Dynamic simulation of regulatory networks using SQUAD

Background: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. Results: We developed SQUAD, a software for the dynamic simulation of signaling networks ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza
• Keywords: Behavior, BMCBI 2007, Dynamical System, Steady States