Standards, databases, and modeling tools in systems biology

Abstract

Modeling is a means for integrating the results from Genomics, Transcriptomics, Proteomics, and Metabolomics experiments and for gaining insights into the interaction of the constituents of biological systems. However, sharing such large amounts of frequently heterogeneous and distributed experimental data needs both standard data formats and public repositories. Standardization and a public storage system are also important for modeling due to the possibility of sharing models irrespective of the used software tools. Furthermore, rapid model development strongly benefits from available software packages that relieve the modeler of recurring tasks like numerical integration of rate equations or parameter estimation. In this chapter, the most common standard formats used for model encoding and some of the major public databases in this scientific field are presented. The main features of currently available modeling software are discussed and proposals for the application of such tools are given.