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title Dynamical and mechanistic reconstructive approaches of T lymphocyte dynamics:Using visual modelling languages to bridge the gap between immunologists, theoreticians and programmers.
Authors Thomas-Vaslin, V., A. Six, J. G. Ganascia and H. Bersini
Source Frontiers in Immunology 01 October 2013 | doi: 10.3389/fimmu.2013.00300
34 http://www.frontiersin.org/Journal/Abstract.aspx?s=1177&name=t_cell_biology&ART_DOI=10.3389/fimmu.2013.00300
Year 2013
Type Journal
Type of publication ISC-PIF scholar

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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.
Created Wednesday 02 April, 2014 19:37:41

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