Trends and Tools for Modeling in Modern Biology

Computational modeling in biology requires sophisticated software tools. Precise communication and effective sharing of the models developed by researchers requires standard formats for storing, annotating, and exchanging models between software systems. Developing such standards is the driving vision behind the Systems Biology Markup Language (SBML) and several related efforts that we discuss in this chapter. At the same time, such standards are only enablers and ideally should be hidden "under the hood" of modeling environments that provide users with high-level, flexible facilities for working with computational models. As an example of the modern software systems available today, we discuss the Virtual Cell and illustrate its support for typical modeling activities in biology.