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

Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV - BMC Syst Biol (2010)

Bottom Line: 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.Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology SPb, Sankt-Peterburgh, Russia. gizzatkulov@gmail.com

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.

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Architecture of the DBSolve Optimum Developer Environment. Abbreviations: IO - Input/Output module, DAT, SLV, SBML, RCT - data file formats, IV - Initial values, RHS - Right hand sides, CSV - text file of CSV format.
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Figure 1: Architecture of the DBSolve Optimum Developer Environment. Abbreviations: IO - Input/Output module, DAT, SLV, SBML, RCT - data file formats, IV - Initial values, RHS - Right hand sides, CSV - text file of CSV format.

Mentions: Figs 1 and 2 represent architecture of DODE and DOP, correspondently. DODE workflow (Fig. 1) consists of data input (IO module), creation and editing model (Model Construction module), its verification and analysis (Solver module) and output of simulation results (Output module) and their visualization (Visualization module). Work with DODE starts with creation of new model or download existing file in "SLV" or "SBML" format. "SLV" (SoLVe) is internal format of DBSolve Optimum which includes both detail information about kinetic model and description of user settings. "SBML" (Systems Biology Markup Language) format [6] is designed for storage of kinetic models and their exchange between modelers which use various software packages for model development and analysis. DODE supports SBML version L2V4 (Level 2 Version 4) and uses libSBML library for Import/Export of SBML files.


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

Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV - BMC Syst Biol (2010)

Architecture of the DBSolve Optimum Developer Environment. Abbreviations: IO - Input/Output module, DAT, SLV, SBML, RCT - data file formats, IV - Initial values, RHS - Right hand sides, CSV - text file of CSV format.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2925829&req=5

Figure 1: Architecture of the DBSolve Optimum Developer Environment. Abbreviations: IO - Input/Output module, DAT, SLV, SBML, RCT - data file formats, IV - Initial values, RHS - Right hand sides, CSV - text file of CSV format.
Mentions: Figs 1 and 2 represent architecture of DODE and DOP, correspondently. DODE workflow (Fig. 1) consists of data input (IO module), creation and editing model (Model Construction module), its verification and analysis (Solver module) and output of simulation results (Output module) and their visualization (Visualization module). Work with DODE starts with creation of new model or download existing file in "SLV" or "SBML" format. "SLV" (SoLVe) is internal format of DBSolve Optimum which includes both detail information about kinetic model and description of user settings. "SBML" (Systems Biology Markup Language) format [6] is designed for storage of kinetic models and their exchange between modelers which use various software packages for model development and analysis. DODE supports SBML version L2V4 (Level 2 Version 4) and uses libSBML library for Import/Export of SBML files.

Bottom Line: 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.Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Systems Biology SPb, Sankt-Peterburgh, Russia. gizzatkulov@gmail.com

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.

Show MeSH
Related in: MedlinePlus