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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 model representing the enzymatic reaction of CI synthesis. The reactions CI_dimerisation and OR1_binding are reversible, so they have the appropriate attribute. The reactions CI_RNA_synth and CI_synth are non reversible and have the appropriate attribute.
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Figure 4: A MIN model representing the enzymatic reaction of CI synthesis. The reactions CI_dimerisation and OR1_binding are reversible, so they have the appropriate attribute. The reactions CI_RNA_synth and CI_synth are non reversible and have the appropriate attribute.

Mentions: A MIN model having a highest level of detail has the property that each regulatory site corresponds to a (single) chemical reaction. We present an example of such a model in Figure 4. It illustrates the CI protein synthesis from the CI gene regulated by the OR1 regulatory site in function of the presence of CI protein dimer.


Incremental and unifying modelling formalism for biological interaction networks.

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

A MIN model representing the enzymatic reaction of CI synthesis. The reactions CI_dimerisation and OR1_binding are reversible, so they have the appropriate attribute. The reactions CI_RNA_synth and CI_synth are non reversible and have the appropriate attribute.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: A MIN model representing the enzymatic reaction of CI synthesis. The reactions CI_dimerisation and OR1_binding are reversible, so they have the appropriate attribute. The reactions CI_RNA_synth and CI_synth are non reversible and have the appropriate attribute.
Mentions: A MIN model having a highest level of detail has the property that each regulatory site corresponds to a (single) chemical reaction. We present an example of such a model in Figure 4. It illustrates the CI protein synthesis from the CI gene regulated by the OR1 regulatory site in function of the presence of CI protein dimer.

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