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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.

Show MeSH
A MIN representing the genetic switch of the λ phage. Species CRO and CI represent proteins which bind with the affinity OR to the regulatory sites OR1, OR2 and OR3. These sites are present in the regulatory regions of genes encoding both proteins, so that they influence the corresponding species CI and CRO. The relation  is the same as in Figure 8.
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Figure 10: A MIN representing the genetic switch of the λ phage. Species CRO and CI represent proteins which bind with the affinity OR to the regulatory sites OR1, OR2 and OR3. These sites are present in the regulatory regions of genes encoding both proteins, so that they influence the corresponding species CI and CRO. The relation is the same as in Figure 8.

Mentions: The resulting MIN is represented in Figure 10.


Incremental and unifying modelling formalism for biological interaction networks.

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

A MIN representing the genetic switch of the λ phage. Species CRO and CI represent proteins which bind with the affinity OR to the regulatory sites OR1, OR2 and OR3. These sites are present in the regulatory regions of genes encoding both proteins, so that they influence the corresponding species CI and CRO. The relation  is the same as in Figure 8.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 10: A MIN representing the genetic switch of the λ phage. Species CRO and CI represent proteins which bind with the affinity OR to the regulatory sites OR1, OR2 and OR3. These sites are present in the regulatory regions of genes encoding both proteins, so that they influence the corresponding species CI and CRO. The relation is the same as in Figure 8.
Mentions: The resulting MIN is represented in Figure 10.

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