DOTcvpSB, a software toolbox for dynamic optimization in systems biology. Optimization aims to make a system or design as effective or functional as possible. In systems biology, most models have a dynamic nature, usually consisting of sets of differential equations. Dynamic optimization seeks the computation of optimal time-varying conditions (called control variables) for this type of systems. These control variables allow us to stimulate a given biosystem so as to achieve a desired dynamic behavior, e.g. stimulate a cell signaling cascade to maximize amplitude strength and/or duration, stimulate an oscillatory system to synchronize oscillations, remove oscillations, etc. In other words, DO allows the computation of optimal operating policies for processes or systems which maximize (or minimize) a pre-defined performance index subject to the system dynamics and other possible constraints. DO may be solved by several methods, including the control vector parameterization (CVP) method, which has demonstrated excellent performance for a wide variety of problems. Here we present a software toolbox, DOTcvpSB, which uses the CVP approach for handling continuous and mixed integer DO problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering. The toolbox is written in MATLAB and provides an easy to use environment while maintaining a quite good performance. DOTcvpSB is designed for the Windows operating systems. The toolbox also contains a function for importing SBML models.
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References in zbMATH (referenced in 4 articles )
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- Hirmajer, Tomás; Balsa-Canto, Eva; Banga, Julio R.: Dotcvpsb, a software toolbox for dynamic optimization in systems biology (2009) ioport