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Qualitative simulation of genetic regulatory networks using piecewise-linear models

Qualitative simulation of genetic regulatory networks using piecewise-linear models,H. De Jong,J. L. Gouz'e,C. Hernan-dez,M. Page,T. Sari,J. Geiselman

Qualitative simulation of genetic regulatory networks using piecewise-linear models   (Citations: 52)
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Abstract In order to cope with the large amounts of data that have become,available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks, based on a class of piecewise-linear (PL) differential equations that has been well-studied in mathematical biology. The simulation method,is well-adapted to state-of-the-art measurement techniques in genomics, which often provide qualitative and coarsegrained descriptions of genetic regulatory networks. Given a qualitative model of a genetic regulatory network, consisting of a system of PL differential equations and inequality constraints on the parameter values, the method produces a graph of qualitative states and transitions between qualitative states, summarizing the qualitative dynamics of the system. The qualitative simulation method has been implemented in Java in the computer tool Genetic Network Analyzer.
Published in 2004.
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    • ...Pioneering work towards automated qualitative analysis and simulation of GRNs has resulted in a computational tool, called GNA[9]...
    • ...In the case D Œ Δr, like in traditional QR methods and in GNA[9], possible transitions are determined by the signs of & xi .A s &i are defined by linear expressions, such signs are easily determined by exploiting the inequalities that define the parameter space domain...

    Liliana Ironiet al. A computational framework for qualitative simulation of nonlinear dyna...

    • ...A first effort in this direction is given by a qualitative simulator, called GNA [4]...
    • ...State Transitions. The possible transitions from D are determined by different strategies according to whether D ∈ ΔR or D ∈ ΔS. In the former case, like in traditional QR methods and in GNA [4], transitions are determined by the signs of ˙ xi .A s˙ xi are defined by linear expressions, such signs are easily determined by exploiting the inequalities that define the parameter space domain, and constrain the RSPs to belong to specific ...

    Liliana Ironiet al. An Algorithm for Qualitative Simulation of Gene Regulatory Networks wi...

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