Constructing a SMBL-based S-system simulation platform

XML (eXtensible Markup Language) is a commonly used markup language for electronic data exchange. XML has been extended to systems biology. SBML (systems biology markup language) (M. Hucka et al., 2004) is developed by ERATO Kitano project, California Institute of Technology, USA. SBML take XML and UML modeling as common element to describe and analyze systems biology, and it can be used for biologists for exchanging biological pathway data among different systems biology modeling and simulation software. There are many existing tools can manipulate SBML formats, e.g. KEGG2SBML (A. Funahashi et al., 2004) CellDesigner, and MathSBML (B. Shapiro et al., 2004). The combination of these software tools facilitates the analysis of the mathematical modeling for biological reactions. However, it is still an open issue to develop a integrated platform to provide the transformation of data formats, editing, simulation, and analysis in real time. In this study, we design an integrated Web service to fetch biological pathway data, convert to visual graphical interface, transform to mathematical modeling, and solve the model in real time.