Integrating Simulation Packages via Systems Biology Mark-Up Language

Abstract

Programs that simulate large-scale biochemical networks are diverse, each of them with their strengths and weaknesses. The typical in-silico scenario in Metabolomics consists of the combination of different packages, so that they provide a more holistic view of the simulated model. However, this has led to problems of incompatibilities, especially when trying to adapt results from one package into another. Until recently, the way to solve this problem was by hand, in a time consuming and error-prone process. Systems Biology Markup Language (SBML) has arisen as a standard platform for information exchange in the Systems Biology community. A parser was created to allow the automatic exchange of information via SBML. This parser was tested with GEPASI (a General Pathway Simulator). It was found that only 9% of all the parameters of the specification file produced by GEPASI could be successfully translated into the variables described by the SBML Level 1 specification. Further development of SBML Level 1 is suggested in order to produce a more complete representation of biochemical information.