title: ViSiBooL-visualization and simulation of Boolean networks with temporal constraints.
abstract: 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.
  
  
  
  ViSiBooL (Java 8) is freely available at http://sysbio.uni-ulm.de/?Software:ViSiBooL .
  
  
  
  hans.kestler@uni-ulm.de.
authors: Institute of Medical Systems Biology.|International Graduate School of Molecular Medicine, Ulm University, Ulm 89081, Germany.
authors: Julian
authors: J
authors: Schwab
authors: Institute of Medical Systems Biology.|International Graduate School of Molecular Medicine, Ulm University, Ulm 89081, Germany.
authors: Andre
authors: A
authors: Burkovski
authors: Institute of Medical Systems Biology.
authors: Lea
authors: L
authors: Siegle
authors: Institute of Medical Systems Biology.
authors: Christoph
authors: C
authors: Müssel
authors: Institute of Medical Systems Biology.|Leibniz Institute on Aging - Fritz Lipmann Institute, Jena 07745, Germany.
authors: Hans A
authors: HA
authors: Kestler
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D006801:Humans; D008957:Models, Genetic; D008962:Models, Theoretical; D012984:Software