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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 translation of a MIN from Figure 10 into MLM. The variables CI and CRO of the MLM are obtained from the species CI and CRO of the MIN combined with the regulatory sites OR1, OR2 and OR3. The MLM interactions are obtained from pairs (ICR + IRC) present in the MIN. For example, there is an arc (CI, CRO) in the MLM because there is a pair (ICR + IRC) = (CI, CRO) in the MIN presented in Figure 10. The dynamic parameters and arc labels of the MLM are calculated from the relation  of the MIN.
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Figure 11: A translation of a MIN from Figure 10 into MLM. The variables CI and CRO of the MLM are obtained from the species CI and CRO of the MIN combined with the regulatory sites OR1, OR2 and OR3. The MLM interactions are obtained from pairs (ICR + IRC) present in the MIN. For example, there is an arc (CI, CRO) in the MLM because there is a pair (ICR + IRC) = (CI, CRO) in the MIN presented in Figure 10. The dynamic parameters and arc labels of the MLM are calculated from the relation of the MIN.

Mentions: Here we can take an assumption that the MLM can not distinguish between the variable values "present" and "low" and we will attribute the same numerical values to them. Replacing the MIN value "absent" by MLM value 0 and thresholds "low"/"present" and "high" by numerical values {1 and 2}, the family of interaction graphs of the translated MLM of the λ switch is obtained (see the Figure 11).


Incremental and unifying modelling formalism for biological interaction networks.

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

A translation of a MIN from Figure 10 into MLM. The variables CI and CRO of the MLM are obtained from the species CI and CRO of the MIN combined with the regulatory sites OR1, OR2 and OR3. The MLM interactions are obtained from pairs (ICR + IRC) present in the MIN. For example, there is an arc (CI, CRO) in the MLM because there is a pair (ICR + IRC) = (CI, CRO) in the MIN presented in Figure 10. The dynamic parameters and arc labels of the MLM are calculated from the relation  of the MIN.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 11: A translation of a MIN from Figure 10 into MLM. The variables CI and CRO of the MLM are obtained from the species CI and CRO of the MIN combined with the regulatory sites OR1, OR2 and OR3. The MLM interactions are obtained from pairs (ICR + IRC) present in the MIN. For example, there is an arc (CI, CRO) in the MLM because there is a pair (ICR + IRC) = (CI, CRO) in the MIN presented in Figure 10. The dynamic parameters and arc labels of the MLM are calculated from the relation of the MIN.
Mentions: Here we can take an assumption that the MLM can not distinguish between the variable values "present" and "low" and we will attribute the same numerical values to them. Replacing the MIN value "absent" by MLM value 0 and thresholds "low"/"present" and "high" by numerical values {1 and 2}, the family of interaction graphs of the translated MLM of the λ switch is obtained (see the Figure 11).

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