ViSiBooL—visualization and simulation of Boolean networks with temporal constraints

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Abstract

Summary:

Mathematical models and their simulation are increasingly used to gain insights into cellular pathways and regulatory networks. Dynamics of regulatory factors can be modeled using Boolean networks (BNs), among others. Text-based representations of models are precise descriptions, but hard to understand and interpret. ViSiBooL aims at providing a graphical way of modeling and simulating networks. By providing visualizations of static and dynamic network properties simultaneously, it is possible to directly observe the effects of changes in the network structure on the behavior. In order to address the challenges of clear design and a user-friendly graphical user interface (GUI), ViSiBooL implements visual representations of BNs. Additionally temporal extensions of the BNs for the modeling of regulatory time delays are incorporated. The GUI of ViSiBooL allows to model, organize, simulate and visualize BNs as well as corresponding simulation results such as attractors. Attractor searches are performed in parallel to the modeling process. Hence, changes in the network behavior are visualized at the same time.

Availability and Implementation:

ViSiBooL (Java 8) is freely available at http://sysbio.uni-ulm.de/?Software:ViSiBooL.

Contact:

hans.kestler@uni-ulm.de

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