MORPHEX NEST Pathfinder Virtual Experimentation © European Commission, 2007 (The Commission accepts no responsibility or liability whatsoever with regard to the information presented in this document).
Official Title	Morphogenesis and Gene Regulatory Networks in Plants and Animals: a Complex Systems Modelling Approach - Acronym: MORPHEX
Coordinator	Centre National de la Recherche Scientifique – Délégation Rhône Auvergne (France)
Partners	• Universiteit van Amsterdam (The Netherlands) • Chalmers University of Technology (Sweden) • Corporacion de Ciencias y de la Educacion – Instituto de Sistemas Complejos de Valparaíso (Chile) • Johannes Gutenberg Univesity Mainz (Germany) • Unversität Stuttgart (Germany) • Ecole Polytechnique (France) • OSLO (France)
Further Information	Prof Michel Morvan Centre National de la Recherche Scientifique – Délégation Rhône Auvergne Laboratoire de l'Informatique du parallélisme, Institut des Systèmes Complexes Allée d'Italie 46 69364 Lyon France email: michel.morvan@ens-lyon.fr fax: +33 4 7272 8080
Project cost	€ 2 222 961.60
EU funding	€ 1 599 990.40
Project reference	Contract No 043322 (NEST)

Growth of biological organisms is influenced by genes in individual cells and by interactions between cells. MORPHEX seeks to understand how interactions between genes cause cells to differentiate, grow and divide, and how exchanges between cells contribute to this process. The results should improve understanding of why the growing process sometimes fails, and how to overcome this. It will also lead to the expansion of computer-based experimentation on virtual organisms, and to the development of a generic platform for model-driven experimentation.

Abstract

The main objective of the project is to obtain via a modelling and simulation approach a better understanding of the structure and dynamics of metabolic pathways of gene regulatory networks involved in the morphogenesis of animals and plants. We will concentrate on the development of two kind of sponges and on the organogenesis of carpel and anthers of a flowering plant. We will tackle the complexity involved in these processes by using concepts and tools arising from complex systems science. On the one side morphogenesis of sponges and organogenesis in flowering plants share many common concerns and approaches which justify the feasability of tackling them within a common complex systems framework. On the other side they consider distinguished features and methods of analysis that will guarantee a minimal genericity in the tools designed for the modelling process. The following problems will be addressed: provide a general model allowing to describe the underlying complex systems at different hiearchical levels in the same formalism; provide tools to extract concrete models description from experimental data; provide a way to conduct in-silico experiments. These tools will be applied on real data in order to significatively progress on the initial biological problems and will also be used to develop a model-guided data collection process. Moreover, the simulation tools will be modular enough to be customised or extended in the future for modelling complex systems arising from other fields. Our global goals can be summarised by three measurable and verifiable objectives: to build spatiotemporal atlases of gene expression for flowering plants (for carpel and anther) and one for sponges; to design, implement and finely tune models of development for reproductive organs in flowering plants and for sponges; to develop a customisable modelling and simulation platform adapted to the study of complex systems in the context of development biology.

ISCV participation on the project

The Chilean group is organised around ISCV from Chile, one of the few complex systems institutes in the world. The group is at a world leading level in the theoretical study of different dynamical models. In particular, it has a leading expertise on the theoretical understanding of regulatory networks, either on a discrete, continuous or hybrid context, this competence having been built around the seminal work of Eric Goles on neural and automata networks. In particular, the group's vision of these systems will be of very important value for the consortium on the following aspects:

Furthermore, the group has more recently worked in the application of theoretical results in the modelling of biological systems, more precisely in the construction of a genetic regulatory network in Drosophila Melanogaster and a metabolic and genetic network in E. Coli. In a retroaction process, this work has lead to identifying new deep directions in the theoretical studies and to reinforce the Chilean group expertise on the formal models.

The project is structured around eight partners, each having been chosen for its recognized competence in at least one major aspect of the project (corresponding to work packages).
The specific Chilean ISCV participation corresponds to WP3: “Complex Systems Modeling”, working in tight collaboration with CHAL, CNRS-LIP, POLY and UVA. All the partners will be in charge of developing different models, tools and protocols, each one preferably in its major field of competence, in the case of ISCV on simplistic gene regulation networks.
Main goal of this WP: Propose a (general enough) meta-model and provide associated implementable concepts for designing tools and protocols targeted to solving the considered biological problems.
Tasks:
a. Characterization of the meta model.
b. Formalisation and conception of tools and protocols.
Pre-simulation tools.
Post-simulation tools.
Protocols.
c. Elaboration of protocols
d. Model and tool validation

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