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Transitions in developing systems: from theory to experiments – Course and Conference Office

EMBL Course

Transitions in developing systems: from theory to experiments

Overview

Course overview

Developing systems at all biological scales are subject to transitions between states of collective organisation that are critical for their function and evolution. The study of transitions requires bridging biological scales and integrating diverse disciplines, including statistical physics, nonlinear dynamics, and developmental biology. Recent technological advances in quantitative biology, the acquisition of big data and machine-learning based analysis now make it possible to study this topic.

This course will give applicants the unique opportunity to closely interact with a diverse group of renowned scientists (speakers/trainers) who work on biological transitions in fundamental developmental processes including morphogenesis, signal transduction, gene expression, collective cell and animal behaviour. Participants will be introduced to the theoretical knowledge of biological transitions and get hands-on training using state-of-the-art methods applied in-depth in different model systems.

Audience

This course is intended for graduate students and post-doctoral fellows with a STEM background. We aim to balance the number of participants with hands-on experience and theoretical background. A key criterion for selection is the potential benefit of adding novel developmental biology and biophysics methods to the participant’s own research.

Modules/resources

  • Theory of phase transitions, critical and bifurcation points
  • Uni- to multi- cellular transitions in slime molds
  • Material phase transitions in zebrafish embryos
  • Life cycle transitions in planarian flatworms
  • Body shape transitions in cnidarians

Learning outcomes

  • Inter-disciplinary methods
  • Highly multiplexed RNA fluorescent in situ hybridisation
  • Quantitative imaging and analysis
  • Machine learning based image segmentation
  • Biophysics analysis
  • Dynamical systems theory
  • Feedback microscopy
  • Hands on with single cell RNA-sequencing
  • Diverse organisms, incl zebrafish, dicty, nematostella, medaka, planaria

What past participants say about the course

Attending ‘Plasticity in developing systems’ [previous title] was a fantastic experience as an ECR. We took part in hands-on practical sessions exploring the relationship between environment and development in a range of organisms, attended inspired curiosity-driven research lectures and had the opportunity to meet and work alongside incredible young scientists. This is the future of Developmental Biology!” – Jennifer Love, University of Manchester, UK

As a PhD student coming from an engineering background, the exposure to a wide variety of experimental techniques and organisms played a crucial role in shaping my postdoc and future research aspirations. Additionally, the remarkable quality of speakers and trainers added to the overall excellence of the experience.” – Guillermo Yáñez Feliú, Newcastle University, UK

Please see EMBL’s COVID-19 safety recommendations for testing and other requirements to attend this on-site course.

Speakers

Speakers, trainers, and staff

Karen Alim

TU Munich

Germany

Alexander Aulehla

EMBL Heidelberg

Germany

Matthew Benton

EMBL Heidelberg

Germany

James Briscoe

The Francis Crick Institute

UK

Thibaut Brunet

Institut Pasteur

France

Iain Couzin

Max Planck Institute of Animal Behaviour

Germany

Mireia Garriga-Canut

EMBL Heidelberg

Germany

Isabella Graf

EMBL Heidelberg

Germany

Aissam Ikmi

EMBL Heidelberg

Germany

Caren Norden

Gulbenkian Institute for Molecular Medicine

Portugal

Nicoletta Petridou

EMBL Heidelberg

Germany

Guillaume Salbreux

Université de Genève

Switzerland

Jordi van Gestel

EMBL Heidelberg

Germany

Hanh Vu

EMBL Heidelberg

Germany

Scientific organisers

Karen Alim

TU Munich

Germany

James Briscoe

The Francis Crick Institute

UK

Nicoletta Petridou

EMBL Heidelberg

Germany

Jordi van Gestel

EMBL Heidelberg

Germany

Hanh Vu

EMBL Heidelberg

Germany

Course organisers

Luana Ribeiro

Course and Conference Officer

EMBL Heidelberg

Germany

Swetlana Krez

Swetlana Krez

Scientific Training

Officer

EMBL Heidelberg

Germany

Alessandra Reversi

EMBL Heidelberg

Germany

Preliminary programme

Are you on social media? Post using #EMBLDevBio and don’t forget to tag @EMBLEvents.

  • Some pre-course work (such as watching pre-recordings and protocol reading) 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 – Wednesday 2 July 2025

Time (Europe/Berlin)Speaker
08:40 – 09:30Welcome, house notes and course overview
09:30 – 10:30Flashtalks
10:30 – 11:00Coffee break
11:00 – 12:00Lecture: From unicellularity to multicellularity
Thibaut Brunet – Institut Pasteur, France
12:00 – 13:00Lunch
13:00 – 14:00Meet the speaker
Thibaut Brunet – Institut Pasteur, France
14:00 – 15:00Introduction to practical 1: Theory of phase transitions, critical and bifurcation points
Isabella Graf – EMBL Heidelberg, Germany
James Briscoe – The Francis Crick Institute, UK
15:00 – 19:00Practical session 1: Theory of phase transitions, critical and bifurcation points
Isabella Graf – EMBL Heidelberg, Germany
James Briscoe – The Francis Crick Institute, UK
1 trainer from Briscoe lab
1 trainer from Alim lab
2 trainers from the Graf group
19:00 – 20:00Dinner
Day 2 – Thursday 3 July 2025

Time (Europe/Berlin)Speaker
09:20 – 09:30Overview of the day
Nicoletta Petridou – EMBL Heidelberg, Germany
09:30 – 10:30Lecture: Biological physics and morphogenesis
Karen Alim – TU Munich, Germany
10:30 – 11:00Coffee break
11:00 – 12:00Meet the speaker
Karen Alim – TU Munich, Germany
12:00 – 13:00Lunch
13:00 – 13:30Introduction to practical 2: Aggregative development in wildtype slime mold species
Jordi van Gestel – EMBL Heidelberg, Germany
13:30 – 18:00Practical session 2: Aggregative development in wildtype slime
mold species
Jordi van Gestel – EMBL Heidelberg, Germany
4 trainers from the van Gestel group
18:00 – 19:00Dinner
19:00 – 21:00Poster Session 1 (odd numbers)
Day 3 – Friday 4 July 2025

Time (Europe/Berlin)Speaker
09:20 – 09:30Overview of the day
James Briscoe – The Francis Crick Institute, UK
09:30 – 10:30Lecture: Theoretical physics of biological development
Guillaume Salbreux – University of Geneva, Switzerland
10:30 – 11:00Coffee break
11:00 – 12:00Meet the speaker
Guillaume Salbreux – University of Geneva, Switzerland
12:00 – 13:00Lunch
13:00 – 13:30Introduction to practical 3A: Tissue material phase transitions in developing zebrafish embryos
Nicoletta Petridou – EMBL Heidelberg, Germany
13:30 – 14:00Introduction to practical 3B: TBC
Alexander Aulehla – EMBL Heidelberg, Germany
14:00 – 18:30Practical session 3A: Tissue material phase transitions in developing zebrafish embryos
Nicoletta Petridou – EMBL Heidelberg, Germany
2 trainers from the Petridou group
14:00 – 18:30Practical session 3B: TBC
Alexander Aulehla – EMBL Heidelberg, Germany
2 trainers from the Aulehla group
18:30 – 19:30Dinner
19:30 – 21:30Poster Session 2 (even numbers)
Day 4 – Saturday 5 July 2025

Time (Europe/Berlin)Speaker
08:50 – 09:00Overview of the day
Karen Alim – TU Munich, Germany
09:00 – 12:00Data analysis for Practicals 2, 3 A & B
Trainers from van Gestel, Petridou and Aulehla groups
12:00 – 13:00Lunch
13:00 – 13:30Introduction to practical 4: Size-dependent physiological changes during
the life cycle of planarian flatworms
Hanh Vu – EMBL Heidelberg, Germany
13:30 – 18:00Practical session 4: Size-dependent physiological changes during the life cycle of planarian flatworms
Hanh Vu – EMBL Heidelberg, Germany
4 trainers from the Vu group
18:00 – 19:00Dinner
Day 5 – Sunday 6 July 2025

Time (Europe/Berlin)Speaker
00:00 – 00:00Free day
Day 6 – Monday 7 July 2025
Time (Europe/Berlin)Speaker
09:20 – 09:30Overview of the day
Jordi van Gestel – EMBL Heidelberg, Germany
09:30 – 10:30Lecture: TBC
Caren Norden – Gulbenkian Institute for Molecular Medicine, Portugal
10:30 – 11:00Coffee break
11:00 – 12:00Meet the speaker
Caren Norden – Gulbenkian Institute for Molecular Medicine, Portugal
12:00 – 13:00Lunch
13:00 – 13:30Introduction to practical 5: Control of the larva-polyp transition via nerve-derived factors
Aissam Ikmi – EMBL Heidelberg, Germany
13:30 – 18:00Practical session 5: Control of the larva-polyp transition via nerve-derived factors
Aissam Ikmi – EMBL Heidelberg, Germany
4 trainers from the Ikmi group
18:00 – 19:00Dinner
19:00 – 21:00Discussion: Responsible conduct of Research led by the organisers
Day 7 – Tuesday 8 July 2025
Time (Europe/Berlin)Speaker
09:20 – 09:30Overview of the day
Hanh Vu – EMBL Heidelberg, Germany
09:30 – 10:30Lecture: Fundamental principles of collective animal behaviour
Iain Couzin – MPI, Germany
10:30 – 11:00Coffee break
11:00 – 12:00Meet the speaker
Iain Couzin – MPI, Germany
12:00 – 13:00Lunch
13:00 – 15:00Data analysis for practicals 4 and 5
Trainers from Vu and Ikmi groups
15:00 – 18:00Preparation time for student presentations/extra time to visit the lab and ask questions to the DB trainers
18:00 – 22:00BBQ and Party
Day 8 – Wednesday 9 July 2025

Time (Europe/Berlin)Speaker
08:50 – 09:00Overview of the day
09:00 – 10:30Student presentations
10:30 – 11:00Coffee break
11:00 – 12:00Feedback session
12:00 – 13:00Lunch

Practical information

Registration fees and motivation letter

The course is limited to 16 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, meals and coffee breaks.

This course includes accommodation and transportation to and from the ISG Hotel to the venue. The reduced fees and accommodation are covered thanks to the Theory@EMBL Transversal Theme.

Academia€550
PhD Student€550
Industry€1200

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

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 the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waiverstravel grants and childcare grants

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.

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 participants travelling to an EMBL Course within Europe.

– up to €1000 for participants travelling to an EMBL Course from outside Europe.

– up to €500 for any participant travelling to an EMBO Practical Course.

– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.

*Registration fees are only covered for EMBO Practical Courses

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 grants

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. Please note that priority will be given to early-stage researchers. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

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 to 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

If you are attending virtually, you can apply for financial assistance in the submission portal by the abstract deadline. Read the instructions on how to apply for financial assistance. Only submissions for financial assistance will be accepted. Presentation abstracts cannot be submitted here and will be declined. 

In your application you will be asked to summarise your current work,  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 some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the participant selection process for courses. 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 for registration fee waivers and travel grants is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Childcare grants will be allocated in the same timeframe (6-8 weeks before the event start date). Please note that priority will be given to early-stage researchers.

Further details

Check out this list of external funding opportunities.

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

Accommodation and travel

Hotel

Accommodation is not included in the registration fee. Participants are expected to book and pay for their own accommodation.

A mix of single and twin rooms have been reserved for 8 nights from 1 to 9 July 2025 at the ISG Hotel. Single rooms are limited and will be available on a first come, first served basis.

After the selection process, selected participants should contact the hotel directly to make a booking with a booking code (PTD25-01) by the deadline of 31 May 2025.

We recommend that all course participants stay at the dedicated hotel for the course.

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

Local transport

Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.

Further details

Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

For more information about accommodation and travel, please refer to the FAQ page.

On-site information

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the laboratories.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk..

EMBL Merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order or get in contact with your Course Organiser.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

Health and safety notes

Please read EMBL’s COVID-19 safety policy for on-site events.
Do not smoke in any EMBL building.
Eating and drinking is prohibited in all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

  • The first aid room is located next to the ATC Registration Desk (room 10- 205).
  • Dial the Emergency number 222 from any EMBL internal phone only.
  • Where is the accident? What happened? How many injured?
  • Emergency number 06221-387 7821 from mobile phones.
  • Please report all accidents to the conference officer at the registration desk.

In case of fire …

  • Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
  • A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
  • Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus. Log in using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga, and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Event software

Additional 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. 

Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.

Other information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Additional information

Please find additional information including FAQs and terms and conditions on our Information for Participants page.

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: 2 - 9 Jul 2025

Location: EMBL Heidelberg

Venue: EMBL Advanced Training Centre


Deadline(s):

Application: 26 Mar 2025


Organisers:

  • Karen Alim
    Technical University of Munich, Germany
    • James Briscoe
      The Francis Crick Institute, UK

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