AMIGO swMATH ID: 15248 Software Authors: Balsa-Canto, Eva; Banga, Julio R. Description: AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Motivation: Mathematical models of complex biological systems usually consist of sets of differential equations which depend on several parameters which are not accessible to experimentation. These parameters must be estimated by fitting the model to experimental data. This estimation problem is very challenging due to the non-linear character of the dynamics, the large number of parameters and the frequently poor information content of the experimental data (poor practical identifiability). The design of optimal (more informative) experiments is an associated problem of the highest interest. Results: This work presents AMIGO, a toolbox which facilitates parametric identification by means of advanced numerical techniques which cover the full iterative identification procedure putting especial emphasis on robust methods for parameter estimation and practical identifiability analyses, plus flexible capabilities for optimal experimental design. Availability: The toolbox and the corresponding documentation may be downloaded from: http://www.iim.csic.es/ amigo Homepage: http://bioinformatics.oxfordjournals.org/content/27/16/2311.short Related Software: Data2Dynamics; COPASI; PESTO; MEIGO; DAISY; R; pyPESTO; PEtab; GenSSI; Julia; BioNetGen; PyBioNetFit; Matlab; Qlopt; SUNDIALS; msolve; TaylorSeries.jl; ParameterEstimation.jl; sbtoolbox; DifferentialEquations.jl Cited in: 8 Documents all top 5 Cited by 23 Authors 2 Abdulla, Ugur G. 2 Balsa-Canto, Eva 2 Poteau, Roby 1 Alonso, Antonio A. 1 Arias-Méndez, Ana 1 Atkinson, Anthony C. 1 Banga, Julio R. 1 Chis, Oana-Teodora 1 Clermont, Gilles 1 Duarte, Belmiro P. M. 1 García, Míriam R. 1 Granjo, José F. O. 1 Hasenauer, Jan 1 López-Núñez, Alejandro 1 Mosquera-Fernández, Maruxa 1 Oliveira, Nuno M. C. 1 Schmiester, Leonard 1 Thomaseth, Karl 1 Vázquez Cendón, Carlos 1 Vilas, Carlos 1 Villaverde, Alejandro Fernández 1 Weindl, Daniel 1 Zenker, Sven Cited in 5 Serials 3 Mathematical Biosciences 1 Journal of Computational Physics 1 Journal of Mathematical Biology 1 Journal of the American Statistical Association 1 Complexity all top 5 Cited in 7 Fields 5 Biology and other natural sciences (92-XX) 2 Ordinary differential equations (34-XX) 2 Operations research, mathematical programming (90-XX) 2 Systems theory; control (93-XX) 1 Dynamical systems and ergodic theory (37-XX) 1 Statistics (62-XX) 1 Numerical analysis (65-XX) Citations by Year