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Computational modelling of multicellular systems – Course and Conference Office

EMBO Practical Course

Computational modelling of multicellular systems

Overview

Overview

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).

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.

Audience

This practical course is aimed at experimental biologists, including those with little or no experience in computer modelling, to become confident and familiar with these approaches and tools. We encourage applicants interested in exploring whether their current projects might benefit from computational modelling.

Modules/resources

  • Pattern formation I (gradients & interpretation).
  • Pattern formation II (self-organisation).
  • 2D vertex models of epithelia.
  • Finite Element Modelling of 3D tissues.
  • Agent-based Modelling of complex tissues.

Speakers

Speakers, trainers, and staff

Katie Bentley

The Francis Crick Institute, King’s College London

UK

Scientific organisers

Katie Bentley

The Francis Crick Institute, Kings College London

UK

Course organisers

Chris Stocks

Course and Conference Team Lead

EMBL Heidelberg

Preliminary Programme

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  • Some pre-course work (such as watching pre-recordings, protocol reading and computational exercises) with estimated time 0-10 hours will be required and will be shared in advance of the course.
  • Some speakers may need to join virtually to give their lecture or Q&A, and the programme is subject to change.
Day 1 – Sunday 18 June 2023
Time (Europe/Berlin)Speaker
17:30 – 19:00Course Overview and Meet and Greet
19:30 – 21:30Dinner
Day 2 – Monday 19 June 2023
Time (Europe/Berlin)Speaker
Topic for Day 2 – Pattern formation I (gradients & interpretation), primary trainer: Jordi Garcia Ojalvo
09:00 – 09:45Lecture 1: Gene regulation, ODEs, phase portraits, negative feedback homeostasis, mutual inhibition
Jordi Garcia Ojalvo – Pompeu Fabra University, Spain
09:45 – 10:45Practical 1: Practical exercises on laptops on the topics of the lecture: Gene regulation, ODEs, phase portraits, negative feedback homeostasis, mutual inhibition.
Software: python code

Jordi Garcia Ojalvo – Pompeu Fabra University, Spain + 4 assistants
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 2: Spatial systems, PDEs, discretised continuum modelling of space / diffusion, different types of gradient formation, interpretation of a gradient – solving the French Flag Problem, sScale invariance, positional information
Jordi Garcia Ojalvo – Pompeu Fabra University, Spain
12:00 – 13:00Practical 2: Practical exercises on laptops on the topics of lecture 2 (listed above). Software: python code
Jordi Garcia Ojalvo – Pompeu Fabra University, Spain + 4 assistants
13:00 – 14:00Lunch break
14:00 – 14:45Lecture 3: More complex spatial systems, Drosophila gap gene patterns, temporal integration, Sonic hedgehog in the neural tube, multiple gradients.
Limitations of modelling – what it can and cannot do.

Jordi Garcia Ojalvo – Pompeu Fabra University, Spain
14:45 – 15:45Practical 3: Practical exercises on laptops on the topics of lecture 3 (listed above). Software: python code
Jordi Garcia Ojalvo – Pompeu Fabra University, Spain + 4 assistants
15:45 – 16:15Coffee break
16:15 – 19:00Practical: Group Project Session
19:00 – 20:00Keynote lecture 1: Using phase portraits to understand molecular pattern formation
Berta Verd – Oxford University, UK
20:00 – 22:00Dinner
Day 3 – Tuesday 20 June 2023
Time (Europe/Berlin)Speaker
Topic for Day 3 – Pattern formation II (self-organisation), primary trainer: James Sharpe
09:00 – 09:45Lecture 4: Reaction-diffusion systems, diffusion-driven instability, Turing space within parameter space, how to adjust the wavelength
James Sharpe – EMBL Barcelona, Spain
09:45 – 10:45Practical 4: Practical exercises on laptops on the topics of lecture 4 (listed above). Software: SIMBIONT (online).
James Sharpe – EMBL Barcelona, Spain + 4 assistants
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 5: Main classes of Turing pattern, spots versus stripes, boundary conditions, creating a Pearson plot, travelling waves versus stable patterns
James Sharpe – EMBL Barcelona, Spain
12:00 – 13:00Practical 5: Practical exercises on laptops on the topics of lecture 5 (listed above). Software: SIMBIONT (online)
James Sharpe – EMBL Barcelona, Spain + 4 assistants
13:00 – 14:00Lunch break
14:00 – 14:45Lecture 6: 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. Controversies, and when modelling goes wrong (the mistaken Turing modelling of Drosophila segmentation).
James Sharpe – EMBL Barcelona, Spain
14:45 – 15:45Practical 6: Practical exercises on laptops on the topics of lecture 6 (listed above). Software: SIMBIONT (online)
James Sharpe – EMBL Barcelona, Spain + 4 assistants
15:45 – 16:15Coffee break
16:15 – 19:00Group Project Session
19:00 – 20:00Keynote lecture 2: Turing models to explain various examples of embryonic pattern formation
Tom Hiscock – Aberdeen University, UK
14:00 – 14:30Networking session (e.g. student talks, or quizz)
Day 4 – Wednesday 21 June 2023
Time (Europe/Berlin)Speaker
Topic for Day 4 – 2D vertex models of epithelia, primary trainer: Alex Fletcher
09:00 – 09:45Lecture 7: The basics and maths of vertex models, growth / proliferation, differential growth, shape creation. The simplifying assumptions, and possible pitfalls of vertex models.
Alex Fletcher – Sheffield University, UK
09:45 – 10:45Practical 7: Practical exercises on laptops on the topics of lecture 7 (listed above). Software: Chaste.
Alex Fletcher – Sheffield University, UK + 4 assistants
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 8: Morphogenesis, anisotropic growth / intercalation / T1,2,3 transitions, planar polarity
Alex Fletcher – Sheffield University, UK
12:00 – 13:00Practical 8: Practical exercises on laptops on the topics of lecture 7 (listed above). Software: Chaste.
Alex Fletcher – Sheffield University, UK + 4 assistants
13:00 – 14:00Lunch
14:00 – 14:30Networking session (e.g. student talks, or quizz)
14:00 – 14:45Lecture 9: Combining molecules with mechanics, molecular patterning in vertex models, using molecular patterns to control growth/morphogenesis, boundary sharpening, combining signalling and cell behaviour
Alex Fletcher – Sheffield University, UK
14:45 – 15:45Practical 9: Practical exercises on laptops on the topics of lecture 9 (listed above). Software: Chaste.
Alex Fletcher – Sheffield University, UK + 4 assistants
15:45 – 16:15Coffee break
16:15 – 18:15Flash talks – All participants will give a 3 minute presentation about their project most relevant to the course, with 2 minutes for questions.
18:15 – 19:00Informal discussions / networking
19:00 – 20:00Keynote lecture 3: Vertex modelling to explain epithelial development
Javier Buceta – Alicante University, Spain
20:00Free evening
Day 5 – Thursday 22 June 2023
Time (Europe/Berlin)Speaker
Topic for Day 5 – Finite Element Modelling of 3D tissues, primary trainer: Alejandro Torres Sanchez
09:00 – 09:45Lecture 10: The basics and maths of finite element models, force vectors and stress tensors etc. linear elasticity and the stokes equations, basic example of non-uniform growth
Alejandro Torres Sanchez – EMBL Barcelona, Spain
09:45 – 10:45Practical 10: Practical exercises on laptops on the topics of lecture 10 (listed above). Software: Fenics.
Alejandro Torres Sanchez – EMBL Barcelona, Spain + 4 assistants
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 11: 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
12:00 – 13:00Practical 11: Practical exercises on laptops on the topics of lecture 11 (listed above). Software: Fenics.
Alejandro Torres Sanchez – EMBL Barcelona, Spain + 4 assistants
13:00 – 14:00Lunch
14:00 – 14:30Networking session (e.g. student talks, or quizz)
14:00 – 14:45Lecture 12: Combining molecules with mechanics, molecular diffusion in FEM, simple example of feedback between molecular gradient and morphogenesis.
Alejandro Torres Sanchez – EMBL Barcelona, Spain
14:45 – 15:45Practical 12: Practical exercises on laptops on the topics of lecture 12 (listed above). Software: Fenics.
Alejandro Torres Sanchez – EMBL Barcelona, Spain + 4 assistants
15:45 – 16:15Coffee break
16:15 – 19:00Group Project Session
19:00 – 20:00Informal discussions / networking
19:00 – 20:00Keynote lecture 4: Using FEM to model how non-uniform proliferation rates lead to controlled buckling and bending of wing disc epithlium
Yanlan Mao – University College London, UK
20:00 – 22:00Dinner
Day 6 – Friday 23 June 2023
Time (Europe/Berlin)Speaker
Topic for Day 6 – Agent-based Modelling of complex tissues, primary trainer: Katie Bentley
09:00 – 09:45Lecture 13: 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
Katie Bentley – The Francis Crick Institute, Kings College London, UK
09:45 – 10:45Practical 13: Practical exercises on laptops on the topics of lecture 13 (listed above). Software: NetLogo (online).
Katie Bentley – The Francis Crick Institute, Kings College London, UK + 4 assistants
10:45 – 11:15Coffee break
11:15 – 12:00Lecture 14: Modelling pattern formation in an agent-based model, diffusion, gene regulation networks, and feedback on morphogenesis
Katie Bentley – The Francis Crick Institute, Kings College London, UK
12:00 – 13:00Practical 14: Practical exercises on laptops on the topics of lecture 14 (listed above). Software: NetLogo (online).
Katie Bentley – The Francis Crick Institute, Kings College London, UK + 4 assistants
13:00 – 14:00Lunch
14:00 – 14:45Lecture 15: Modelling complex tissues – vasculogenesis
Katie Bentley – The Francis Crick Institute, Kings College London, UK
14:45 – 15:45Practical 15: Practical exercises on laptops on the topics of lecture 15 (listed above). Software: NetLogo (online).
Katie Bentley – The Francis Crick Institute, Kings College London, UK + 4 assistants
15:45 – 16:15Coffee break
16:15 – 17:15Keynote lecture 5: Using Agent-based Models to explain stripe formation in zebrafish
Alexandria Volkening – Purdue University, USA
17:15 – 18:45Group Project Session
19:00 – 20:00Final wrap-up discussion
20:00 – 22:00Dinner & Farewell

Practical Information

Registration fees and motivation letter

The course is limited to 24 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€450
PhD Student€450
Industry€1000

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 €500 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 18 June to 23 June (6 nights). Please note that the course registration fee includes coverage of accommodation costs in twin rooms, including breakfast.

Local transport

The hotel is just an 8 minute walk from the Collaboratorium space where the practical course will be held

Further details

Address: Hotel H10 Marina; Olympic Village, Av. del Bogatell, 64, 68, 08005 Barcelona, Spain

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: 18 - 23 Jun 2023

Location: EMBL Barcelona


Deadline(s):

Application: Closed


Organisers:

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

EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

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