Snazer: the simulations and networks analyzer

From a pure dynamical perspective, simulation represents a relevant way-out. Many simulator tools capitalized on the "noisy" behavior of some systems and used formal models to represent cellular activities as temporal trajectories. Statistical methods have been applied to a fairly large number of replicated trajectories in order to infer knowledge.A tool which both graphically manipulates reactive models and deals with sets of simulation time-course data by aggregation, interpretation and statistical analysis is missing and could add value to simulators.We designed and implemented Snazer, the simulations and networks analyzer. Its goal is to aid the processes of visualizing and manipulating reactive models, as well as to share and interpret time-course data produced by stochastic simulators or by any other means.Snazer is a solid prototype that integrates biological network and simulation time-course data analysis techniques.Proteins and genes play fundamental roles in most organic functions. They cooperate to keep the entire organism's machinery working and prevent breakdowns. Globally, their social relationships give rise to minutely organized networks, currently the target of meticulous studies [1]. Genetic Regulatory Networks (GRNs) [2,3] and Protein-to-Protein Interaction networks (PPIs) are the most representative classes of biological networks.GRNs represent collections of DNA segments which functionally interact with each other as well as with the chemicals that govern the transcription of genes into RNA sequences. From another perspective, GRNs can be seen as input-output machineries which produce an output (i.e. the expression level of a gene) by a combined application of basic functions to input stimuli. PPIs are comprised of proteins that form chains in which each protein reacts to a stimulus of its predecessor to produce a signal directed to its successor. Reactions in such chains are usually seen as directionally oriented because often they are not rev