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by allowing the programming to come closer to the way human perceives this reality
(the first OO language was indeed called “SIMULA”) instead of being constrained by
the processor set of elementary instructions. There is a today trend which makes more
and more possible to abstract software engineering from the processor by naturally
using high-level human concepts and percepts, simply mapping the actors of the pro-
blem on the bricks of the algorithm. Even the way these concepts are cognitively
organized (generalization, semantic relations) can be transposed as such in the soft-
ware. This goes together with the increased use of the standard visual modeling
language called UML [16, 24]. UML proposes a set of well defined diagrams (tran-
scending any specific OO programming language) to naturally describe and resolve
problems with the high level concepts inherent to the formulation of the problem. It is
enough to discover and draw the main actors of the problem and how they do mutual-
ly relate and interact in time to build the algorithmic solution of this problem. Depart-
ing from these diagrams, more and more automatic code generation tools appear on
the market, contributing to make this whole computational frame even more appeal-
ing to biologists. On the other hand, Design Patterns (DP) [18, 17, 24] are very con-
venient and well experimented software recipes to face and resolve programming
difficulties often encountered during the development of complex software. The next
section of this paper will illustrate how immune knowledge is already intrinsically
OO and how accordingly UML and DP should ease the construction of OO models of
immune system. In the third section, these OO tricks will be put into practice in a very
simplified model of the immune clonal selection and memory, limited to B cells,
antigens and antibodies.
2 UML and Design Patterns
Obviously, it is impossible to even briefly give an overview of the hundred modeling
symbols composing the 13 UML diagrams. A very simple and didactical introduction
to UML is the purpose of Folwer's topic [16]. However these symbols are far from
being all necessary and a couple of days is enough to acquire those allowing the con-
ception of Class, State and Sequence diagrams, the most useful ones for the simula-
tion of biological systems. For didactics' sake, two excerpts of the Janeway et al's
immune system bible [20] will be mapped onto the corresponding UML class dia-
gram. “
The antigen-specific activation of these effector T cells is aided by co-
receptors on the T-cell surface that distinguish between the two classes of MHC
molecule; cytotoxic cells express the CD8 co-receptor, which binds MHC class I
molecules, whereas MHC Class II molecules specific T cells express the CD4 co-
receptor, which has specificity for MHC Class II molecules
”. In figure 1, the link
between the classes “T cell” and “Receptor” means a “composition” relationship, the
receptor being physically and intimately part of the T cell, while the arrow joining the
classes “MHC class I” to “MHC Molecule” means a inheritance or specialization
relationship, class I and class II being two sub-classes of MHC molecule. The corre-
spondence of figure 1 with the text should be obvious.
