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SIMBIONT SIGNED

A data-driven multiscale simulation of organogenesis

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

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.

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

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 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.	DE (HEIDELBERG)	coordinator	1˙492˙803.00
2	FUNDACIO CENTRE DE REGULACIO GENOMICA FUNDACIO CENTRE DE REGULACIO GENOMICA Organization address address: CARRER DOCTOR AIGUADER 88 city: BARCELONA postcode: 8003 website: www.crg.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	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

List of publications.
year	authors and title	journal	last update
2018	Xavier Diego, Luciano Marcon, Patrick MÃ¼ller, 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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The information about "SIMBIONT" are provided by the European Opendata Portal: CORDIS opendata.