Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes.

From functional genomics to systems biology: concepts and practices.

Systems biology is the iterative and integrative study of biological systems as systems in response to perturbations. It is founded on hypotheses formalized in models built from the results of global functional genomics analyses of the complexity of the genome, transcriptome, proteome, metabolome, etc. Its implementation by cross-disciplinary teams in a standardized mode under quality assurance should allow accessing the small variations of the large number of elements determining functioning of biological systems.

Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time.

Living systems have paradoxical thermodynamic stability, the intrinsic property of self-organization, fluctuation and adaptation to their changing environment. Knowledge accumulated in the analytical reductionist framework has provided useful systematic descriptions of biological systems which appear to be insufficient to gain deep understanding of their behaviour in physiologic conditions and diseases. A state-of-the-art functional genomics study in yeast points to the current inability to appraise 'biological noise', leading to focus on few genes, transcripts and proteins subject to major detectable changes, while currently inaccessible small fluctuations may be major determinants of the behaviour of biological systems.

The systemic paradigm and its relevance to the modelling of biological functions.

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.