Software Infrastructure for Effective Communication and Reuse of Computational Models

Abstract

Until recently, the majority of computational models in biology were implemented in custom programs and published as statements of the underlying mathematics. However, to be useful as formal embodiments of our understanding of biological systems, computational models must be put into a consistent form that can be communicated more directly between the software tools used to work with them. In this chapter, we describe the Systems Biology Markup Language (SBML), a format for representing models in a way that can be used by different software systems to communicate and exchange those models. By supporting SBML as an input and output format, different software tools can all operate on an identical representation of a model, removing opportunities for errors in translation and assuring a common starting point for analyses and simulations. We also take this opportunity to discuss some of the resources available for working with SBML as well as ongoing efforts in SBML’s continuing evolution.