biological systems: gene regulatory networks

Jordi Garcia-Ojalvo – Universitat Pompeu Fabra, Spain
Seminar Room (Aula de Seminari)
12:00 – 13:00Practical 10
main trainer: Jordi Garcia-Ojalvo + 4 assistants
Practical exercises on laptops on Modelling oscillations in gene expression. Limit cycles. Hopf bifurcations
Software: python code.
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture 11
Understanding the sources and impact of noise in biological systems: spatial patterning

Jordi Garcia-Ojalvo – Universitat Pompeu Fabra, Spain
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 11
main trainer: Jordi Garcia-Ojalvo + 4 assistants
Practical exercises on laptops on Spatial systems, partial differential equations, discretized continuum modelling of space / diffusion, different types of gradient formation, interpretation of a gradient – solving the French Flag Problem, scale invariance, positional information.
Software: python code.
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 19:00Group project session IIBreakout Area
19:00 – 20:00Keynote II: Embryonic pattern formation
James Briscoe – Francis Crick Institute, United Kingdom
Seminar Room (Aula de Seminari)
20:00Free evening
Day 5 – Wednesday 18 June 2025
Time (Barcelona/Europe)SpeakerLocation
09:00 – 09:45Lecture 12
Basics of agent based modelling (ABM), different types of agent interaction, emergent behaviour in flocking. The simplifying assumptions, and possible pitfalls of the ABM approach

Alexandria Volkening – Purdue University, USA
Seminar Room (Aula de Seminari)
09:45 – 10:45Practical 12
main trainer: Alexandria Volkening – Purdue University, USA (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 13 (listed above)
Software: NetLogo (online)
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 13
Modelling pattern formation in an agent-based model, diffusion, gene regulation networks, and feedback on morphogenesis

Katie Bentley – Francis Crick Institute, UK
Seminar Room (Aula de Seminari)
12:00 – 13:00Practical 13
main trainer: Katie Bentley – Francis Crick Institute, UK (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 14 (listed above)
Software: NetLogo (online)
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture 14
Modelling complex tissues – stripe formation in zebrafish

Alexandria Volkening – Purdue University, USA
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 14
main trainer: Alexandria Volkening – Purdue University, USA (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 15 (listed above)
Software: NetLogo (online)
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 18:15Flash talksBreakout Area
18:15 – 19:00Networking and Meet the speakersBreakout Area
19:00 – 20:00Keynote III: Using Agent-based Models to explain vasculogenesis
Katie Bentley – Francis Crick Institute, UK
Seminar Room (Aula de Seminari)
20:00 – 22:00DinnerOffsite
Day 6 – Thursday 19 June 2025
Time (Barcelona/Europe)SpeakerLocation
09:00 – 09:45Lecture 15
Combining molecules with mechanics, molecular patterning in vertex models, using molecular patterns to control growth/morphogenesis, boundary sharpening, combining signalling and cell behaviour

Javier Buceta – I²SysBio, CSIC-UV, Spain
Seminar Room (Aula de Seminari)
09:45 – 10:45Practical 15
main trainer: Javier Buceta – I²SysBio, CSIC-UV, Spain (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 7 (listed above)
Software: Chaste
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 16
Morphogenesis, anisotropic growth / intercalation / T1,2,3 transitions, planar polarity

Javier Buceta – I²SysBio, CSIC-UV, Spain
Seminar Room (Aula de Seminari)
12:00 – 13:00Practical 16
main trainer: Javier Buceta – I²SysBio, CSIC-UV, Spain (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 8 (listed above)
Software: Chaste
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture 17
Combining molecules with mechanics, molecular patterning in vertex models, using molecular patterns to control growth/morphogenesis, boundary sharpening, combining signalling and cell behaviour

Javier Buceta – I²SysBio, CSIC-UV, Spain
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 17
main trainer: Javier Buceta – I²SysBio, CSIC-UV, Spain (+ 4 assistants)
Practical exercises on laptops on the topics of lecture 9 (listed above)
Software: Chaste
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 19:00Group project session IIIBreakout Area
19:00 – 20:00Keynote IV: Vertex modelling to explain epithelial development
Alex Fletcher – University of Sheffield, UK
Seminar Room (Aula de Seminari)
20:00Free evening
Day 6 – Friday 20 June 2025
Time (Barcelona/Europe)SpeakerLocation
09:00 – 09:45Lecture 18
The basics and maths of continuum mechanics, force vectors and stress tensors etc. linear elasticity and the stokes equations, basic example of non-uniform growth

Alejandro Torres Sanchez – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
09:45 – 10:45Practical 18
main trainer: Alejandro Torres-Sánchez – EMBL Barcelona, Spain

Practical exercises on laptops on the topics of lecture 10 (listed above)
Software: hiperlife.
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 19
Defining tissue geometries, manual creation of geometries / meshes, segmentation of tissue geometry from image data, triangulation / tetrahedralization, solving basic equations

Alejandro Torres Sanchez – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
12:00 – 13:00Practical 19
main trainer: Alejandro Torres-Sánchez – EMBL Barcelona, Spain

Practical exercises on laptops on the topics of lecture 11 (listed above)
Software: hiperlife
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture 20
Combining molecules with mechanics, molecular diffusion in FEM, simple example of feedback between molecular gradient and morphogenesis

Alejandro Torres Sanchez – EMBL Barcelona, Spain
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 20
main trainer: Alejandro Torres-Sánchez – EMBL Barcelona, Spain

Practical exercises on laptops on the topics of lecture 12 (listed above)
Software: hiperlife
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee break
16:15 – 17:15Keynote V: Using FEM to model how non-uniform proliferation rates lead to controlled buckling and bending of wing disc epithelium
Yanlan Mao – University College London, UK
Seminar Room (Aula de Seminari)
17:15 – 18:45Group project presentationsSeminar Room (Aula de Seminari)
18:45 – 19:45Wrap up discussion and course debrief
19:45 – 21:45DinnerOffsite

Practical Information

Registration fees and motivation letter

The course is limited to 20 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.

Registration

Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. This EMBO course includes accommodation and transportation to and from the hotel to the venue.

Academia€550
PhD Student€550
Industry€1100

NO visa support letters will be issued until payment of the registration fee is confirmed.

Confirmation and payment

The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.

Motivation letter submission

After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.

Instructions

  1. Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
  2. Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.

Please note:

  • The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
  • If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
  • If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

For detailed instructions, please watch our video on how to submit a course motivation letter.

Further details

For further information about registration and motivation letter submission please refer to the FAQ page.

Financial assistance

Financial assistance

Limited financial assistance is provided by EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site events and will be indicated during the abstract or motivation letter submission process.

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course or conference.

Travel grant

The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:
– up to €400 for any participant travelling to an EMBO Practical Course or EMBO Workshop.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course or EMBO Workshop.

*Registration fees are only covered for EMBO Practical Courses or EMBO Workshops

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap 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. Scanned copies cannot be accepted.

Childcare grant (EMBO Practical Courses and Workshops only)

For EMBO Practical Course or EMBO Workshop participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course or conference. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of 500 EUR can be awarded per participant applying for an EMBO Childcare Grant. In order to apply for this grant for EMBO Workshops, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds travel grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance at the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

You may apply for financial assistance when submitting your motivation letter for courses, and abstract for conferences. In your application, you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

For the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.

Selection

The scientific organisers will select the recipients of all financial assistance during the motivation letter or abstract selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection is based on your current work or study location, the reasons for needing financial support and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

See our list of external funding opportunities and information on attending a conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Accommodation and shuttles

Hotel

Accommodation has been pre-booked for you at a nearby hotel for the default dates of 14 June to 21 June 2025 (7 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfast.

Local transport

The hotel is just a few minutes from the Collaboratorium space where the practical course will be held

Further details

The address of the hotel will be communicated later in the process.

Event software

Event software

The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus. 

Sponsors

Sponsorship opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other events, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Warning

EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.

Please also note that:

  • EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
  • EMBL will never call or email you to ask for your credit card details or to request a payment.
  • All payments are on invoice.

Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.

Media kit

Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.

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Date: 14 - 20 Jun 2025

Location: EMBL Barcelona


Deadline(s):

Application: 8 Mar 2025


Organisers:

  • Katie Bentley
    The Francis Crick Institute, Kings College London, UK

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