Abstract

Dynamic modeling of lymphocyte behavior has primarily been based on populations based differential equations or on cellular agents moving in space and interacting each other. The final steps of this modeling effort are expressed in a code written in a programing language. On account of the complete lack of standardization of the different steps to proceed, we have to deplore poor communication and sharing between experimentalists, theoreticians and programmers. The adoption of diagrammatic visual computer language should however greatly help the immunologists to better communicate, to more easily identify the models similarities and facilitate the reuse and extension of existing software models. Since immunologists often conceptualize the dynamical evolution of immune systems in terms of “state-transitions” of biological objects, we promote the use of unified modeling language (UML) state-transition diagram. To demonstrate the feasibility of this approach, we present a UML refactoring of two published models on thymocyte differentiation. Originally built with different modeling strategies, a mathematical ordinary differential equation-based model and a cellular automata model, the two models are now in the same visual formalism and can be compared.

Highlights

  • The perspective is to encourage immunologists involved into mathematical modeling or software productions, to adopt a visual graphical language, here mainly the unified modeling language (UML) “state-transition” diagram to ease the communication, the reuse and the extension of their models

  • LACK OF INTEROPERABILITY, UNDER-USE OF SOFTWARE MODELS in Immunology there is more than 20-years tradition of software and mathematical modeling, very few of them have been the object of further exploitation once published and made available [30]

  • Frontiers in Immunology | T Cell Biology allowed by these diagrams makes possible to distinguish more the “entities” as T cells and the “processes” that occur at different levels such as differentiation, migration and cell cycle. Such “state-transition diagrams” allow computing parallel pathways at various scales to avoid redundancy that is inherent in the formal description of multi-level, heterogeneous and concurrent systems and to model heterogeneity in a very simplified and economical form [31].We have used the well-established Unified Modelling Language (UML – a sofware standard) that still remains approachable to the lab-immunologist, convenient for the theoretician and that can be directly adopted for the high-level graphical depiction [31, 34]

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Summary

Introduction

The perspective is to encourage immunologists involved into mathematical modeling or software productions, to adopt a visual graphical language, here mainly the unified modeling language (UML) “state-transition” diagram to ease the communication, the reuse and the extension of their models. Integrating the heterogeneity of cell populations, phenotypes, lineages, cell location and interactions, cell differentiation across generations [16] in the different biological, and time scales, is problematic in such a mathematical form, which make these models difficult to handle.

Results
Conclusion

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