Modeling Shape and Size in Biological Development

- This workshop is organized online -

24 - 28 August 2020

Venue: Lorentz Center@Oort

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

On Wednesday 26 August at 20:00 an online lecture is organized by James Sharpe. If you would like to attend this online lecture, please register here.  

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

    Theme: Stochastic discrete dynamical systems

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

    Recorded Keynote Lecture 1 - Exemplary research project - Speaker pending confirmation
    Recorded Keynote Lecture 2 -  Introduction to in silico experimentation - TBA
    Recorded Educational Lectures: Physics-based modeling: Mark Alber, UC Riverside & Roeland Merks, U Leiden

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    09:3010:00 LIVE- Arrival to the Kalture Live Room, informal chats and coffee
    10:0010:15 Welcome and intruction by Lorentz Center
    10:1510:45 LIVE- Introduction of workshop goals by organizers
    10:4514:30 

    Asynchronous events / Working collaboration groups

    14:3015:30 Q&A session with speakers
    15:3017:00 LIVE- Students teams introduce themselves and present their plans in ten minute presentations as prepared in advance of the course
    17:0018:00 LIVE- "Wine & Cheese" - informal online chats

    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 - Philip Maini, U Oxford
    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
    Breakout Groups (Kaltura Liveroom)  - Students discuss projects
    Work on projects Record and watch -  Informal update team progress (10 minutes each)

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

    10:0010:30 

    Virtual walk-in coffee break. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advise from the other participants

    10:3017:00 

    Asynchronous events / Working collaboration groups

    17:0018:00 Live Q&A session with speakers

    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 1 - Exemplary research project - Speaker pending confirmation
    Recorded Keynote Lecture 2 -  Introduction to in silico experimentation - TBA
    Recorded Educational Lectures: Physics-based modeling: Mark Alber, UC Riverside & Roeland Merks, U Leiden

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    More information about the online lecture by James Sharpe: https://www.lorentzcenter.nl/turing-patterns-on-turing-machines.html

     

    10:0010:30 

    Virtual walk-in coffee break.

    10:3017:00 

    Asynchronous events / Working collaboration groups

    17:0018:00 LIVE Q&A Session with speakers
    18:0019:00 

    Online social 'dinner' event

    19:4520:00 

    Entering the virtual Lorentz Center room

    20:0020:45 

    Start lecture by James Sharpe

    20:4521:00 

    Questions and discussion

    21:0021:00 

    End

    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
    Recorded keynote lecture on exemplary research project -Verônica Grieneisen, U Cardiff
    Recorded lectures: Modeling shoot apical development: concepts, computational and mathematical tools - Christophe Godin
    Students work on projects
    Record and watch -  Informal update presentation of teams (10 minutes each)

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    10:3017:00 Asynchronous event / Collaboration working groups
    10:3010:30 Virtual walk-in coffee break. Share experiences about the project, how students are progressing, what are the difficulties, to find help and advise from the other participants
    17:0018:00 Live Q&A session with speakers

    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 methodolo

     ------Asynchronous events------

    Recorded Keynote lecture on exemplary research project - Emmanuel Faure
    Recorded lecture on computational implementation issues  - Alexander Fletcher, U Sheffield
    Students work on project 

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    10:3014:30 Asynchronous events / Working collaboration groups
    10:3010:30 Virtual walk-in coffee break.
    14:3015:30 Live Q&A and Discussion on Implementation Issues
    15:3018:30 Live Final presentations of projects and plans for follow-up
    18:3018:45 Wrap-up
    Please log in to view the participants information...

    Roeland Merks, Leiden University  

    Mark Alber, University of California Riverside  

    Christophe Godin, INRIA and ENS of Lyon  

    Philip Maini, University of Oxford  


Michelle Grandia

+31 71-5275579

grandia@lorentzcenter.nl

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