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DOTcvpSB, a software toolbox for dynamic optimization in systems biology
|Autor:||Hirmajer, Tomáš; Balsa-Canto, Eva ; Banga, Julio R.|
|Fecha de publicación:||29-jun-2009|
|Citación:||BMC Bioinformatics 10:199 (2009)|
|Resumen:||[Background] 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.|
[Results] 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.
[Conclusion] 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.
|Descripción:||14 pages, 8 figures, 2 tables.|
|Versión del editor:||http://dx.doi.org/10.1186/1471-2105-10-199|
|Aparece en las colecciones:||(IIM) Artículos|
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|1471-2105-10-199.pdf||437,79 kB||Adobe PDF|