Time course simulation replicability of SBML-supporting biochemical network simulation tools
Abstract (Summary)Background: Modelling and simulation are important tools for understanding biological systems. Numerous modelling and simulation software tools have been developed for integrating knowledge regarding the behaviour of a dynamic biological system described in mathematical form. The Systems Biology Markup Language (SBML) was created as a standard format for exchanging biochemical network models among tools. However, it is not certain yet whether actual usage and exchange of SBML models among the tools of different purpose and interfaces is assessable. Particularly, it is not clear whether dynamic simulations of SBML models using different modelling and simulation packages are replicable.Results: Time series simulations of published biological models in SBML format are performed using four modelling and simulation tools which support SBML to evaluate whether the tools correctly replicate the simulation results. Some of the tools do not successfully integrate some models. In the time series output of the successfulsimulations, there are differences between the tools.Conclusions: Although SBML is widely supported among biochemical modelling and simulation tools, not all simulators can replicate time-course simulations of SBML models exactly. This incapability of replicating simulation results may harm the peer-review process of biological modelling and simulation activities and should be addressed accordingly, for example by specifying in the SBML model the exact algorithm or simulator used for replicating the simulation result.
School:Högskolan i Skövde
Source Type:Master's Thesis
Date of Publication:11/06/2006