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Incremental and unifying modelling formalism for biological interaction networks.

Yartseva A, Klaudel H, Devillers R, Képès F - BMC Bioinformatics (2007)

Bottom Line: We also show how to extract from our model a classical ODE description of the dynamics of a system.This approach provides an additional level of description between the biological and mathematical ones.It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.

View Article: PubMed Central - HTML - PubMed

Affiliation: IBISC - Université d'Evry Val d'Essonne, Tour Evry 2, 523 place des Terrasses de l'Agora, F-91000 Evry, France. iartseva@gmail.com

ABSTRACT

Background: An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.

Results: We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the lambda phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system.

Conclusion: This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.

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Examples of Kohn Maps building blocks and their MIN representations.
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Figure 14: Examples of Kohn Maps building blocks and their MIN representations.

Mentions: Over the last few years, some work has been carried out in the field of integration of biological and, in particular, biochemical data which includes rich but informal visualisation conventions [17,18]. Even if MIN is not designed as a graphical model, it provides a quite simple visualisation convention with two types of nodes and two types of links. However, combined with textual information encoded in the attributes of links and nodes, it can represent biological features encoded as Kohn Maps [17], as it is illustrated for three examples of Kohn Maps building blocks in Figure 14.


Incremental and unifying modelling formalism for biological interaction networks.

Yartseva A, Klaudel H, Devillers R, Képès F - BMC Bioinformatics (2007)

Examples of Kohn Maps building blocks and their MIN representations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2200675&req=5

Figure 14: Examples of Kohn Maps building blocks and their MIN representations.
Mentions: Over the last few years, some work has been carried out in the field of integration of biological and, in particular, biochemical data which includes rich but informal visualisation conventions [17,18]. Even if MIN is not designed as a graphical model, it provides a quite simple visualisation convention with two types of nodes and two types of links. However, combined with textual information encoded in the attributes of links and nodes, it can represent biological features encoded as Kohn Maps [17], as it is illustrated for three examples of Kohn Maps building blocks in Figure 14.

Bottom Line: We also show how to extract from our model a classical ODE description of the dynamics of a system.This approach provides an additional level of description between the biological and mathematical ones.It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.

View Article: PubMed Central - HTML - PubMed

Affiliation: IBISC - Université d'Evry Val d'Essonne, Tour Evry 2, 523 place des Terrasses de l'Agora, F-91000 Evry, France. iartseva@gmail.com

ABSTRACT

Background: An appropriate choice of the modeling formalism from the broad range of existing ones may be crucial for efficiently describing and analyzing biological systems.

Results: We propose a new unifying and incremental formalism for the representation and modeling of biological interaction networks. This formalism allows automated translations into other formalisms, thus enabling a thorough study of the dynamic properties of a biological system. As a first illustration, we propose a translation into the R. Thomas' multivalued logical formalism which provides a possible semantics; a methodology for constructing such models is presented on a classical benchmark: the lambda phage genetic switch. We also show how to extract from our model a classical ODE description of the dynamics of a system.

Conclusion: This approach provides an additional level of description between the biological and mathematical ones. It yields, on the one hand, a knowledge expression in a form which is intuitive for biologists and, on the other hand, its representation in a formal and structured way.

Show MeSH