DOTcvpSB: a Matlab Toolbox for Dynamic Optimization in Systems ...

DOTcvpSB: a Matlab Toolbox for Dynamic Optimization in Systems Biology• optimization modules: offering several optimization strategies, namely single optimization, multi-start, successivere-optimization, and hybrid optimization modules.1.2.1 Utility modulesThe utility modules offer several facilities for the definition, checking, and handling of problems. Thetoolbox can be operated through two equivalent approaches: by the use of the GUI, or directly from the commandline (from where scripts with problem definitions can be created and executed). It also offers a module to importdynamic models from SBML files, and the imported models can be checked by a simulation module.• Graphical User Interface (GUI) module: this module was developed in order to help users in the definitionand execution of problems. With the help of this module, which follows an intuitive wizard-like approach,problem definitions and modifications are guided in an easy and convenient stepwise manner, especiallyindicated for entry users.• Simulation module: this module carries out the dynamic simulation of the user-defined dynamics (plusassigned initial conditions and controls) generating the corresponding state trajectories. This module isespecially useful for checking the model correctness during the definition phase, which is particularly errorprone.Typical errors like those related with units inconsistencies can be readily identified with this procedure.• SBML to DOTcvpSB module: this module allows DOTcvpSB to import the systems dynamics from SBML(Systems Biology Markup Language) models [18; 20]. Once a dynamic model is imported, it is necessaryto check the model correctness by simulation (previous module). If everything works correctly, the usercan proceed with the definition of the other terms of the dynamic optimization problem (performance index,constraints) and, finally, with its numerical solution.1.2.2 Optimization modulesThe optimization modules offers a suite of four different optimization strategies, each one with differentoptions for the optimization solvers, following the "Swiss Army knife" approach mentioned previously. All thesemodules are described in more detail below.• Single optimization module: this module makes a single call to one of the optimization solvers, which canbe either a local deterministic or global stochastic method (see available solvers below). This procedure canbe sufficient for well conditioned, convex problems, or non-convex problems which are cheap to evaluate.In any case, it is recommended as the first strategy to try with any new problem.• Multi-start optimization module: this modules runs a selected optimization solver (typically a local one)repeatedly. The set of solutions (performance index values) obtained can then be analyzed (e.g. plottinga histogram) in order to check the multimodality of the problem.• Sucessive re-optimization module: Sucessive re-optimization can be used to speed up the convergence forproblems where a high discretization level is desired (e.g. those where the control profiles behave wildly).This procedure runs several successive single optimizations automatically increasing the control discretization,NLP, and IVP tolerances after each run.• Hybrid optimization module: Hybrid optimization is characterized by the combination of a stochasticglobal method plus a deterministic local method. This procedures ensures a compromise between the robustnessof global methods and the efficiency of local ones. This module is especially indicated for difficultmultimodal problems. In any case, tweaking the hybrid method requires a deep knowledge of the solvers,and this approach will be almost always more costly (in CPU time) than the single optimization proceduresusing local methods (the price to pay for the increased robustness).1.3 NUMERICAL OPTIMIZATION METHODS (NLP AND MINLP SOLVERS)The toolbox provides interfaces to several optimization state-of-the-art solvers:• local deterministic1. IPOPT [37] (Interior Point OPTimizer) implements a primal-dual interior point method, and uses linesearches based on Filter methods;Page – 8