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DBSolve Optimum：一款用于动力学建模的软件包，可实现模拟结果的动态可视化。

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

作者信息

Gizzatkulov Nail M, Goryanin Igor I, Metelkin Eugeny A, Mogilevskaya Ekaterina A, Peskov Kirill V, Demin Oleg V

机构信息

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

出版信息

BMC Syst Biol. 2010 Aug 10;4:109. doi: 10.1186/1752-0509-4-109.

DOI:10.1186/1752-0509-4-109
PMID:20698988
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2925829/
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.

摘要

背景：系统生物学研究与应用需要创建、验证和广泛使用数学模型，并由最终用户对模拟结果进行可视化展示。我们的目标是开发一种新颖的模拟结果可视化方法，并将其应用于配备了用于模型开发、验证和参数拟合的复杂数学和计算技术的模拟软件包中。 结果：我们展示了数学模拟工作台DBSolve Optimum，它是著名模拟软件DBSolve5显著改进和扩展后的继任者。在DBSolve Optimum中开发并实现了模拟结果的“动态可视化”概念。在该概念框架下，代表代谢物浓度和反应的图形对象会根据模拟结果改变其体积和形状。此技术用于可视化模型的动力学响应及其稳态对参数的依赖性。通过三羧酸循环的动力学模型说明了动态可视化的应用。 结论：DBSolve Optimum是一个用户友好的模拟软件包，能够简化动力学模型的构建、验证、分析和可视化。软件中实现的动态可视化工具允许用户对模拟结果进行动画展示，从而以更易于理解的方式呈现它们。DBSolve Optimum及其内置的动态可视化模块可供学术和商业免费使用。可直接从http://www.insysbio.ru下载。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/3e7a91e02306/1752-0509-4-109-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/b5b00f642aa2/1752-0509-4-109-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/32311ed8c042/1752-0509-4-109-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/6cf88dab81cb/1752-0509-4-109-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/b7e2fef6b320/1752-0509-4-109-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/4aadc82f83ed/1752-0509-4-109-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/3e7a91e02306/1752-0509-4-109-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/b5b00f642aa2/1752-0509-4-109-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/32311ed8c042/1752-0509-4-109-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/6cf88dab81cb/1752-0509-4-109-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/b7e2fef6b320/1752-0509-4-109-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/4aadc82f83ed/1752-0509-4-109-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6a2/2925829/3e7a91e02306/1752-0509-4-109-6.jpg

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