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  Director : ROUX-ROUQUIE Magali (mroux@pasteur.fr)


  abstract

 

Our unit works on the formalization of biological processes with the aim of developing and implementing computer models. We use the experience that we have accumulated in systemic modeling in the representation of processes, to develop a biological modeling language.



  report

cale

The activity of the BioSystemics Modeling Engineering Unit is based on the modeling and implementing of processes, considering biological systems to be reactive systems. Reactive systems constitute a good approximation to biological systems because both types of system are subjected to external and internal events that condition their behavior. Thus, the functioning of these systems over time cannot be specified solely in terms of inputs and outputs, but must take into account these events, which may be synchronous and/or concurrent, and which determine morphological and spatio-temporal changes in the system over time.

The specification of such systems is based on numerous methods, of two main types: formal graphic languages (including Petri nets) and algebraic and logical methods. Among the graphic methods, Unified Modeling Language (UML) is an object-oriented language that can be used, which allows to model structure, function and evolution. We use the experience that acquired in data processing in the modeling of the reactive systems. This enables us to develop feasible procedures for representing biological systems, focusing on their functional characteristics (function and evolution).

This involves a mixture of conceptual and methodological approaches (systemic modeling), instrumental experiments (relevance of the modeling languages, for example UML) and interpretation procedures (multicriterion searches and inferences). These studies make it possible to express explicitly and unambiguously, the various aspects of a biological system: the static view of its components, the synchronic view of its states, the diachronic view of state changes. A process (for example: cell cycle, protein trafficking, etc.) is modeled by connecting these three aspects. These activities are carried out within a framework of interdisciplinary collaboration, bringing together biologists, mathematicians, computer scientists and epistemologists.



  publications

puce Publications of the unit on Pasteur's references database


  personnel

  Office staff Researchers Scientific trainees Other personnel
   

Roux-Rouquié, Magali, CNRS (DR2, mroux@pasteur.fr)

Yéramian, Edouard, CNRS (DR2)

Huynh, Nina (DESS)

Hicham Selouane

 

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