title: DOTcvpSB, a software toolbox for dynamic optimization in systems biology.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors: Instituto de Investigaciones Marinas, IIM-CSIC, Spanish Council for Scientific Research, C/Eduardo Cabello 6, 36208 Vigo, Spain. thirmajer@gmail.com
authors: Tomás
authors: T
authors: Hirmajer
authors: Eva
authors: E
authors: Balsa-Canto
authors: Julio R
authors: JR
authors: Banga
mesh_terms: D016208:Databases, Factual; D020407:Internet; D012984:Software; D049490:Systems Biology / Q000379:methods*