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Open Access Highly Accessed Software

Snazer: the simulations and networks analyzer

Tommaso Mazza1*, Gennaro Iaccarino1 and Corrado Priami12

Author Affiliations

1 The Microsoft Research University of Trento, CoSBi, Trento, Italy

2 DISI - University of Trento, Trento, Italy

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BMC Systems Biology 2010, 4:1  doi:10.1186/1752-0509-4-1

Published: 7 January 2010

Abstract

Background

Networks are widely recognized as key determinants of structure and function in systems that span the biological, physical, and social sciences. They are static pictures of the interactions among the components of complex systems. Often, much effort is required to identify networks as part of particular patterns as well as to visualize and interpret them.

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.

Results

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.

Conclusions

Snazer is a solid prototype that integrates biological network and simulation time-course data analysis techniques.