DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
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DOI：
10.1186/1471-2105-10-199
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发表时间：
2009-06-29
影响因子：
3
通讯作者：
Banga JR
中科院分区：
文献类型：
--
作者：
Hirmajer T;Balsa-Canto E;Banga JR
数学优化旨在使系统或设计尽可能有效或实用，使用数学模型计算不同备选方案的质量。系统生物学中的大多数模型都具有动态性质，通常由微分方程组描述。动态优化解决了这类系统，寻求最佳时变条件（控制变量）的计算，以最小化或最大化某个性能指标。动态优化可以解决系统生物学中的许多重要问题，包括获得期望生物性能的最优控制、网络设计分析和生物单元的计算机辅助设计。在这里，我们提出了一个软件工具箱，DOTcvpSB，它使用了丰富的合奏国家的最先进的数值方法来解决连续和混合整数动态优化（MIDO）问题。该工具箱是用MATLAB编写的，提供了一个简单和用户友好的环境，包括图形用户界面，同时确保了良好的数值性能。由于紧凑的输入定义，问题很容易说明。该工具箱还提供了导入SBML模型的可能性，从而使其成为系统生物学建模软件包的强大优化伙伴。它也是处理一般黑盒模型的一种方法。在这里，我们说明了DOTcvpSB的能力和性能，通过解决几个具有挑战性的优化问题与生物反应器的优化，最佳药物输注到患者和细胞内振荡的最小化。结果表明，该套件的求解器可以有效地解决一类广泛的动态优化问题，包括具有挑战性的多模态问题。该工具箱可免费供学术使用。
Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations. Dynamic optimization addresses this class of systems, seeking the computation of the optimal time-varying conditions (control variables) to minimize or maximize a certain performance index. Dynamic optimization can solve many important problems in systems biology, including optimal control for obtaining a desired biological performance, the analysis of network designs and computer aided design of biological units. Here, we present a software toolbox, DOTcvpSB, which uses a rich ensemble of state-of-the-art numerical methods for solving continuous and mixed-integer dynamic optimization (MIDO) problems. The toolbox has been written in MATLAB and provides an easy and user friendly environment, including a graphical user interface, while ensuring a good numerical performance. Problems are easily stated thanks to the compact input definition. The toolbox also offers the possibility of importing SBML models, thus enabling it as a powerful optimization companion to modelling packages in systems biology. It serves as a means of handling generic black-box models as well. Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use.
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影响因子：
14.3
作者：
Runarsson, TP;Yao, X
通讯作者：
Yao, X
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
影响因子：
4.3
作者：
Bansal, V;Sakizlis, V;Pistikopoulos, EN
通讯作者：
Pistikopoulos, EN
DOI：
10.1073/pnas.88.16.7328
发表时间：
1991-08-01
影响因子：
11.1
作者：
TYSON, JJ
通讯作者：
TYSON, JJ
影响因子：
2.7
作者：
Hindmarsh, AC;Brown, PN;Woodward, CS
通讯作者：
Woodward, CS