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SIMBIONT SIGNED

A data-driven multiscale simulation of organogenesis

Total Cost €

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EC-Contrib. €

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Partnership

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 SIMBIONT project word cloud

Explore the words cloud of the SIMBIONT project. It provides you a very rough idea of what is the project "SIMBIONT" about.

grow    patterns    structures    enormous    carefully    interact    bud    modeling    functions    scales    integrate    cell    coordinated    question    differentiate    tomo    levels    types    understand    quantitative    optispim    latest    mouse    robustness    framework    organogensis    simbiont    gradients    putting    physically    gather    medicine    engineering    tissues    molecular    mammalian    scientifically    first    techniques    cellular    mechanical    perturbations    grand    morphogen    mutants    single    molecularly    heart    pieces    global    simulation    eg    simulate    generation    gene    puzzle    regenerative    brain    model    deep    questions    tissue    genes    ask    fundamental    seq    experimentally    predictions    molecules    multicellular    serve    data    cells    medically    vitro    3d    parallel    expression    purpose    signaling    shape    limb    scientific    organogenesis    constructed    organ    movements    helped    intercalation    patterning    create    rates    computer    interactions    multiple   

Project "SIMBIONT" data sheet

The following table provides information about the project.

Coordinator
EUROPEAN MOLECULAR BIOLOGY LABORATORY 

Organization address
address: Meyerhofstrasse 1
city: HEIDELBERG
postcode: 69117
website: http://www.embl.de

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Germany [DE]
 Total cost 2˙075˙055 €
 EC max contribution 2˙075˙055 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2015
 Duration (year-month-day) from 2015-09-01   to  2020-08-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) coordinator 1˙492˙803.00
2    FUNDACIO CENTRE DE REGULACIO GENOMICA ES (BARCELONA) participant 582˙251.00

Map

 Project objective

Organogensis is the process by which multiple different cell types grow, differentiate and interact with each other (both molecularly and physically) to create large complex structures with integrated functions, such as the heart, brain or limb. Understanding this process has enormous potential impact, both scientifically and medically. The SIMBIONT project represents both a grand technical challenge, and a fundamental scientific question. The grand technical challenge is to build the first ever multi-scale computer model of mammalian organogenesis, specifically limb development. This purpose of the model is to help us address the deep scientific question: How are the complex interactions at multiple scales (genes, molecules, cells and tissues) coordinated so as to build a carefully constructed 3D organ? So far, computer modelling has helped to understand some of the pieces of this puzzle, eg. morphogen gradients, or control of tissue growth. However, putting multiple pieces together into a single multi-scale simulation remains a challenge. We will use the latest state-of-the-art quantitative data-generation techniques (including Tomo-Seq and OPTiSPIM), to gather 3D data at multiple levels: gene expression patterns, cell signaling, cellular growth rates, intercalation patterns, and global tissue movements. In parallel we will develop a new multi-scale modeling framework which can integrate this quantitative data, to simulate both the molecular patterning and the mechanical growth of the developing limb bud. Doing so will allow us to ask new systems-level questions about (i) the molecular control of organ shape, (ii) coordination of patterning and growth, and (iii) the multi-scale robustness of the system. We will test the key predictions of the model experimentally (both with mouse mutants, and in vitro perturbations). SIMBIONT will serve as an example for modeling other complex multicellular processes in the future, eg. tissue engineering and regenerative medicine.

 Publications

year authors and title journal last update
List of publications.
2018 Xavier Diego, Luciano Marcon, Patrick Müller, James Sharpe
Key Features of Turing Systems are Determined Purely by Network Topology
published pages: , ISSN: 2160-3308, DOI: 10.1103/physrevx.8.021071
Physical Review X 8/2 2019-09-04
2019 Philipp Germann, Miquel Marin-Riera, James Sharpe
ya||a: GPU-Powered Spheroid Models for Mesenchyme and Epithelium
published pages: 261-266.e3, ISSN: 2405-4712, DOI: 10.1016/j.cels.2019.02.007
Cell Systems 8/3 2019-09-04

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