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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
An MLM instance: its regulatory graph (left, top), the corresponding state graph (left, bottom) and the table of its dynamic parameters (right).
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Figure 7: An MLM instance: its regulatory graph (left, top), the corresponding state graph (left, bottom) and the table of its dynamic parameters (right).

Mentions: The following definition describes an instance of MLM as introduced by R. Thomas. It is composed of a regulatory graph (U, E) and a table K of dynamic parameters (see Figure 7). Each node u of the graph corresponds to a variable with integer values between 0 and the boundary bu of the variable, which drives the topology of the corresponding state graph. The influences between variables in MLM can be positive (inducing) or negative (inhibiting).


Incremental and unifying modelling formalism for biological interaction networks.

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

An MLM instance: its regulatory graph (left, top), the corresponding state graph (left, bottom) and the table of its dynamic parameters (right).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: An MLM instance: its regulatory graph (left, top), the corresponding state graph (left, bottom) and the table of its dynamic parameters (right).
Mentions: The following definition describes an instance of MLM as introduced by R. Thomas. It is composed of a regulatory graph (U, E) and a table K of dynamic parameters (see Figure 7). Each node u of the graph corresponds to a variable with integer values between 0 and the boundary bu of the variable, which drives the topology of the corresponding state graph. The influences between variables in MLM can be positive (inducing) or negative (inhibiting).

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