AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology

Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynam...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) Vol. 32; no. 21; pp. 3357 - 3359
Main Authors: Balsa-Canto, Eva, Henriques, David, Gábor, Attila, Banga, Julio R.
Format: Journal Article
Language:English
Published: England Oxford University Press 01.11.2016
Subjects:
Algorithms
Animals
Applications Notes
Humans
Metabolic Engineering
Models, Biological
Software
Systems Biology
ISSN:1367-4803, 1367-4811, 1367-4811
Online Access:Get full text
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Summary:Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynamic flux balance analysis. In the context of control, model-based metabolic engineering or drug dose optimization problems can be formulated as (multi-objective) optimal control problems. Finding a solution to those problems is a very challenging task which requires advanced numerical methods. Results: This work presents the AMIGO2 toolbox: the first multiplatform software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimizers and advanced simulation approaches. Availability and Implementation: The toolbox and its documentation are available at: sites.google.com/site/amigo2toolbox . Contact:  ebalsa@iim.csic.es Supplementary information:  Supplementary data are available at Bioinformatics online.
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Associate Editor: Jonathan Wren
ISSN:1367-4803
1367-4811
1367-4811
DOI:10.1093/bioinformatics/btw411