DBSolve Optimum represents program tool for model creation, analysis, and estimation of the parameters with experimental data. This program is a heiress of DBSolve5 program developed by I. Goryanin and DBSolve7 developed in ISBSPb. Considerable changes were included into the program because of new requirements and standards in the modeling.

Description:

DBSolve Optimum represents program tool for model creation, analysis, and estimation of the parameters with experimental data. This program is a heiress of DBSolve5 program developed by I. Goryanin and DBSolve7 developed in ISBSPb. Considerable changes were included into the program because of new requirements and standards in the modeling.

We have tested the new version for kinetic model of metabolism, signal transduction and genetic regulation development (see references). The new version included:

• Integrated "C" compiler for calculation rate increase. This modification turned out necessary for system of large dimension (1000 and more equations)
• New fitting methods, including "multi-shuting" and genetic algorithms.
• Pathways optimization by methods of fluxes analysis.
• User-friendly interface and errors search in the model.
• Visualization tools of metabolic pathways
• Instruments for dynamic reflection of rates and concentrations change
• Import/export of *.xls files, containing data set
• Import/export of models in SBML format.
• By results of users’ remarks, were corrected errors having presented in the old version.

Supplementary material and versions of the program:

The last version of the DBSolve Optimum, manual and detail description of the DBSolve Optimum visualization tool you can download from our website.

Screenshots of DbSolve Optimum Visualization:

AVI Demos of DBSolve Optimum visualization:

Acknowledgments

At different times various people contributed to DBSolve Optimum development and improvement.

Source code generation and numerical methods implementation: Nail Gizzatkulov, Alexander Galtchenko, Sergey Dronov and Igor Goryanin.

References

• Goryanin, O. Demin, F. Tobin, Applications of whole cell and large pathway mathematical models in the pharmaceutical industry. IN: Metabolic Engineering in the Post Genomic Era,(2004), p. 321-356
• Moehren, G., Markevich, N., Demin, O, Kiyatkin, A., Goryanin, I., Hoek, J., Kholodenko, B.N. Temperature dependence of epidermal growth factor receptor signaling network can be accounted for using a kinetic model (2002) Biochemistry, 41(1), 306-320
• Nail M Gizzatkulov, Igor I Goryanin, Eugeny A Metelkin, Ekaterina A Mogilevskaya, Kirill V Peskov and Oleg V Demin. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Systems Biology (2010), 4:109.