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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

Javier Buceta

Institute for Integrative Systems Biology (I2SysBio)

CSIC-UV

Spain

Scientific organisers

Katie Bentley

The Francis Crick Institute, Kings College London

UK

Course organisers

Chris Stocks

Course and Conference Team Lead

EMBL Heidelberg

Julia Pi Lopez

Collaboratorium Project Manager

EMBL Barcelona, Spain

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 Location
18:00 – 19:00Course Overview and Meet and GreetH10 Marina
19:30 – 21:30DinnerH10 Marina
Day 2 – Monday 19 June 2023
Time (Europe/Berlin)SpeakerLocation
08:30 – 09:00Welcome to Collaboratorium Barcelona Collaboratorium
Topic for Day 2 – Agent based modelling
Primary trainer: Katie Bentley
Collaboratorium Edifici Pasqual Maragall, 2nd Floor
09:00 – 10:45Lecture 1 & Practical 1: Introduction to designing ABMSSeminar Room (Aula de Seminari)
10:45 – 11:15Coffee breakBreakout Area
11:15 – 13:00Lecture & Practical 2 “calibrating, validating and analysing ABMs”
Seminar Room (Aula de Seminari)
13:00 – 14:00Lunch breakUPF Canteen
14:00 – 15:45Lecture & Practical 3 “advanced concepts”Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee breakBreakout Area
16:15 – 19:00Practical: Group Project Session
1) ABM project
2) Vertex model project
3) Pattern Formation in tissues
4) Patterning on moving cells
5) FEM project


1 – Aula Seminari
2 – Sala de Reunions 1
3 – Sala de Reunions 2
4 – Break Out Area 1 (right wing)
5- Break Out Area 2 (left wing)
19:00 – 20:00Keynote lecture 1: Using Agent-based Models to explain stripe formation in zebrafish
Alexandria Volkening – Purdue University, USA
**this talk is remote**
20:30 – 22:00Dinner at Flax & Kale
Day 3 – Tuesday 20 June 2023
Time (Europe/Berlin)SpeakerLocation
Topic for Day 3 – Vertex Models.
Primary trainer: Alex Fletcher
09:00 – 10:45Lecture & Practical 1 “Basics”Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee breakBreakout Area
11:15 – 13:00Lecture & Practical 2 “Morphogenesis” Seminar Room (Aula de Seminari)
13:00 – 14:00Lunch breakUPF Canteen
14:00 – 15:45Lecture & Practical 3 “Combining molecules with mechanics” Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee breakBreakout Area
16:15 – 19:00Practical: Group Project Session
1) ABM project
2) Vertex model project
3) Pattern Formation in tissues
4) Patterning on moving cells
5) FEM project

1 – Aula Seminari
2 – Sala de Reunions 1
3 – Sala de Reunions 2
4 – Break Out Area 1 (right wing)
5- Break Out Area 2 (left wing)
19:00 – 20:00Keynote lecture 2: Vertex modelling to explain epithelial development
Javier Buceta – Alicante University, Spain
Seminar Room (Aula de Seminari)
20:00 – 22:30Dinner at Café Menssana
Day 4 – Wednesday 21 June 2023
Time (Europe/Berlin)SpeakerLocation
Topic for Day 4 – Pattern Formation
Primary trainer: James Sharpe
09:00 – 10:45Lecture & Practical 1
– Introduction to molecular patterning and the LimbNET tool
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee breakBreakout Area
11:15 – 13:00Lecture & Practical 2
– Morphogen gradients and downstream targets
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 14:45Lecture & Practical 3 – Regionalisation in a 2D domainSeminar Room (Aula de Seminari)
14:45 – 15:45Lecture & Practical 4 – Periodic patterns from reaction-diffusion circuitsSeminar Room (Aula de Seminari)
15:45 – 16:15Coffee breakBreakout Area
16:15 – 19:00Networking & Flash talks Seminar Room (Aula de Seminari)
19:00 – 20:00Keynote lecture 3: Title to be confirmed
Tom Hiscock – Aberdeen University (UK)
Seminar Room (Aula de Seminari)
20:00Free evening
Day 5 – Thursday 22 June 2023
Time (Europe/Berlin)SpeakerLocation
Topic for Day 5 – GRN Dynamics and cellular movements Primary trainer: Berta Verd
09:00 – 10:45Lecture & Practical 1
Exploring the relationship between network topology, network parameters, phase space geometry, initial conditions and expression dynamics
Seminar Room (Aula de Seminari)
10:45 – 11:15Coffee breakBreakout Area
11:15 – 13:00Lecture & Practical 2
– Dynamical systems and simulating on moving cells
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:00 – 15:45Lecture & Practical on VEDO
– A python module for scientific analysis and visualization of 3D objects
Seminar Room (Aula de Seminari)
14:45 – 15:45Practical 12: Practical exercises on laptops Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee breakBreakout Area
16:15 – 19:00Practical: Group Project Session
1) ABM project
2) Vertex model project
3) Pattern Formation in tissues
4) Patterning on moving cells
5) FEM project


1 – Aula Seminari
2 – Sala de Reunions 1
3 – Sala de Reunions 2
4 – Break Out Area 1 (right wing)
5- Break Out Area 2 (left wing)
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
**This talk is virtual**
20:30 – 22:00Dinner at Ovella Negra
Day 6 – Friday 23 June 2023
Time (Europe/Berlin)SpeakerLocation
Topic for Day 6 – Finite element models,
Primary trainer: Alejandro Torres-Sánchez
09:00 – 10:45Lecture & Practical 1 – Introduction to elasticity, viscosity and plasticity in cell and tissue mechanicsSeminar Room (Aula de Seminari)
10:45 – 11:15Coffee breakBreakout Area
11:15 – 13:00Lecture & Practical 2
– Continuum modelling. Stress, strain; stress rate, strain rate.
– Finite element simulations. Indentation test.
Seminar Room (Aula de Seminari)
13:00 – 14:00LunchUPF Canteen
14:45 – 15:45Lecture & Practical 3
– Modelling activity: active gel models.
– Finite element simulations of mechanical patterning.
Seminar Room (Aula de Seminari)
15:45 – 16:15Coffee breakBreakout Area
16:15 – 19:00Group Project PresentationsSeminar Room (Aula de Seminari)
19:00 – 20:00Final wrap-up discussionSeminar Room (Aula de Seminari)
21:00 – 22:30Dinner & FarewellH10 Marina

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

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