Genetic Network Analyzer (GNA) is a computer tool for the modeling and simulation of genetic regulatory networks. The aim of GNA is to assist biologists in constructing a model of a genetic regulatory network using knowledge about regulatory interactions in combination with gene expression data. Genetic Network Analyzer consists of a simulator of qualitative models of genetic regulatory networks in the form of piecewise-linear differential equations. Instead of exact numerical values for the parameters, which are often not available for networks of biological interest, the user of GNA specifies inequality constraints. This information is sufficient to generate a state transition graph that describes the qualitative dynamics of the network. The simulator has been implemented in Java and has been applied to the analysis of various regulatory systems, such as the networks controlling the initiation of sporulation in B. subtilis, the carbon starvation response in E. coli, and biodegradation of polluants by P. putida. See the list of publications below for references to these and other examples.

References in zbMATH (referenced in 26 articles )

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  1. Mera, Manuel; Bejarano, Francisco Javier: On mode reconstructability and reconstructability sets of piecewise linear systems (2021)
  2. Bernot, G.; Comet, J.-P.; Khalis, Z.; Richard, A.; Roux, O.: A genetically modified Hoare logic (2019)
  3. Glass, Leon; Edwards, Roderick: Hybrid models of genetic networks: mathematical challenges and biological relevance (2018)
  4. Figueiredo, Daniel; Martins, Manuel A.; Chaves, Madalena: Applying differential dynamic logic to reconfigurable biological networks (2017)
  5. Fages, François; Martinez, Thierry; Rosenblueth, David A.; Soliman, Sylvain: Influence systems vs reaction systems (2016)
  6. Ironi, Liliana; Tran, Diana X.: Nonlinear and temporal multiscale dynamics of gene regulatory networks: a qualitative simulator (2016)
  7. Brim, Luboš; Demko, Martin; Pastva, Samuel; Šafránek, David: High-performance discrete bifurcation analysis for piecewise-affine dynamical systems (2015)
  8. Carta, Alfonso; Chaves, Madalena; Gouzé, Jean-Luc: Continuous-switch piecewise quadratic models of biological networks: application to bacterial growth (2015)
  9. Fitime, Louis Fippo; Schuster, Christian; Angel, Peter; Roux, Olivier; Guziolowski, Carito: Integrating time-series data in large-scale discrete cell-based models (2015)
  10. Hrydziuszko, Olga; Balbus, Joanna; Żulpo, Magdalena; Wrona, Artur; Kubica, Krystian: Mathematical analyses of two-compartment model of human cholesterol circulatory transport in application to high blood cholesterol prevention, diagnosis and treatment (2015)
  11. Ito, Sohei; Ichinose, Takuma; Shimakawa, Masaya; Izumi, Naoko; Hagihara, Shigeki; Yonezaki, Naoki: Qualitative analysis of gene regulatory networks by temporal logic (2015)
  12. Acary, Vincent; de Jong, Hidde; Brogliato, Bernard: Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems (2014)
  13. Edwards, Roderick; Ironi, Liliana: Periodic solutions of gene networks with steep sigmoidal regulatory functions (2014)
  14. Ironi, Liliana; Lanzarone, Ettore: Assigning probabilities to qualitative dynamics of gene regulatory networks (2014)
  15. Tonnelier, Arnaud: Cyclic negative feedback systems: what is the chance of oscillation? (2014)
  16. Van Goethem, S.; Jacquet, J.-M.; Brim, L.; Šafránek, D.: Timed modelling of gene networks with arbitrarily precise expression discretization (2013) ioport
  17. Baldazzi, Valentina; Ropers, Delphine; Geiselmann, Johannes; Kahn, Daniel; de Jong, Hidde: Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in \textitEscherichiacoli (2012)
  18. Hu, Manfeng; Cao, Jinde; Yang, Yongqing: Stability of genetic networks with hybrid regulatory mechanism (2012)
  19. Ironi, Liliana; Panzeri, Luigi; Plahte, Erik; Simoncini, Valeria: Dynamics of actively regulated gene networks (2011)
  20. Mabrouki, Mbarka; Aiguier, Marc; Comet, Jean-Paul; Le Gall, Pascale; Richard, Adrien: Embedding of biological regulatory networks and property preservation (2011)

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