Abstract
SummaryPESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objective function in MATLAB.Availability and implementationPESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https://github.com/ICB-DCM/PESTO/.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
In many disciplines such as computational biology, engineering and operations research, researchers are faced with the problem of finding a set of parameters optimizing a given objective function and determining uncertainties of those estimates
In an effort to provide a universally applicable parameter estimation toolbox, we developed PESTO
PESTO is a freely available MATLAB toolbox offering scalable state-of-the-art algorithms for optimization, uncertainty and identifiability analysis, which do not depend on any problemspecific assumptions
Summary
In many disciplines such as computational biology, engineering and operations research, researchers are faced with the problem of finding a set of parameters optimizing a given objective function and determining uncertainties of those estimates. There are various toolboxes available which offer this functionality, most of them focus either on individual aspects or are tailored to specific model types, e.g. ordinary differential equations (ODEs) or partial differential equations (PDEs). The user must adapt to different tools, depending on the current problem structure. A feature comparison of a selection of toolboxes related to parameter estimation is provided as Supplementary Table S1. In an effort to provide a universally applicable parameter estimation toolbox, we developed PESTO. PESTO is a freely available MATLAB toolbox offering scalable state-of-the-art algorithms for optimization, uncertainty and identifiability analysis, which do not depend on any problemspecific assumptions
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