GRegNetSim : A Tool for the Discrete Simulation and Analysis of Genetic Regulatory Networks

Background: Discrete simulations of genetic regulatory networks have been used to study subsystems of yeast successfully. However, implementations of the two models underlying these simulations do not support a graphic interface, are not freely available, and require computations necessary to analyze their results to be done manually. Furthermore, differences between these two models suggest that an enriched model, encompassing both existing models, is needed. Results: We developed a software tool, called GRegNetSim, that allows the end-user (a biologist) to describe genetic regulatory networks graphically. The input is graphic (as an input to Cytoscape, an open-source platform for the representation and analysis of biological networks). The user can specify various transition functions at different nodes of the network, supporting, for example, threshold and gradient effects, and then apply the network to a variety of inputs. GRegNetSim displays the relationship between the inputs and the mode of behavior of the network in a graphic form that is easy to interpret. Furthermore, it can automatically extract statistical data necessary to analyze the simulations. Conclusions: The discrete simulations performed by GRegNetSim can be used to elucidate and predict the behavior, structure and properties of genetic regulatory networks in a unified manner. GRegNetSim is implemented as a Cytoscape App. Installation files, examples and source code, along with a detailed user guide, are freely available at https://sites.google.com/site/gregnetsim/.