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Open Access Software

DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

Nail M Gizzatkulov1*, Igor I Goryanin2, Eugeny A Metelkin1, Ekaterina A Mogilevskaya1, Kirill V Peskov1 and Oleg V Demin13

Author Affiliations

1 Institute for Systems Biology SPb, Sankt-Peterburgh, Russia

2 University of Edinburgh, Edinburgh, UK

3 A.N. Belozersky Institute of Physico-Chemical Biology of Moscow State University, Moscow, Russia

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BMC Systems Biology 2010, 4:109  doi:10.1186/1752-0509-4-109

Published: 10 August 2010

Abstract

Background

Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting.

Results

We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle.

Conclusion

DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru webcite.