Computational Tools for Modeling Protein Networks

There are a large number of software packages available, both commercial and academic, to assist researchers in modeling protein networks. In this paper, we briefly review some of the more commonly used tools and focus on the current state of the Systems Biology Workbench (SBW), a modular framework that connects modeling and analysis applications, enabling tools to reuse each others capabilities. We describe how users and developers perceive SBW and then describe the currently available SBW modules. Keywords: Systems biology workbench, Java-based simulation and animation environment, Complex pathway simulator, Virtual cell, Systems biology markup language