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 21 articles )

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  1. Bernot, G.; Comet, J.-P.; Khalis, Z.; Richard, A.; Roux, O.: A genetically modified Hoare logic (2019)
  2. Glass, Leon; Edwards, Roderick: Hybrid models of genetic networks: mathematical challenges and biological relevance (2018)
  3. Figueiredo, Daniel; Martins, Manuel A.; Chaves, Madalena: Applying differential dynamic logic to reconfigurable biological networks (2017)
  4. Carta, Alfonso; Chaves, Madalena; Gouzé, Jean-Luc: Continuous-switch piecewise quadratic models of biological networks: application to bacterial growth (2015)
  5. 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)
  6. Ito, Sohei; Ichinose, Takuma; Shimakawa, Masaya; Izumi, Naoko; Hagihara, Shigeki; Yonezaki, Naoki: Qualitative analysis of gene regulatory networks by temporal logic (2015)
  7. Acary, Vincent; de Jong, Hidde; Brogliato, Bernard: Numerical simulation of piecewise-linear models of gene regulatory networks using complementarity systems (2014)
  8. Edwards, Roderick; Ironi, Liliana: Periodic solutions of gene networks with steep sigmoidal regulatory functions (2014)
  9. Ironi, Liliana; Lanzarone, Ettore: Assigning probabilities to qualitative dynamics of gene regulatory networks (2014)
  10. Tonnelier, Arnaud: Cyclic negative feedback systems: what is the chance of oscillation? (2014)
  11. Van Goethem, S.; Jacquet, J.-M.; Brim, L.; Šafránek, D.: Timed modelling of gene networks with arbitrarily precise expression discretization (2013) ioport
  12. 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)
  13. Hu, Manfeng; Cao, Jinde; Yang, Yongqing: Stability of genetic networks with hybrid regulatory mechanism (2012)
  14. Ironi, Liliana; Panzeri, Luigi; Plahte, Erik; Simoncini, Valeria: Dynamics of actively regulated gene networks (2011)
  15. Mabrouki, Mbarka; Aiguier, Marc; Comet, Jean-Paul; Le Gall, Pascale; Richard, Adrien: Embedding of biological regulatory networks and property preservation (2011)
  16. Barnat, J.; Brim, L.; Černá, I.; Dražan, S.; Fabriková, J.; Šafránek, D.: On algorithmic analysis of transcriptional regulation by LTL model checking (2009)
  17. Tran, Nam; Baral, Chitta: Hypothesizing about signaling networks (2009)
  18. Barnat, J.; Brim, L.; Černá, I.; Dražan, S.; Šafránek, D.: Parallel model checking large-scale genetic regulatory networks with DiVinE (2008)
  19. Gelenbe, Erol: Modelling gene regulatory networks (2008)
  20. Sepulchre, Jacques-A.; Reverchon, Sylvie; Nasser, William: Modeling the onset of virulence in a pectinolytic bacterium (2007)

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