Modelling of complex biological systems in the context of genomics: an account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005

Plant morphology: creating plant morphological ideotypes with respect to genetic and environmental factors. Although 3D structure and morphogenetic processes are now numerically simulated, the capacity for capturing both environment and function is less explored. Modelling might make it possible to link plant structures, functions and morphogeneses. Scrutinizing the integrated function of a plant via a modelling approach is a challenge in plant biology. For instance, better understanding of nitrogen management by plants is of crucial interest when lowering agricultural nitrogen consumption is of concern. There is a need for a global vision for nitrogen management with respect to, for instance, the various plant organs and coupling of nitrogen with carbon. Use of transcriptomic tools is envisaged to implement modelling to different levels of plant function. Elaboration of strategies for enhancing fruit quality might be facilitated through modelling. Thus, parameters such as organoleptics, wall fruit, and saccharose import would be linked to plant global functions. There is no experimental plant model for studying the interactions of plants with bio-aggressors. Thus, modelling is needed for linking structure, function and morphogenesis of a plant with respect to bio-aggressor attacks. Manipulating unicellular organisms is easier, allowing the use of a dynamic model. When considering pluricellular organisms, the metabolic network can be linked to the gene network. However, such types of modelling do not address the global integration of plant functions. Investment in bioinformatics at the Institut National sur la Recherche Agronomique (INRA) particularly focuses on metabolic, proteomic or genomic representation. However, quantitative modelling is poor. It seems necessary to implement a program where, first, horizontal integration would make sense of the numerous data provided by proteomic, transcriptomic and metabolomic studies. Second, the program should, as well, address vertical integration, for instance through the links between plant organization and systems. Finally, the program would benefit from studying species diversity relative to the modelled species of agronomic interest, ensuring transversal integration. The challenges and future of the “life complexity” approach in the health domain was introduced by B. Pau. The quest for the infinitely small is not sufficient to address life’s complexity, which appears fractal relative to the monomolecular scale. Modelling might help in combining the monomolecular aspects and the complexity of life. For instance, neuroscience should, in addition to synaptic transmission, take into consideration the steric and temporal dimensions of neurones and their organization. Modelling of complex biological systems in the context of genomics: an account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005 Alain R. Thierry,1 Francois Kepes,2,3 Patrick Amar,2,4 Georgia Barlovatz,5 Gilles Bernot,2,6 Marie BeurtonAimar,7 Marie Dutreix,8 Jean-Louis Giavitto,6 Janine Guespin,9 Jean-Pierre Mazat,7 Vic Norris,2,10 Vincent Schafter,11 Philippe Tracqui,12 Christophe Godin13 and Franck Molina14,* 1 Laboratoire des Defenses Antivirales et Antitumorales, UMR 5124 CNRS, CC 086, Universite Montpellier 2, Place Eugene Bataillon, 34095 Montpellier, France. 2 Epigenomics Project / Genopole, 91057 Evry, France. 3 Ateliers de Genomique Cognitive, CNRS UPR 2355, Gif, France. 4 Laboratoire de Recherche en l’Informatique, Universite de Paris Sud, Centre d’Orsay, France. 5 Dynamic / INSERM, Creteil, France. 6 Laboratoire de Methodes Informatiques, CNRS UMR8042 / Genopole, 523 Terrasses de l’Agora 9 000 Evry, France. 7 Labri-INSERM U688, Universite Bordeaux 2, 33405 Talence, France. 8 Institut Curie, CNRS UMR 2027, 91405 Orsay, France. 9 Laboratoire de Microbiologie du Froid, Universite de Rouen, Faculte des Sciences et Techniques, Universite de Rouen, 76821 Mont-Saint-Aignan, France. 10 FRE CNRS 2829, University of Rouen, 76821 Mont Saint Aignan, France 11 Genoscope, CNS Genopole, CP5706 Evry, France 12 CNRS, TIMC/DynaCell, Faculte de Medecine, 38706 La Tronche, France 13 INRIA, CIRAD, INRA, CNRS, Universite Montpellier 2, Botanique et Bio-informatique de l’Architecture des Plantes, Boulevard de la Lironde, 34398 Montpellier, France 14 Centre de Pharmacologie et Biotechnologie pour la Sante, UMR 5160 CNRS, Faculte de Pharmacie, 34093 Montpellier, France.