Modeling Shape and Size in Biological Development

- This workshop is organized online -

24 - 28 August 2020

Venue: Lorentz Center@Virtual

If you are invited or already registered for this workshop, you have received login details by email.

On Thursday 27 August at 20:00 an online lecture is organized by James Sharpe. https://video.leidenuniv.nl/media/1_gqixuilc

One of the key central questions in biology is the emergence of shape and pattern during embryo development, in the process known as morphogenesis.  How can the sequential information in the genome translate to three-dimensional biological form and function? To answer this question, developmental biology has recently seen a shift in focus to coupling molecular and genomic level processes with the biomechanics of cells and tissues. This shift has in part been driven by the availability of advanced live imaging methodology, as well as by techniques that have made it possible to mechanically probe and perturb embryos at the single-cell, as well as the whole tissue scale.

To interpret these data and to develop hypotheses that can be tested using these techniques, multiscale mathematical and computational modeling have become central tools in this new field that can be called “Multiscale mathematical and computational developmental biology”, for lack of a better, shorter name.   Modeling in developmental biology differs from the mathematical modeling of other aspects in biology, in that the background topology and geometry on which the dynamics of patterning and information processing play out are themselves dynamic. Some of the latest results in this field were presented in the recently published Special Issue of the Bulletin of Mathematical Biology “Multi-scale Modeling of Tissue Growth and Shape ”Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, Eric Mjolsness, Editors, Volume 81, Issue 8, August 2019.

Scientific Aims: The summer school will focus on multiscale models in Developmental Biology rooted in the cellular level, i.e. models making links between cellular processes such as cellular growth and division, cell movement and interaction with the extracellular matrix (ECM), mechanical or chemical signaling between cells, etc. and organ shape development at higher spatial scales. This summer school will focus on mechanistic modeling skills, while integration of imaging and data analysis tools (e.g., deep learning) - however important - can only be illustrated in the keynote lectures.
The scientific aim will be to establish Multiscale Mathematical and Computational Developmental Biology as a field, and to define the theoretical foundations and practical skills that need to be mastered for researchers to be successful in this field.

Educational Aims: As a student in the school, you will be exposed to state-of-the-art examples of multiscale modeling in development. Through project work in collaboration with one of the lecturers, you will get hands-on experience with the development of mathematical and computational models. In a small team, you will develop a simple, but novel example model to answer an open scientific question proposed by the lecturers. For example, the lecturer could show interesting imaging data. In your team you will then discuss what existing models are available to explain the phenomena shown by the data, and develop predictive models based on these.

You will be required to have already some experience in modeling, but will be asked to work with a method that is new to you.

Follow-up of the workshop: Scientific aims and educational aims will be integrated with the final aim to define this emerging field, and mark its development with an educational textbook that will help train new students in the field. The book will be research oriented: examples will be developed from actual, state-of-the-art as well as novel research questions. Based on the final output of the workshop, we will solicit input and advice from the community, including contributors who were unable to participate in the workshop.

Speakers of the workshop are:

Arjen Doelman, James Sharpe, Alexandria Volkening, Jeremiah Zartman, Richard Smith, Veronica Grieneisen, Emmanuel Fuare and Alexander Fletcher.

Read more...

    Monday 24 August

    The links to the online lectures are included in the "Updated Program with lecture links” that you can find under “Workshop Files”, after logging in with the user name and password that you have obtained from the Lorentz Center. 

    All times indicated in the live programme are at Central European Summer Time (CEST)

     

    Theme: Stochastic discrete dynamical systems

    ------Asynchronous events------

    Keynote lecture on exemplary research project - Philip Maini, U Oxford

    Recorded Educational Lectures:
    Physics-based modeling I: Roeland Merks, U Leiden

    Physics-based modeling II: Mark Alber, U Leiden

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    All times indicated in the live programme are at Central European Summer Time (CEST)

    09:30 - 10:00 LIVE-CEST-time zone arrival to the Kalture Live Room informal chats and coffee
    10:00 - 10:15 LIVE & prerecorded -Welcome and instruction by Lorentz Center 
    10:15 - 10:45 LIVE- Introduction of workshop goals by organizers (will be recorded) 
    10:45 - 14:30 Asynchronous events / Working collaboration groups (European Time Zones)
    These take place in the individual Live Rooms that have been prepared for each team. See list "Live Rooms Kaltura" on Lorentz Workshop site (password protected part)

    17:00 - 18:00 Kaltura LIVE- Students introduce themselves and present their plans in one-minute presentations as prepared in advance of the course - chair Roeland Merks
    18:00 - 19:00 Kaltura Live Q&A session with speakers - ask questions through Slack in channel #questions4speakers - chair Christophe Godin
    20:00 - 22:00 Kaltura LIVE- "Wine & Cheese, Muffins & Coffee " - informal after-breakfast/after dinner chats - on Kaltura

    22:00 - 03:00 Asynchronous events / Working collaboration groups (California Time Zones)

     

    The programme will be announced shortly.

    Tuesday 25 August

    Theme: Continuous dynamical systems

    Themes for the day:
    ● Continuous mathematical models of pattern formation
    ● Mathematical techniques: ODEs, PDEs 

    ------Asynchronous events------

    Keynote Lecture on exemplary research project - Arjen Doelman, U Leiden, reaction-diffusion systems of pattern formation
    Keynote lecture on an exemplary research project - James Sharpe, EMBL Barcelona
    Keynote Lecture 1 - Exemplary research project: Alexandria Volkening, Northwestern University, Evanston, IL, USA

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    8:30 - 9:30    Kaltura Virtual walk-in coffee break/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advice from the other participants
    9:30 - 17:00  Kaltura Asynchronous events / Working collaboration groups (European Time Zones)

    17:00 -18:00  Kaltura Live Q&A session with speakers - ask questions through Slack in channel #questions4speakers - chair Philip Maini
    18:00 - 23:30 Kaltura - Asynchronous events / Working collaboration groups (Californian Time Zones)

    23:30 - 0:00   Kaltura - Virtual walk-in afternoon tea/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advice from the other participants

     

     

    The programme will be announced shortly.

    Wednesday 26 August

    Theme: Animal Developmental Biology

    ● Cell-based modeling of animal pattern formation
    ● Application of machine learning to microscopical image analysis
    ● Mathematical modeling techniques: Cellular Potts model, vertex-based modeling, subcellular element modeling, techniques for modeling the extracellular matrix, hybrid and multiscale modeling, etc.

    ------Asynchronous events------

    Recorded Keynote Lecture - Exemplary Research Project: Jeremy Zartman, Department of Chemical and Biomolecular Engineering, University of Notre Dame, IN, USA

    Recorded Keynote Lecture - Exemplary Research Project: René Doursat, Complex Systems Institute, Paris Ile-de-France (ISC-PIF), CNRS

     ------------------------------------------------------------------------------------------------------------------------------

      8:30 - 9:00   Kaltura - Virtual walk-in coffee break/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advise from the other participants
    10:30 - 17:00 Kaltura - Asynchronous events / Working collaboration groups
    17:00 - 18:00 Kaltura - LIVE Q&A Session with speakers - ask questions through Slack in channel #questionsforspeakers - chair Mark Alber
    18:00 - 19:00 Kaltura - Online social 'dinner' event

    21:00 - 03:30 Kaltura - Asynchronous events / Working collaboration groups (Californian Time Zones)
    23:30 - 00:00 Kaltura - Virtual walk-in afternoon tea/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advise from the other participants

      

    The programme will be announced shortly.

    Thursday 27 August

    Theme: Plant Developmental Biology 

    ● Mathematical modeling of auxin fluxes in plants
    ● Modeling of the shoot apical meristem development and phyllotaxis
    ● Mathematical modeling techniques:  3D vertex-based models, coupled ODEs and PDEs, L-systems, etc. 

    ------Asynchronous events------

    Recorded keynote lecture on exemplary research project in plant research - Richard Smith, John Innes Centre

    Computational MorphoMechanX part 1
    Computational MorphoMechanX part 2
    Computational MorphoMechanX part 3 

    Recorded keynote lecture on exemplary research project -Verônica Grieneisen, U Cardiff
    Recorded Educational lecture: Modeling shoot apical development: concepts, computational and mathematical tools - Christophe Godin

    LIVE Public Lecture James Sharpe: https://www.lorentzcenter.nl/turing-patterns-on-turing-machines.html
    https://video.leidenuniv.nl/media/1_gqixuilc

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      8:30 - 9:00    Kaltura - Virtual walk-in coffee break/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advice from the other participants
      9:00 - 17:00  Kaltura - Asynchronous events / Collaboration working groups (Central European Time Zone)
    17:00 - 18:00  kaltura - Live Q&A session with speakers - ask questions through Slack in channel #questions4speakers (Chair: Gabriela Mosca (t.b.c))

    19:45 - 20:00 Kaltura - Entering the virtual Lorentz Center room (Register first, see below)
    20:00 - 20:45 Kaltura - Start lecture by James Sharpe: Register here: https://www.lorentzcenter.nl/turing-patterns-on-turing-machines.html
    20:45 - 21:00 Kaltura - Questions and discussion

    18:00 - 00:30  Kaltura - Asynchronous events / Working collaboration groups (Californian Time Zones)
    23:30 - 00:00  Kaltura - Virtual walk-in afternoon tea/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advise from the other participants

     

    The programme will be announced shortly.

    Friday 28 August

    Theme: Computational Implementation 

    ● Visualizing complex data” 4D exploration of embryo development, 4D atlases of gene to shape connection, connection to databases
    ● Use of machine learning for segmentation and augmentation of complex data
    ● Reproducibility of models,  research ethics in mathematical modeling.

    ● Implementation issues & energy-efficient computing: numerical methodology

     ------Asynchronous events------

    Recorded Keynote lecture 1 on exemplary research project - Emmanuel Faure -Recorded Keynote Lecture 2 - Exemplary Research Project: Emmanuel Faure, CNRS , Laboratoire d’Informatique, de Robotique et de Microélectronique de Montpellier

    Recorded Keynote Lecture 2 on computational implementation issues - Alexander Fletcher, U Sheffield

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      8:30 - 9:00   Kaltura - Virtual walk-in coffee break/late-night snack. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advice from the other participants
      9:00 - 16:00 Kaltura -  Asynchronous events / Collaboration working groups (Central European Time Zone)
    16:00 - 18:00 Kaltura - Live Final Presentations of Projects and Plans for Follow Up (10 minutes)

    1. Modelling Multicellular Tissue 
    2. Modeling lateral inhibition patterning 
    3. Mechanisms underlying cell growth and cell division involved in stem cell homeostasis in plants 
    4. Dependence of the shape of epithelial tissue on subcellular mechanics and  signaling gradients 
    5. Finite element modeling for experimental simulation and structural analysis in plants 
    6. Reconciling hypotheses for vasculogenic network formation 
    7. Building stochastic cell interactions into agent-based models of zebrafish skin patterns 
    8. Collective cell movements and cell sorting in morphogenesis 
    9. LimbNET - A one week online practical from the Sharpe lab
    10. Modelling the morphogenesis of multicellular rosettes 
    11. `Turing before Tipping' in spatially extended models 
    12. An introduction to the Cellular Potts Model & a Growing Organoid Model

    18: 00 - 19:00 Live Q&A and Discussion on Implementation Issues - ask questions through Slack in channel #questions4speakers - chair Hadrien Oliveri (t.b.c.)

    19:00 - 22:00 Asynchronous events / Working collaboration groups (Californian Time Zones)

    22:00 - 00:00 Live Final Presentations of Projects (recorded)

    After the meeting: Plans for Follow Up - reschedule until after the meeting

    The programme will be announced shortly.
    Please log in to view the participants information...
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    Roeland Merks, Leiden University  

    Mark Alber, University of California Riverside  

    Christophe Godin, INRIA and ENS of Lyon  

    Philip Maini, University of Oxford  


Maria Krebbers

+31 71 572 5578

krebbers@lorentzcenter.nl

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