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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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Different modes of the dynamic visualization: "Arrow animation" mode. An example of visualization: time response of the concentrations and fluxes of the Krebs cycle resulted from changes in external glutamate concentration from 2 mM to 10 mM. Changes in width of arrows and circles radius visualize changes in reaction rates and metabolites concentrations correspondingly.
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Figure 6: Different modes of the dynamic visualization: "Arrow animation" mode. An example of visualization: time response of the concentrations and fluxes of the Krebs cycle resulted from changes in external glutamate concentration from 2 mM to 10 mM. Changes in width of arrows and circles radius visualize changes in reaction rates and metabolites concentrations correspondingly.

Mentions: DBSolve Optimum allows visualization of simulation results in two different ways: "Bar animation" and "Arrow animation" (see corresponding options for construction of visual map in DVM interface Fig. 3). "Bar animation" mode (Fig. 5) allows modeler to create a set of the bars corresponding to reactions and entities of the system. The height of the rectangles corresponds to the value of either reaction rate or concentration. Animation in this mode implemented in DOP as changes in heights of the bars in accordance to data provided by simulations. "Arrow animation" mode (Fig. 6) allows us to create static map consisting of nodes (biological entities) and the directed edges (reactions). Variation of concentration of i-th metabolite, Ci, is represented by change in circle radius, ri, around the corresponding node in such a way that the concentration is directly proportional to circle radius:


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)

Different modes of the dynamic visualization: "Arrow animation" mode. An example of visualization: time response of the concentrations and fluxes of the Krebs cycle resulted from changes in external glutamate concentration from 2 mM to 10 mM. Changes in width of arrows and circles radius visualize changes in reaction rates and metabolites concentrations correspondingly.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Different modes of the dynamic visualization: "Arrow animation" mode. An example of visualization: time response of the concentrations and fluxes of the Krebs cycle resulted from changes in external glutamate concentration from 2 mM to 10 mM. Changes in width of arrows and circles radius visualize changes in reaction rates and metabolites concentrations correspondingly.
Mentions: DBSolve Optimum allows visualization of simulation results in two different ways: "Bar animation" and "Arrow animation" (see corresponding options for construction of visual map in DVM interface Fig. 3). "Bar animation" mode (Fig. 5) allows modeler to create a set of the bars corresponding to reactions and entities of the system. The height of the rectangles corresponds to the value of either reaction rate or concentration. Animation in this mode implemented in DOP as changes in heights of the bars in accordance to data provided by simulations. "Arrow animation" mode (Fig. 6) allows us to create static map consisting of nodes (biological entities) and the directed edges (reactions). Variation of concentration of i-th metabolite, Ci, is represented by change in circle radius, ri, around the corresponding node in such a way that the concentration is directly proportional to circle radius:

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