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The cooperation on SBML qual further fostered synergistic efforts to articulate and improve existing tools, leading to the launching of the Common Logical Modelling Tools (CoLoMoTo) project (http://co.mbine.org/colomoto/), which gathers many groups developing and using logical modelling software tools.
The logical modelling framework is described in the Methods section.
Additional file 1 Supplementary information on logical modelling formalism including Figures S1 and Tables S1 and S2.
FBA and logical modelling are classical methods used to perform simulations on large-scale metabolic and regulatory networks, respectively.
Regarding regulatory networks, a broad spectrum of methods are dedicated to their analysis although logical modelling remains the major method to take charge of large-scale networks.
A number of logical modelling tools allow properties of the state transition graphs to be verified by means of existing model-checking tools, such as NuSMV [ 44- 47].
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Interaction graphs, logical models and logic-based ODE models are tightly linked since every logical model has an underlying interaction graph (from which it was constructed) and every logic-based ODE an underlying logical model and thus also a corresponding interaction graph.
This article reviews legal applications of logic, with a particularly marked concern for logical models of legal argument.
More refined qualitative modeling approaches include constraint-based modeling [ 7], Petri nets [ 8, 9], and logical modeling [ 10- 12].
Claude Lévi-Strauss once wrote that "the object of myth is to provide a logical model capable of overcoming a contradiction".
"We've based our promotion of exercise on a medical and logical model," she said.
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