DBSolveOptimum is a stand-alone software tool for construction and analysis of mathematical models of biological systems. It is a succession and extension of DBSolve 5 and DBSolve 7, which were popular tools for systems biology. In addition to the capabilities of these software packages, DBSolveOptimum is implemented with new tools for extended data analysis and multiple simulations, which are important for simulation of virtual clinical trials and application of modern modeling techniques, like quantitative systems pharmacology, to problems arising in drug research and development. By this time, DBSolveOptimum has been successfully tested and applied for the development and analysis of both systems pharmacology and conventional PK/PD models of drugs. It is free for academic and industrial use.
- Automatic generation of structural kinetic models on the basis of stoichiometric matrices or reaction lists;
- SBML import/export (including L2V4);
- Flexible capabilities for working on rate and conservation laws;
- Numerical parameter optimization on the basis of experimental data (including global fitting);
- Singular points and bifurcation analysis;
- Analysis of variability in parameter values;
- Identifiability analysis and confidence intervals/regions estimation;
- Extended static and dynamic visualization tools;
- Integration with third-part visualization and statistical tools.
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): 1—11.
Igor I Goryanin, Oleg V Demin, and Frank 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.