title: The systemic paradigm and its relevance to the modelling of biological functions.
abstract: If we are to make advances in the design of information systems for the processing of functional genomic data, we must carefully examine the concepts of gene and function. Therefore, we must consider the biological models that are used to acquire these data from an epistemological point of view. This article introduces three elements of this view: (i) we reviewed the major concepts and the axioms of the systemic paradigm; (ii) we considered their relevance for the modelling of the biological functions within the framework of an intracellular signalling process; (iii) we present an operational input founded on this methodological viewpoint to illustrate the coherence of a theoretical framework and the use of its formalism for the description and the representation of biological activities. This formalism will guide the modelling and the interpretation of molecular interactions in terms of organisational operations producing and transforming the genetic information; thus, providing a better understanding of the complex relationship between the generation, the circulation and the computation of information when biological systems are set up.
authors.affiliation: Centre de bioinformatique, institut Pasteur, 25-28, rue du Docteur-Roux, 75724 Paris, France. mroux@pasteur.fr
authors.forename: Magali
authors.initials: M
authors.lastname: Roux-Rouquié
authors.forename: Jean-Louis
authors.initials: JL
authors.lastname: Le Moigne
mesh_terms: D000818:Animals; D005075:Biological Evolution; D016208:Databases, Factual; D005796:Genes / Q000502:physiology; D005968:Glutamate Decarboxylase / Q000235:genetics; D006801:Humans; D007527:Isoenzymes / Q000235:genetics; D019359:Knowledge; D008954:Models, Biological; D016571:Neural Networks, Computer; D015398:Signal Transduction; D016212:Transforming Growth Factor beta / Q000502:physiology
chemical_list: D007527:Isoenzymes; D016212:Transforming Growth Factor beta; D005968:Glutamate Decarboxylase